Citrus Sinensis ID: 006282

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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--
Protein Sequence
MAQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
Secondary Structure (PSIPRED)
cccccHHHHHHcccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHcccccccEEEEEEEEcccccccccccccEEEccccccccHHHHHHHHHccccccEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccccccEEEEEEEccccHHHHHHHHcccccEEEEccccccccHHHHHHHHcccccEEEEEEEEccccccEEEEEEEcccHHHHHHHHHHHcccEEccEEEEEEEccccHHHHHHHHHHHHHHHHHHcccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccEEccEEEEEEEEccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHcHHHHHHHccccccccHHHHHccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEccccHHHHHccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEcccccccccEEEEcccHHHHHHHHHHHccccccccEEEEEccccHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEcccHHHHHHHHHHHccccccccEEEEEccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEEccHHHHHHHHHHHcccEcccccEEEEHHccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
MAQIQVQHQaqmsgpngvaagasgnqflttslyvgdldfnvtdsqLYDLFSQVGQVLSVRVcrdlstrrslgygyvnyanpadaaraldvlnftplnnksirimyshrdpsirksgtgnifiknldksidhkalhdtfssFGNILSckiatdgsgqskgfgfvqfeNKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFvknldesttdedLKKIFGEYGTITSAVvmrdgdgkskcfgfvnfenADDAAKAVEALngkkfddrewyvgkaqkksEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFgtitsckvmrdpsgiskgsgfvafstPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFsqmrpvamgpsvpprmpmyppgpsglgqqflygqappaiippqagfgyqqqlvpgmrpagapmpnffvpvvsqgqqgqrpggrrgagpvqqtqqplpimphqmpprghayryplgrnmqdfpfdmgagsmlpvpvdmgagiprrdasvgqpmpITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQqannpadqlaslslnenlvs
Flexible Loop (DISEMBL)
MAQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRimyshrdpsirksgtgNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERetvaiktkfnnvfvknldesttdedlkkiFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEalngkkfddrewyvgkaqkksereqeLKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLqaqfsqmrpvamgpsvpPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQannpadqlaslslnenlvs
Low Complexity Region (SEG)
MAQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMgpsvpprmpmyppgpsgLGQQFLYGqappaiippqaGFGYQQQLVPGMRPAGAPMPNFFvpvvsqgqqgqrpggrrgagpvqqTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
Disordered region (IsUnstruct)
***********************GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV************************VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR**********FV*****************KMIVSKPLYVAV********************************************FLYGQAPPAIIPPQAGFGYQQQLV***********NFFVP*******************************************************************************************************LGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLE******************************************
Disordered Region (DISOPRED)
*******************************LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI****************IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG******************NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV******************************LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV*************************************************************************************************************************************************************************************EQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME****************************
Disordered Region (DISEMBL)
***************NGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK**************FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA**********QAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVV*******************QTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
Disordered Region (DISPRO)
*************GPN**A*GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYP*GR*MQD*******************************MPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQ*******************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKxxxxxxxxxxxxxxxxxxxxxTVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
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	652	2.2.26 [Sep-21-2011]
P42731	629	Polyadenylate-binding pro	yes	no	0.949	0.984	0.678	0.0
O64380	660	Polyadenylate-binding pro	no	no	0.884	0.874	0.549	1e-176
Q05196	682	Polyadenylate-binding pro	no	no	0.929	0.888	0.543	1e-174
P29341	636	Polyadenylate-binding pro	no	no	0.911	0.933	0.467	1e-149
P11940	636	Polyadenylate-binding pro	no	no	0.911	0.933	0.467	1e-148
P61286	636	Polyadenylate-binding pro	yes	no	0.911	0.933	0.467	1e-148
Q5R8F7	636	Polyadenylate-binding pro	yes	no	0.911	0.933	0.466	1e-148
Q9EPH8	636	Polyadenylate-binding pro	yes	no	0.915	0.938	0.468	1e-147
Q6IP09	633	Polyadenylate-binding pro	N/A	no	0.912	0.939	0.465	1e-146
Q5B630	732	Polyadenylate-binding pro	yes	no	0.914	0.814	0.429	1e-145

>sp|P42731|PABP2_ARATH Polyadenylate-binding protein 2 OS=Arabidopsis thaliana GN=PAB2 PE=1 SV=1

 Score =  870 bits (2247), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/657 (67%), Positives = 524/657 (79%), Gaps = 38/657 (5%)

Query: 1   MAQIQVQHQAQMSGPNGVAA----------GASGNQFLTTSLYVGDLDFNVTDSQLYDLF 50
           MAQ+Q+Q Q     PNG  A          GA+  QF  TSLYVGDLDFNVTDSQL+D F
Sbjct: 1   MAQVQLQGQT----PNGSTAAVTSAPATSGGATATQFGNTSLYVGDLDFNVTDSQLFDAF 56

Query: 51  SQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP 110
            Q+G V++VRVCRDL TRRSLGYGYVN+ NP DAARA+  LN+ PL  K IR+MYSHRDP
Sbjct: 57  GQMGTVVTVRVCRDLVTRRSLGYGYVNFTNPQDAARAIQELNYIPLYGKPIRVMYSHRDP 116

Query: 111 SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKES 170
           S+R+SG GNIFIKNLD+SIDHKALHDTFSSFGNI+SCK+A D SGQSKG+GFVQ+ N+ES
Sbjct: 117 SVRRSGAGNIFIKNLDESIDHKALHDTFSSFGNIVSCKVAVDSSGQSKGYGFVQYANEES 176

Query: 171 AQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFG 230
           AQ AI+KLNGML+NDKQV+VG FLR+QER++ A KTKF NV+VKNL ESTTD+DLK  FG
Sbjct: 177 AQKAIEKLNGMLLNDKQVYVGPFLRRQERDSTANKTKFTNVYVKNLAESTTDDDLKNAFG 236

Query: 231 EYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSER 290
           EYG ITSAVVM+DG+GKSK FGFVNFENADDAA+AVE+LNG KFDD+EWYVG+AQKKSER
Sbjct: 237 EYGKITSAVVMKDGEGKSKGFGFVNFENADDAARAVESLNGHKFDDKEWYVGRAQKKSER 296

Query: 291 EQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI 350
           E EL+ ++EQ +KE  DKFQ  NLY+KNL  SI DEKLKE+FS FGT+TS KVMRDP+G 
Sbjct: 297 ETELRVRYEQNLKEAADKFQSSNLYVKNLDPSISDEKLKEIFSPFGTVTSSKVMRDPNGT 356

Query: 351 SKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMG 410
           SKGSGFVAF+TPEEA+ A+++++GKMI SKPLYVA+AQRKE+RR RLQAQFSQ+RPVAM 
Sbjct: 357 SKGSGFVAFATPEEATEAMSQLSGKMIESKPLYVAIAQRKEDRRVRLQAQFSQVRPVAMQ 416

Query: 411 PSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVP 470
           PSV PRMP+YPPG  G+GQQ  YGQAPPA+IPPQ G+GYQQQLVPGMRP G P+P+FF+P
Sbjct: 417 PSVGPRMPVYPPGGPGIGQQMFYGQAPPAMIPPQPGYGYQQQLVPGMRPGGGPVPSFFMP 476

Query: 471 VVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGS 530
           +V   QQ     G R  G +Q +QQ  P+M  QM PRG  +RYP GR         G   
Sbjct: 477 MVQPQQQRPG--GGRRPGGIQHSQQQNPMMQQQMHPRGRMFRYPQGR---------GGSG 525

Query: 531 MLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAA 590
            +P P DMG  +         P+ I AL++ L+NA+PEQQRT+LGE LYPLVEQ+E ++A
Sbjct: 526 DVP-PYDMGNNM---------PLTIGALASNLSNATPEQQRTMLGEVLYPLVEQVEAESA 575

Query: 591 AKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLN 647
           AKVTGMLLEMDQTEVLHLLESPEALKAKVAEAM+VLRSVA   A    +QLASL+L+
Sbjct: 576 AKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMDVLRSVA---AGGATEQLASLNLS 629

Binds the poly(A) tail of mRNA.
Arabidopsis thaliana (taxid: 3702)

>sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 OS=Arabidopsis thaliana GN=PAB3 PE=2 SV=1

 Score =  619 bits (1596), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 339/617 (54%), Positives = 424/617 (68%), Gaps = 40/617 (6%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           +SLY GDLD  VT++ L+DLF  V  V+SVRVCRD   RRSLGY Y+N++NP DA RA++
Sbjct: 49  SSLYAGDLDPKVTEAHLFDLFKHVANVVSVRVCRD-QNRRSLGYAYINFSNPNDAYRAME 107

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            LN+TPL ++ IRIM S+RDPS R SG GNIFIKNLD SID+KAL +TFSSFG ILSCK+
Sbjct: 108 ALNYTPLFDRPIRIMLSNRDPSTRLSGKGNIFIKNLDASIDNKALFETFSSFGTILSCKV 167

Query: 150 ATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER--ETVAIKTK 207
           A D +G+SKG+GFVQFE +ESAQ AIDKLNGML+NDKQVFVGHF+R+QER  +      +
Sbjct: 168 AMDVTGRSKGYGFVQFEKEESAQAAIDKLNGMLMNDKQVFVGHFIRRQERARDENTPTPR 227

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           F NV+VKNL +   +++L+K FG++G I+SAVVMRD  G S+CFGFVNFE  + AA AVE
Sbjct: 228 FTNVYVKNLPKEIGEDELRKTFGKFGVISSAVVMRDQSGNSRCFGFVNFECTEAAASAVE 287

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEK 327
            +NG    D   YVG+AQKKSERE+EL+ +FEQ      +K QG NLY+KNL DS+DDEK
Sbjct: 288 KMNGISLGDDVLYVGRAQKKSEREEELRRKFEQERINRFEKSQGANLYLKNLDDSVDDEK 347

Query: 328 LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA 387
           LKE+FSE+G +TS KVM +P G+S+G GFVA+S PEEA RAL+EMNGKMI  KPLY+A+A
Sbjct: 348 LKEMFSEYGNVTSSKVMLNPQGMSRGFGFVAYSNPEEALRALSEMNGKMIGRKPLYIALA 407

Query: 388 QRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGP-SGL-----------GQQFLYGQ 435
           QRKE+RRA LQA FSQ+R                PGP SG             Q    GQ
Sbjct: 408 QRKEDRRAHLQALFSQIR---------------APGPMSGFHHPPGGPMPGPPQHMYVGQ 452

Query: 436 APPAIIPPQ-AGFGYQQQLVPGMRPAGAPMPNFFV--PVVSQGQQGQRPGGRRGAGPVQQ 492
              +++P Q  G+G+Q Q +PGMRP   P  NF V  P+  Q Q G R G RRGA  VQQ
Sbjct: 453 NGASMVPSQPIGYGFQPQFMPGMRPGSGP-GNFIVPYPLQRQPQTGPRMGFRRGATNVQQ 511

Query: 493 TQQPLPIMPHQMPPRGHAYRYPL--GRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVG 550
             Q   +M H+ P  G  Y      GRN  D     G    +       + I  + A + 
Sbjct: 512 HIQQQQLM-HRNPSPGMRYMNGASNGRNGMDSSVPQGILPPIIPLPIDASSISHQKAPL- 569

Query: 551 QPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLE 610
             +PI+ L+++LA+ASP  +  +LGE LYPLVE+ E    AKVTGMLLEMDQ E+LHL+E
Sbjct: 570 --LPISKLTSSLASASPADRTRMLGEQLYPLVERHEPLHVAKVTGMLLEMDQAEILHLME 627

Query: 611 SPEALKAKVAEAMEVLR 627
           SPEALK+KV+EA++VLR
Sbjct: 628 SPEALKSKVSEALDVLR 644

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q05196|PABP5_ARATH Polyadenylate-binding protein 5 OS=Arabidopsis thaliana GN=PAB5 PE=1 SV=3

 Score =  612 bits (1578), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 347/639 (54%), Positives = 446/639 (69%), Gaps = 33/639 (5%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
            +SLYVGDLD +V +S L DLF+QV  V ++RVCRDL T RSLGY YVN+ANP DA+RA+
Sbjct: 58  NSSLYVGDLDPSVNESHLLDLFNQVAPVHNLRVCRDL-THRSLGYAYVNFANPEDASRAM 116

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCK 148
           + LN+ P+ ++ IRIM S+RDPS R SG GN+FIKNLD SID+KAL++TFSSFG ILSCK
Sbjct: 117 ESLNYAPIRDRPIRIMLSNRDPSTRLSGKGNVFIKNLDASIDNKALYETFSSFGTILSCK 176

Query: 149 IATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER---ETVAIK 205
           +A D  G+SKG+GFVQFE +E+AQ AIDKLNGML+NDKQVFVGHF+R+Q+R   E+ A+ 
Sbjct: 177 VAMDVVGRSKGYGFVQFEKEETAQAAIDKLNGMLLNDKQVFVGHFVRRQDRARSESGAVP 236

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
           + F NV+VKNL +  TD++LKK FG+YG I+SAVVM+D  G S+ FGFVNF + + AA A
Sbjct: 237 S-FTNVYVKNLPKEITDDELKKTFGKYGDISSAVVMKDQSGNSRSFGFVNFVSPEAAAVA 295

Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           VE +NG    +   YVG+AQKKS+RE+EL+ +FEQ      +K QG NLY+KNL DS++D
Sbjct: 296 VEKMNGISLGEDVLYVGRAQKKSDREEELRRKFEQERISRFEKLQGSNLYLKNLDDSVND 355

Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 385
           EKLKE+FSE+G +TSCKVM +  G+S+G GFVA+S PEEA  A+ EMNGKMI  KPLYVA
Sbjct: 356 EKLKEMFSEYGNVTSCKVMMNSQGLSRGFGFVAYSNPEEALLAMKEMNGKMIGRKPLYVA 415

Query: 386 VAQRKEERRARLQAQFSQMR-PVAMGPSVPPRMP---MYPPGP--SGLGQQFLYGQAPPA 439
           +AQRKEER+A LQ+ F+Q+R P  M P VP  M     +PPG   SG       G     
Sbjct: 416 LAQRKEERQAHLQSLFTQIRSPGTMSP-VPSPMSGFHHHPPGGPMSGPHHPMFIGHNGQG 474

Query: 440 IIPPQ-AGFGYQQQLVPGMRPAGAPMPNFFV--PVVSQGQQGQRPGGRRGAGPVQQTQQP 496
           ++P Q  G+GYQ Q +PGMRP   P PNF +  P+  Q Q G R G RRGA  +QQ  Q 
Sbjct: 475 LVPSQPMGYGYQVQFMPGMRPGAGP-PNFMMPFPLQRQTQPGPRVGFRRGANNMQQQFQ- 532

Query: 497 LPIMPHQMPPRGHAYRYPLG----RNMQDFPFDMGAGSMLPVPVDMGA---GIPRRDASV 549
                 Q   + +A R+  G    RN  +     G   ++P+P++  A     P+R +  
Sbjct: 533 -----QQQMLQQNASRFMGGAGNRRNGMEASAPQG---IIPLPLNASANSHNAPQR-SHK 583

Query: 550 GQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLL 609
             P+ I+ L++ LA ASP++   +LG+ LYPLVEQ E   AAKVTGMLLEMDQ E+LHLL
Sbjct: 584 PTPLTISKLASDLALASPDKHPRMLGDHLYPLVEQQEPANAAKVTGMLLEMDQAEILHLL 643

Query: 610 ESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNE 648
           ESPEALKAKV+EA++VLR  A   A +  D   +LS +E
Sbjct: 644 ESPEALKAKVSEALDVLRRSADPAAVSSVDDQFALSSSE 682

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2

 Score =  528 bits (1359), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 298/637 (46%), Positives = 406/637 (63%), Gaps = 43/637 (6%)

Query: 23  SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
           S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PA
Sbjct: 4   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63

Query: 83  DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
           DA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123

Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETV 202
           NILSCK+  D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F  ++ERE  
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182

Query: 203 --AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENAD 260
             A   +F NV++KN  E   DE LK++FG++G   S  VM D  GKSK FGFV+FE  +
Sbjct: 183 LGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHE 242

Query: 261 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 320
           DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +FEQ  ++ + ++QG+NLY+KNL 
Sbjct: 243 DAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLD 302

Query: 321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
           D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS+PEEA++A+ EMNG+++ +K
Sbjct: 303 DGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 361

Query: 381 PLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFL-YGQAPPA 439
           PLYVA+AQRKEER+A L  Q+ Q          P   P  P  PSG     +   Q   A
Sbjct: 362 PLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAA 421

Query: 440 IIPP--------------QAGFGYQQQLVPG-MRPAGAPMPNFFVPVVSQGQQGQRPGGR 484
             PP              Q    +  Q +PG +RPA AP P F     +  Q  +    +
Sbjct: 422 YYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-APRPPFSTMRPASSQVPRVMSTQ 480

Query: 485 RGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPR 544
           R A    QT  P P           A   P  R +  + +  G  +    P       P+
Sbjct: 481 RVANTSTQTMGPRPAA-------AAAAATPAVRTVPQYKYAAGVRN----PQQHLNAQPQ 529

Query: 545 RDASVGQPM-------PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGML 597
              ++ QP        P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGML
Sbjct: 530 --VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGML 585

Query: 598 LEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 634
           LE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 586 LEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Mus musculus (taxid: 10090)

>sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=1 SV=2

 Score =  526 bits (1355), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 298/637 (46%), Positives = 405/637 (63%), Gaps = 43/637 (6%)

Query: 23  SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
           S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PA
Sbjct: 4   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63

Query: 83  DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
           DA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123

Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETV 202
           NILSCK+  D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F  ++ERE  
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182

Query: 203 --AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENAD 260
             A   +F NV++KN  E   DE LK +FG++G   S  VM D  GKSK FGFV+FE  +
Sbjct: 183 LGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHE 242

Query: 261 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 320
           DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +FEQ  ++ + ++QG+NLY+KNL 
Sbjct: 243 DAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLD 302

Query: 321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
           D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS+PEEA++A+ EMNG+++ +K
Sbjct: 303 DGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 361

Query: 381 PLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFL-YGQAPPA 439
           PLYVA+AQRKEER+A L  Q+ Q          P   P  P  PSG     +   Q   A
Sbjct: 362 PLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAA 421

Query: 440 IIPP--------------QAGFGYQQQLVPG-MRPAGAPMPNFFVPVVSQGQQGQRPGGR 484
             PP              Q    +  Q +PG +RPA AP P F     +  Q  +    +
Sbjct: 422 YYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-APRPPFSTMRPASSQVPRVMSTQ 480

Query: 485 RGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPR 544
           R A    QT  P P           A   P  R +  + +  G  +    P       P+
Sbjct: 481 RVANTSTQTMGPRPAA-------AAAAATPAVRTVPQYKYAAGVRN----PQQHLNAQPQ 529

Query: 545 RDASVGQPM-------PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGML 597
              ++ QP        P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGML
Sbjct: 530 --VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGML 585

Query: 598 LEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 634
           LE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 586 LEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Homo sapiens (taxid: 9606)

>sp|P61286|PABP1_BOVIN Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1

 Score =  526 bits (1355), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 298/637 (46%), Positives = 405/637 (63%), Gaps = 43/637 (6%)

Query: 23  SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
           S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PA
Sbjct: 4   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63

Query: 83  DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
           DA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123

Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETV 202
           NILSCK+  D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F  ++ERE  
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182

Query: 203 --AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENAD 260
             A   +F NV++KN  E   DE LK +FG++G   S  VM D  GKSK FGFV+FE  +
Sbjct: 183 LGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHE 242

Query: 261 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 320
           DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +FEQ  ++ + ++QG+NLY+KNL 
Sbjct: 243 DAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLD 302

Query: 321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
           D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS+PEEA++A+ EMNG+++ +K
Sbjct: 303 DGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 361

Query: 381 PLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFL-YGQAPPA 439
           PLYVA+AQRKEER+A L  Q+ Q          P   P  P  PSG     +   Q   A
Sbjct: 362 PLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAA 421

Query: 440 IIPP--------------QAGFGYQQQLVPG-MRPAGAPMPNFFVPVVSQGQQGQRPGGR 484
             PP              Q    +  Q +PG +RPA AP P F     +  Q  +    +
Sbjct: 422 YYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-APRPPFSTMRPASSQVPRVMSTQ 480

Query: 485 RGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPR 544
           R A    QT  P P           A   P  R +  + +  G  +    P       P+
Sbjct: 481 RVANTSTQTMGPRPAA-------AAAAATPAVRTVPQYKYAAGVRN----PQQHLNAQPQ 529

Query: 545 RDASVGQPM-------PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGML 597
              ++ QP        P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGML
Sbjct: 530 --VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGML 585

Query: 598 LEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 634
           LE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 586 LEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Bos taurus (taxid: 9913)

>sp|Q5R8F7|PABP1_PONAB Polyadenylate-binding protein 1 OS=Pongo abelii GN=PABPC1 PE=2 SV=1

 Score =  525 bits (1351), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 297/637 (46%), Positives = 404/637 (63%), Gaps = 43/637 (6%)

Query: 23  SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
           S   +   SLYVGDL  + T++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PA
Sbjct: 4   SAPSYPMASLYVGDLHPDATEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63

Query: 83  DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
           DA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123

Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETV 202
           NILSCK+  D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F  ++ERE  
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182

Query: 203 --AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENAD 260
             A   +F NV++KN  E   DE LK +FG++G   S  VM D  GKSK FGFV+FE  +
Sbjct: 183 LGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHE 242

Query: 261 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 320
           DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +FEQ  ++ + ++QG+NLY+KNL 
Sbjct: 243 DAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLD 302

Query: 321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
           D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS+PEEA++A+ EMNG+++ +K
Sbjct: 303 DGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 361

Query: 381 PLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFL-YGQAPPA 439
           PLYVA+AQRKEER+A L  Q+ Q          P   P  P  PSG     +   Q   A
Sbjct: 362 PLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAA 421

Query: 440 IIPP--------------QAGFGYQQQLVPG-MRPAGAPMPNFFVPVVSQGQQGQRPGGR 484
             PP              Q    +  Q +PG +RPA AP P F     +  Q  +    +
Sbjct: 422 YYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-APRPPFSTMRPASSQVPRVMSTQ 480

Query: 485 RGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPR 544
           R A    QT  P P           A   P  R +  + +  G  +    P       P+
Sbjct: 481 RVANTSTQTMGPRPAA-------AAAAATPAVRTVPQYKYAAGVRN----PQQHLNAQPQ 529

Query: 545 RDASVGQPM-------PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGML 597
              ++ QP        P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGML
Sbjct: 530 --VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGML 585

Query: 598 LEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 634
           LE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 586 LEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Pongo abelii (taxid: 9601)

>sp|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=2 SV=1

 Score =  523 bits (1348), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 297/634 (46%), Positives = 404/634 (63%), Gaps = 37/634 (5%)

Query: 23  SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
           S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PA
Sbjct: 4   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63

Query: 83  DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
           DA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123

Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETV 202
           NILSCK+  D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F  ++ERE  
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182

Query: 203 --AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENAD 260
             A   +F NV++KN  E   DE LK++FG++G   S  VM D  GKSK FGFV+FE  +
Sbjct: 183 LGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHE 242

Query: 261 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 320
           DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +FEQ  ++ + ++QG+NLY+KNL 
Sbjct: 243 DAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLD 302

Query: 321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
           D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS+PEEA++A+ EMNG+++ +K
Sbjct: 303 DGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 361

Query: 381 PLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFL-YGQAPPA 439
           PLYVA+AQRKEER+A L  Q+ Q          P   P  P  PSG     +   Q   A
Sbjct: 362 PLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAA 421

Query: 440 IIPP--------------QAGFGYQQQLVPG-MRPAGAPMPNFFVPVVSQGQQGQRPGGR 484
             PP              Q    +  Q +PG +RPA AP P F     +  Q  +    +
Sbjct: 422 YYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-APRPPFSTMRPASSQVPRVMSTQ 480

Query: 485 RGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFP-FDMGAGSMLP---VPVDMGA 540
           R A    QT          M PR  A        ++  P +   AG   P   +      
Sbjct: 481 RVANTSTQT----------MGPRPAAAATAATPAVRTVPQYKYAAGVRNPQQHLNAQPQV 530

Query: 541 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 600
            + +    V    P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+
Sbjct: 531 TMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEI 588

Query: 601 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 634
           D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 589 DNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Rattus norvegicus (taxid: 10116)

>sp|Q6IP09|PABPB_XENLA Polyadenylate-binding protein 1-B OS=Xenopus laevis GN=pabpc1-b PE=2 SV=1

 Score =  520 bits (1340), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 304/653 (46%), Positives = 406/653 (62%), Gaps = 58/653 (8%)

Query: 23  SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
           S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PA
Sbjct: 4   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63

Query: 83  DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
           DA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123

Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETV 202
           NILSCK+  D +G SKG+GFV FE +E+A+ AIDK+NGML+ND++VFVG F  ++ERE  
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIDKMNGMLLNDRKVFVGRFKSRKEREAE 182

Query: 203 --AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENAD 260
             A   +F NV++KN  E   DE LK+ FG+YG   S  VM D  GKS+ FGFV+FE  +
Sbjct: 183 LGARAKEFTNVYIKNFGEDMDDERLKEWFGQYGAALSVKVMTDDHGKSRGFGFVSFERHE 242

Query: 261 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 320
           DA KAV+ +NGK  + +  +VG+AQKK ER+ ELK +FEQ  ++ + ++QG+NLY+KNL 
Sbjct: 243 DAQKAVDDMNGKDLNGKAIFVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLD 302

Query: 321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
           D IDDE+L++ F+ FG+ITS KVM +  G SKG GFV FS+PEEA++A+ EMNG+++ +K
Sbjct: 303 DGIDDERLRKEFTPFGSITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 361

Query: 381 PLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPP-- 438
           PLYVA+AQRKEER+A L  Q+ Q       P+  P +  Y P PS     +     PP  
Sbjct: 362 PLYVALAQRKEERQAHLTNQYMQRMASVRVPN--PVINPYQPPPSS----YFMAAIPPAQ 415

Query: 439 ---AIIPPQAGFGYQQQLVP-------GMRP------AG-----APMPNFFVPVVSQGQQ 477
              A  PP    G   QL P       G RP      AG     AP P  F  +    Q 
Sbjct: 416 NRAAYYPP----GQIAQLRPSPRWTAQGARPHPFQNMAGAIRPSAPRPPTFSTMRPTSQV 471

Query: 478 GQRPGGRRGAGPVQQTQQPLPIMPHQMPPRG----HAYRYPLG-RNMQDFPFDMGAGSML 532
            +    +R A    QT  P P                Y+Y  G RN Q         +M 
Sbjct: 472 PRVMSAQRVANTSTQTMGPRPTTAAAAATSAVRTVPQYKYAAGVRNTQQHLNTQPQVAMQ 531

Query: 533 PVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAK 592
              V +           GQ  P+TA  + LA A P++Q+ +LGE L+PL++ +    A K
Sbjct: 532 QPAVHVQ----------GQE-PLTA--SMLAAAPPQEQKQMLGERLFPLIQAMHPTLAGK 578

Query: 593 VTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLS 645
           +TGMLLE+D +E+LH+LESPE+L++KV EA+ VL++    QA   A ++ S +
Sbjct: 579 ITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQA---HQAKEAAQKVVSAT 628

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.

Xenopus laevis (taxid: 8355)

>sp|Q5B630|PABP_EMENI Polyadenylate-binding protein, cytoplasmic and nuclear OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=pab1 PE=2 SV=2

 Score =  515 bits (1326), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 305/710 (42%), Positives = 408/710 (57%), Gaps = 114/710 (16%)

Query: 18  VAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN 77
           V A A+ +Q  + SLYVG+LD +VT++ LY+LFS +GQV S+RVCRD  TRRSLGY YVN
Sbjct: 30  VEAPATTSQPHSASLYVGELDPSVTEAMLYELFSSIGQVASIRVCRDAVTRRSLGYAYVN 89

Query: 78  YANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDT 137
           Y + A   RALD LN+T +  K  RIM+S RDP++RK+G GN+FIKNLD +ID+KALHDT
Sbjct: 90  YNDTAHGERALDELNYTLIKGKPCRIMWSQRDPALRKTGQGNVFIKNLDSAIDNKALHDT 149

Query: 138 FSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQ 197
           F++FGNILSCK+A D  G SKG+GFV +E  E+A NAI  +NGML+NDK+VFVGH + K+
Sbjct: 150 FAAFGNILSCKVAQDEFGVSKGYGFVHYETAEAANNAIKHVNGMLLNDKKVFVGHHISKK 209

Query: 198 ERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVN 255
           +R++    +K  F N+++KN+D    DE+ +K+F ++G ITSA + RD +GKS+ FGFVN
Sbjct: 210 DRQSKFEEMKANFTNIYIKNIDPEVEDEEFRKLFEKFGEITSATLSRDSEGKSRGFGFVN 269

Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLY 315
           F   + A  AVE +N K+   ++ YVG+AQKK ERE+EL+ Q+E A  E   K+QG+NLY
Sbjct: 270 FSTHESAQAAVEEMNDKEVRSQKLYVGRAQKKHEREEELRKQYEAARMEKASKYQGVNLY 329

Query: 316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRD----------------------------- 346
           +KNL D +DD+KL+ELF  +GTITS KVMRD                             
Sbjct: 330 VKNLTDDVDDDKLRELFGPYGTITSAKVMRDTAPVETATPESETKESANKENEKAAEGEK 389

Query: 347 ----------------------PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
                                 P G SKG GFV FS+P+EAS+A+ EMN +M+  KPLYV
Sbjct: 390 EPAAEEKEKEEKKEAEQKPEKKPLGKSKGFGFVCFSSPDEASKAVTEMNQRMVNGKPLYV 449

Query: 385 AVAQRKEERRARLQAQFSQMRPVA--------------MGPSVPPRMPMYPPGPSGLGQQ 430
           A+AQRK+ RR++L+A       +               M P+V      Y PG  G    
Sbjct: 450 ALAQRKDVRRSQLEASIQARNNIRQQQAAAAAGMGQAYMAPAV-----FYGPGQQG---- 500

Query: 431 FLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPV 490
           F+ G     + PPQ G        PG  P   P P         GQQG      RG GP 
Sbjct: 501 FIPGAQRGGMFPPQPGMMMGMPGRPGQYP--GPFP---------GQQGG-----RGVGPN 544

Query: 491 QQTQ---QPLPIMPHQMPPRGHAYRYPL---------------GRNMQDFPFDMGAGSML 532
           QQ     Q LP+   Q P   +   YP+               G          G    +
Sbjct: 545 QQIPPNFQGLPMGAMQGPGIPNGMGYPMVQGQFGGGRGRGQVPGMGGPMRGGYGGGRGGV 604

Query: 533 PVPVDMGAGIPRRDASVGQPMPITAL----STALANASPEQQRTLLGESLYPLVEQLERD 588
           P+   M  G   R  +VGQP P T +    + AL+ A P+QQ+ +LGE+LYP ++  + +
Sbjct: 605 PLGGQMRPGQGGRGQAVGQPGPETPVGVLTAQALSAAPPQQQKQMLGEALYPKIQATQPE 664

Query: 589 AAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPA 638
            A K+TGMLLEMD TE+L LLE  EAL+AKV EA+ V     + +++ PA
Sbjct: 665 LAGKITGMLLEMDNTELLGLLEDDEALRAKVDEALSVYDEYMKNKSDEPA 714

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

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	652
356564176	654	PREDICTED: polyadenylate-binding protein	0.995	0.992	0.802	0.0
224063493	657	predicted protein [Populus trichocarpa]	0.995	0.987	0.828	0.0
255538240	658	polyadenylate-binding protein, putative	0.996	0.987	0.801	0.0
224137600	632	predicted protein [Populus trichocarpa]	0.967	0.998	0.836	0.0
225458678	640	PREDICTED: polyadenylate-binding protein	0.978	0.996	0.822	0.0
225438781	654	PREDICTED: polyadenylate-binding protein	0.960	0.957	0.802	0.0
356521524	651	PREDICTED: polyadenylate-binding protein	0.996	0.998	0.785	0.0
356499763	646	PREDICTED: polyadenylate-binding protein	0.990	1.0	0.781	0.0
356552218	652	PREDICTED: polyadenylate-binding protein	0.995	0.995	0.806	0.0
386780450	657	poly(A)-binding protein [Nicotiana tabac	0.995	0.987	0.784	0.0

>gi|356564176|ref|XP_003550332.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score = 1060 bits (2742), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 527/657 (80%), Positives = 586/657 (89%), Gaps = 8/657 (1%)

Query: 1   MAQIQVQHQAQMSG---PNGVAAGA--SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ 55
           MA+IQVQHQ+ +S    PNG  A A  + NQF+TTSLYVGDLD NV DSQLYDLF+QVGQ
Sbjct: 1   MAEIQVQHQSPVSAAPPPNGGVANAPNNANQFVTTSLYVGDLDQNVNDSQLYDLFNQVGQ 60

Query: 56  VLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKS 115
           V+SVRVCRDL+TRRSLGYGYVN++NP DAARALDVLNFTPLNN+SIRIMYSHRDPS+RKS
Sbjct: 61  VVSVRVCRDLTTRRSLGYGYVNFSNPQDAARALDVLNFTPLNNRSIRIMYSHRDPSLRKS 120

Query: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           GT NIFIKNLDK+IDHKALHDTFSSFG ILSCKIATD SG SKG+GFVQF+N+E+AQNAI
Sbjct: 121 GTANIFIKNLDKAIDHKALHDTFSSFGLILSCKIATDASGLSKGYGFVQFDNEEAAQNAI 180

Query: 176 DKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTI 235
           DKLNGMLINDKQV+VGHFLRKQ+RE    KTKFNNV+VKNL ESTTDE+L   FGEYGTI
Sbjct: 181 DKLNGMLINDKQVYVGHFLRKQDRENALSKTKFNNVYVKNLSESTTDEELMINFGEYGTI 240

Query: 236 TSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELK 295
           TSA++MRD DGKS+CFGFVNFEN DDAAKAVE LNGKKFDD+EWYVGKAQKKSEREQELK
Sbjct: 241 TSALIMRDADGKSRCFGFVNFENPDDAAKAVEGLNGKKFDDKEWYVGKAQKKSEREQELK 300

Query: 296 GQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSG 355
           G+FEQ++KE  DK+ GLNLY+KNL D+I DEKLKE+F+++GTITSCKVMRDP+GIS+GSG
Sbjct: 301 GRFEQSIKEAADKYPGLNLYLKNLDDTISDEKLKEMFADYGTITSCKVMRDPTGISRGSG 360

Query: 356 FVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPP 415
           FVAFSTPEEA+RAL EMNGKM   KPLYVA+AQRKEERRARLQAQFSQMRPVA+ PSV P
Sbjct: 361 FVAFSTPEEATRALGEMNGKMFAGKPLYVALAQRKEERRARLQAQFSQMRPVAITPSVAP 420

Query: 416 RMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQG 475
           RMP+YPPG  GLGQQFLYGQ PPA++PPQAGFGYQQQLVPGMRP G PMP+FFVP+V QG
Sbjct: 421 RMPLYPPGAPGLGQQFLYGQGPPAMMPPQAGFGYQQQLVPGMRPGGGPMPSFFVPMVQQG 480

Query: 476 QQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVP 535
           QQGQRP GRRG GPVQQ QQP+P+M  QM PRG  YRYP GRNMQD P  + AG ML VP
Sbjct: 481 QQGQRPVGRRGTGPVQQPQQPMPMMQQQMLPRGRVYRYPPGRNMQDVPLQVAAGGMLSVP 540

Query: 536 VDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTG 595
            DMG G+P RDA VGQPMPI AL+TALANA PEQQRT+LGE+LYPLV+QLE D+AAKVTG
Sbjct: 541 YDMG-GLPMRDA-VGQPMPIQALATALANAPPEQQRTMLGEALYPLVDQLEHDSAAKVTG 598

Query: 596 MLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 652
           MLLEMDQ EVLHL+ESP+ALKAKVAEAM+VLR+VAQQQ  NPADQLASLSLN+NLVS
Sbjct: 599 MLLEMDQPEVLHLIESPDALKAKVAEAMDVLRNVAQQQT-NPADQLASLSLNDNLVS 654

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224063493|ref|XP_002301171.1| predicted protein [Populus trichocarpa] gi|222842897|gb|EEE80444.1| predicted protein [Populus trichocarpa]

 Score = 1035 bits (2677), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 542/654 (82%), Positives = 588/654 (89%), Gaps = 5/654 (0%)

Query: 1   MAQIQV-QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSV 59
           MAQIQV Q  A + GPNGVAAG    QF+ TSLYVGDLDFNVTDSQLYDLF+QVGQV+SV
Sbjct: 1   MAQIQVHQAAAPVPGPNGVAAGPGAIQFVPTSLYVGDLDFNVTDSQLYDLFNQVGQVVSV 60

Query: 60  RVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           RVCRDLSTRRSLGYGYVNY+NP DAARALDVLNFTPLNNK +RIMYSHRDPSIRKSG  N
Sbjct: 61  RVCRDLSTRRSLGYGYVNYSNPQDAARALDVLNFTPLNNKPLRIMYSHRDPSIRKSGMAN 120

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IFIKNLDK+IDHKALHDTFSSFGNILSCK+ATD SGQSKG+GFVQF+++E+AQNAIDKLN
Sbjct: 121 IFIKNLDKTIDHKALHDTFSSFGNILSCKVATDASGQSKGYGFVQFDSEEAAQNAIDKLN 180

Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 239
           GMLINDKQV+VG+FLRKQER++     KFNN++VKNL ESTTDEDLK IF E+G ITSAV
Sbjct: 181 GMLINDKQVYVGNFLRKQERDSALSNIKFNNIYVKNLAESTTDEDLKSIFEEHGAITSAV 240

Query: 240 VMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFE 299
           VMRD DGKSKCFGFVNFEN DDAAKAVEALNGKKFDD+EWYVGKAQKKSERE ELKG+FE
Sbjct: 241 VMRDADGKSKCFGFVNFENVDDAAKAVEALNGKKFDDKEWYVGKAQKKSERELELKGRFE 300

Query: 300 QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 359
           Q++ E+V+K+Q +NLYIKNL DS++DEKLKELFS+FGTITSCKVM DPSGIS+GSGFVAF
Sbjct: 301 QSL-ESVEKYQAVNLYIKNLDDSVNDEKLKELFSDFGTITSCKVMHDPSGISRGSGFVAF 359

Query: 360 STPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPM 419
           STPEEASRALAE+NGKM+VSKPLYVA AQRKEERRARLQAQFSQMRPVAM PSV PRM M
Sbjct: 360 STPEEASRALAELNGKMVVSKPLYVAPAQRKEERRARLQAQFSQMRPVAMAPSVAPRMQM 419

Query: 420 YPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQ 479
           YPPG  GLGQQFLYGQ PPA+I PQAGFGYQQQLVPGMRP GAPMPNFFVP+V QGQQGQ
Sbjct: 420 YPPGAPGLGQQFLYGQGPPAMI-PQAGFGYQQQLVPGMRPGGAPMPNFFVPLVQQGQQGQ 478

Query: 480 RPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMG 539
           RPGGRRG GPVQQTQQP+P+M  QM PRG  YRYP GRNM D P    AG ML VP DMG
Sbjct: 479 RPGGRRGGGPVQQTQQPVPLMQQQMLPRGRVYRYPPGRNMPDVPMPGVAGGMLSVPYDMG 538

Query: 540 AGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLE 599
             +P RDA+ GQPMPITAL+TALANA+PEQQRT+LGE LYPLV+QLE D+AAKVTGMLLE
Sbjct: 539 V-MPIRDAAGGQPMPITALATALANATPEQQRTMLGEGLYPLVDQLEHDSAAKVTGMLLE 597

Query: 600 MDQTEVLHLLESPEALKAKVAEAMEVLRSV-AQQQANNPADQLASLSLNENLVS 652
           MDQTEVLHLLESPEALKAKVAEAMEVLR+V AQQQ NNPAD LASLSLNENLVS
Sbjct: 598 MDQTEVLHLLESPEALKAKVAEAMEVLRTVAAQQQINNPADHLASLSLNENLVS 651

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538240|ref|XP_002510185.1| polyadenylate-binding protein, putative [Ricinus communis] gi|223550886|gb|EEF52372.1| polyadenylate-binding protein, putative [Ricinus communis]

 Score = 1027 bits (2655), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 529/660 (80%), Positives = 579/660 (87%), Gaps = 10/660 (1%)

Query: 1   MAQIQVQHQAQMSG---PNGVAAGASGNQ----FLTTSLYVGDLDFNVTDSQLYDLFSQV 53
           MAQIQVQHQ+  +    P    A A+       ++ TSLYVGDLD NVTDSQLYD+F+QV
Sbjct: 1   MAQIQVQHQSAAAAAPIPGANGAAAAAGSGSVPYMPTSLYVGDLDLNVTDSQLYDVFNQV 60

Query: 54  GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIR 113
           GQV+SVRVCRDL+TRRSLGYGYVNY +P DAARALD+LNFTP NNK IRIMYSHRDPSIR
Sbjct: 61  GQVVSVRVCRDLTTRRSLGYGYVNYTSPQDAARALDILNFTPFNNKPIRIMYSHRDPSIR 120

Query: 114 KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQN 173
           KSGTGNIFIKNLDK+IDHKALHDTFSSFGNILSCK+ATD SGQS+G+GFVQF+N+E+AQN
Sbjct: 121 KSGTGNIFIKNLDKTIDHKALHDTFSSFGNILSCKVATDSSGQSRGYGFVQFDNEEAAQN 180

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG 233
           AIDKLNGML+NDKQV+VGHFLRK ER++ + K KFNNV+VKNL ESTT+EDLK IFGEYG
Sbjct: 181 AIDKLNGMLLNDKQVYVGHFLRKHERDSASNK-KFNNVYVKNLSESTTEEDLKNIFGEYG 239

Query: 234 TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQE 293
            ITSAV+MRD DGKSKCFGFVNFEN D AAKAVE+LNGKK DD+EWYVGKAQKKSERE E
Sbjct: 240 EITSAVIMRDADGKSKCFGFVNFENTDAAAKAVESLNGKKIDDKEWYVGKAQKKSERELE 299

Query: 294 LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKG 353
           LK QFEQ+MKE VDK+QG+NLYIKNL DSI DE LKELFS+FG ITSCKVMRDPSGIS+G
Sbjct: 300 LKSQFEQSMKEAVDKYQGVNLYIKNLDDSISDENLKELFSDFGMITSCKVMRDPSGISRG 359

Query: 354 SGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSV 413
           SGFVAFSTPEEASRALAEMNGKM+VSKPLYVA+AQRKEERRARLQAQFSQMRPVAM PSV
Sbjct: 360 SGFVAFSTPEEASRALAEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPVAMAPSV 419

Query: 414 PPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVS 473
            PRMP+Y PG  G+GQQFLYGQ PP +IPPQ GFGYQQQLVPG+RP GAPMPNFFVP+V 
Sbjct: 420 GPRMPIYSPGAPGMGQQFLYGQGPPTMIPPQGGFGYQQQLVPGIRPGGAPMPNFFVPMVQ 479

Query: 474 QGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLP 533
           QGQQGQR GGRRGA PVQQ QQP+P+M  QM PRG  YRYP GRNM D P    AG ML 
Sbjct: 480 QGQQGQRHGGRRGAVPVQQNQQPVPLMHQQMLPRGRVYRYPPGRNMPDVPMPGVAGGMLS 539

Query: 534 VPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKV 593
           VP DMG G+P RDA+ GQP+PITAL+TALANASPE QRTLLGESLYPLV+QLE ++AAKV
Sbjct: 540 VPYDMG-GMPIRDAAAGQPVPITALATALANASPEHQRTLLGESLYPLVDQLEHESAAKV 598

Query: 594 TGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV-AQQQANNPADQLASLSLNENLVS 652
           TGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV AQQ ANN ADQL SLSLN+ LVS
Sbjct: 599 TGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAAQQHANNTADQLTSLSLNDGLVS 658

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137600|ref|XP_002327166.1| predicted protein [Populus trichocarpa] gi|222835481|gb|EEE73916.1| predicted protein [Populus trichocarpa]

 Score = 1024 bits (2648), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 531/635 (83%), Positives = 573/635 (90%), Gaps = 4/635 (0%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           AAG    QF+ TSLYVGDLDFNVTDSQLYD+F+QVGQV+SVRVCRDLSTRRSLGYGYVNY
Sbjct: 1   AAGPGAIQFVPTSLYVGDLDFNVTDSQLYDVFNQVGQVVSVRVCRDLSTRRSLGYGYVNY 60

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTF 138
           +NP DAARALDVLNFTPLNNK IRIMYSHRDPSIRKSG  NIFIKNLDK IDHKALHDTF
Sbjct: 61  SNPQDAARALDVLNFTPLNNKPIRIMYSHRDPSIRKSGMANIFIKNLDKGIDHKALHDTF 120

Query: 139 SSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQE 198
           SSFGNILSCK+ATD SGQSKG+GFVQF+++E+AQNAIDKLNGML+NDKQV+VGHFLRKQ+
Sbjct: 121 SSFGNILSCKVATDASGQSKGYGFVQFDSEEAAQNAIDKLNGMLVNDKQVYVGHFLRKQD 180

Query: 199 RETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN 258
           R+      KFNNVFVKNL ESTTDE+LK IF E+G ITSAVVMRD DGKSKCFGFVNFE+
Sbjct: 181 RDGALYSIKFNNVFVKNLAESTTDEELKNIFAEHGAITSAVVMRDADGKSKCFGFVNFES 240

Query: 259 ADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKN 318
           ADDAAKAVEALNGKK D  EWYVGKAQKKSERE ELKG+FEQ+MKETVDKFQGLNLYIKN
Sbjct: 241 ADDAAKAVEALNGKKIDGEEWYVGKAQKKSERELELKGRFEQSMKETVDKFQGLNLYIKN 300

Query: 319 LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV 378
           L DSI+DEKLKELFS+FG ITSCKVMRDPSGIS+GSGFVAFSTPEEASRALAEMNGKM++
Sbjct: 301 LDDSINDEKLKELFSDFGAITSCKVMRDPSGISRGSGFVAFSTPEEASRALAEMNGKMLI 360

Query: 379 SKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPP 438
           SKPLYVA+AQRKEERRARLQAQFSQMRPV M PSV  RMPMYPPG  G+GQQFLYGQ PP
Sbjct: 361 SKPLYVALAQRKEERRARLQAQFSQMRPVTMAPSVASRMPMYPPGAPGMGQQFLYGQGPP 420

Query: 439 AIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLP 498
           A++PPQAGFGYQQQLVPGMRP GAPMPNFFVP+V QGQQGQRPGGRRG GPVQQTQQP+P
Sbjct: 421 AMMPPQAGFGYQQQLVPGMRPGGAPMPNFFVPLVQQGQQGQRPGGRRGGGPVQQTQQPVP 480

Query: 499 IMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITAL 558
           +M  QM PRG  YRYP GRNM D P    AG ML VP DMG G+P RDA+  QPMPITAL
Sbjct: 481 LMQQQMLPRGRVYRYPPGRNMPDVPMPGVAGGMLSVPYDMG-GMPIRDAA--QPMPITAL 537

Query: 559 STALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAK 618
           +TALANA+PEQQRT+LGESLYP+V+QLE D+AAKVTGMLLEMDQTEVLHLLESPEALKAK
Sbjct: 538 ATALANATPEQQRTMLGESLYPIVDQLEHDSAAKVTGMLLEMDQTEVLHLLESPEALKAK 597

Query: 619 VAEAMEVLRSV-AQQQANNPADQLASLSLNENLVS 652
           VAEAMEVLR+V AQQQ NN ADQL SLSLN+NLVS
Sbjct: 598 VAEAMEVLRTVAAQQQINNQADQLGSLSLNDNLVS 632

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458678|ref|XP_002284923.1| PREDICTED: polyadenylate-binding protein 2 [Vitis vinifera] gi|147773643|emb|CAN76464.1| hypothetical protein VITISV_017035 [Vitis vinifera]

 Score = 1023 bits (2646), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 536/652 (82%), Positives = 583/652 (89%), Gaps = 14/652 (2%)

Query: 1   MAQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVR 60
           MAQIQ    A ++GPNGVA         T SLYVGDLD N+TDSQLYDLF Q GQVLSVR
Sbjct: 1   MAQIQ----AAVAGPNGVAN--------TASLYVGDLDVNITDSQLYDLFIQAGQVLSVR 48

Query: 61  VCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNI 120
           VCRDLSTRRSLGYGYVNY+NP DAARALD+LNFTPLN K IRIMYSHRDPSIRKSGT NI
Sbjct: 49  VCRDLSTRRSLGYGYVNYSNPQDAARALDLLNFTPLNGKPIRIMYSHRDPSIRKSGTANI 108

Query: 121 FIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNG 180
           FIKNLDKSID+KALHDTFS+FGNILSCKIATD SGQSKG+GFVQF+N+ESAQNAIDKLNG
Sbjct: 109 FIKNLDKSIDNKALHDTFSAFGNILSCKIATDPSGQSKGYGFVQFDNEESAQNAIDKLNG 168

Query: 181 MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 240
           MLINDKQV+VG FLRKQERET   KTKFNNV+VKNL ESTT+EDLK IFGE+G ITS VV
Sbjct: 169 MLINDKQVYVGQFLRKQERETALNKTKFNNVYVKNLSESTTEEDLKNIFGEFGIITSVVV 228

Query: 241 MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 300
           MRDGDGKSKCFGFVNFENADDAA+AVEALNGKKFD++EWYVGKAQKK ERE ELKG+FEQ
Sbjct: 229 MRDGDGKSKCFGFVNFENADDAAEAVEALNGKKFDEKEWYVGKAQKKYERELELKGRFEQ 288

Query: 301 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 360
           +MKE VDKFQG+NLYIKNL DSI D+KLKELFSEFGTITSCKVMRDPSGIS+GSGFVAFS
Sbjct: 289 SMKEVVDKFQGVNLYIKNLDDSIGDDKLKELFSEFGTITSCKVMRDPSGISRGSGFVAFS 348

Query: 361 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 420
           T EEASRAL EMNGKM+VSKPLYVA+AQRKEERRARLQAQFSQMRPV+M PSV PRMPMY
Sbjct: 349 TSEEASRALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPVSMAPSVAPRMPMY 408

Query: 421 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 480
           PPG  GLGQQ  YGQ PPAIIPPQAGFGYQQQLVPGMRP GAPMPNFFVP+V QGQQGQR
Sbjct: 409 PPGAPGLGQQLFYGQGPPAIIPPQAGFGYQQQLVPGMRPGGAPMPNFFVPLVQQGQQGQR 468

Query: 481 PGGRRGAGPVQQTQQPLPIMPHQMPPR-GHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMG 539
           PGGRRGAGPVQQ QQP+P+M  QM PR G  YRYP GRNM D P    AG ML +P DMG
Sbjct: 469 PGGRRGAGPVQQNQQPVPLMQQQMLPRGGRVYRYPPGRNMPDVPMPGVAGGMLSIPYDMG 528

Query: 540 AGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLE 599
            G+P RDA++GQPMPI+AL++ALANA+P+QQRT+LGESLYPLV+QLE + AAKVTGMLLE
Sbjct: 529 -GVPLRDAAIGQPMPISALASALANATPDQQRTMLGESLYPLVDQLEHEMAAKVTGMLLE 587

Query: 600 MDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLV 651
           MDQTEVLHLLESPEALK+KVAEAM+VLR+VAQQQAN+P +QLASLSLN++LV
Sbjct: 588 MDQTEVLHLLESPEALKSKVAEAMDVLRNVAQQQANSPTEQLASLSLNDSLV 639

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438781|ref|XP_002283105.1| PREDICTED: polyadenylate-binding protein 2 [Vitis vinifera] gi|296082381|emb|CBI21386.3| unnamed protein product [Vitis vinifera]

 Score = 1012 bits (2616), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 504/628 (80%), Positives = 555/628 (88%), Gaps = 2/628 (0%)

Query: 26  QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAA 85
           QF++TSLYVGDL+ NVTDS LYDLF Q+G V+SVRVCRDLSTRRSLGYGYVNY N  DAA
Sbjct: 28  QFVSTSLYVGDLESNVTDSHLYDLFGQLGPVVSVRVCRDLSTRRSLGYGYVNYGNTQDAA 87

Query: 86  RALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNIL 145
           RALD+LNFTPLN K IRIMYS RDPSIR+SGT NIFIKNLDK+ID+KAL+DTFS+FG IL
Sbjct: 88  RALDMLNFTPLNGKPIRIMYSFRDPSIRRSGTANIFIKNLDKAIDNKALYDTFSTFGAIL 147

Query: 146 SCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIK 205
           SCKIATD SGQSKG+GFVQF+N+ESA+NA DKLNGML+NDKQV+VG F+RKQERE+   K
Sbjct: 148 SCKIATDASGQSKGYGFVQFDNEESAKNATDKLNGMLLNDKQVYVGPFVRKQERESATNK 207

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
           TKFNNV+VKNL ESTTDEDLK IFGEYG ITSAVVM+DGDGKSKCFGFVNFENADDAA++
Sbjct: 208 TKFNNVYVKNLLESTTDEDLKNIFGEYGPITSAVVMQDGDGKSKCFGFVNFENADDAARS 267

Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           VEALNGKKFDD+EWYVGKAQKK+ERE ELKG+FEQ++KE VDKFQGLNLY+KNL DSI D
Sbjct: 268 VEALNGKKFDDKEWYVGKAQKKTEREVELKGRFEQSLKEAVDKFQGLNLYVKNLDDSIAD 327

Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 385
           +KL+ELFSEFGTITSCKVMRDP+GIS+GSGFVAFST EEASRALA+MNGKM+ SKPLYVA
Sbjct: 328 DKLRELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASRALADMNGKMVASKPLYVA 387

Query: 386 VAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQA 445
           +AQRKE+RRARLQAQFSQMRP AM PSV PRM MYPPG  GLGQQ  YGQ PPA+IPPQ 
Sbjct: 388 LAQRKEDRRARLQAQFSQMRPAAMAPSVGPRMSMYPPGAPGLGQQLFYGQGPPALIPPQP 447

Query: 446 GFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRR-GAGPVQQTQQPLPIMPHQM 504
           GFGYQ QLVPGMRP  APMPNFFVP+V  GQ  QRPGGRR G GPVQQTQQPLP+M  QM
Sbjct: 448 GFGYQHQLVPGMRPGAAPMPNFFVPMVQPGQPNQRPGGRRSGTGPVQQTQQPLPLMQQQM 507

Query: 505 PPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALAN 564
            PRG  YRYP GRNM D P     G ML  P DM AG+P RDA+V QPMPI AL+TALAN
Sbjct: 508 LPRGRVYRYPPGRNMADVPIPGVPGGMLSAPYDM-AGMPFRDAAVSQPMPIGALATALAN 566

Query: 565 ASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME 624
           A P+QQRTLLGE+LYPLV+QLE + AAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME
Sbjct: 567 APPDQQRTLLGENLYPLVDQLEHEMAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME 626

Query: 625 VLRSVAQQQANNPADQLASLSLNENLVS 652
           VLR+VAQQQANNP D++ASLSLN+ L S
Sbjct: 627 VLRNVAQQQANNPTDRMASLSLNDTLTS 654

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521524|ref|XP_003529405.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score = 1010 bits (2611), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 513/653 (78%), Positives = 571/653 (87%), Gaps = 3/653 (0%)

Query: 1   MAQIQVQHQAQMSGPNGVAAGASGN-QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSV 59
           MAQ+QV  Q  M GPNG         QF+TTSLYVGDLD NVTD+QLYDLF+Q+GQV+SV
Sbjct: 1   MAQVQVPPQNAMPGPNGGGGAGGAGNQFVTTSLYVGDLDPNVTDAQLYDLFNQLGQVVSV 60

Query: 60  RVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           RVCRDL++RRSLGYGYVN++NP DAARALDVLNFTPLNN+ IRIMYSHRDPSIRKSG GN
Sbjct: 61  RVCRDLTSRRSLGYGYVNFSNPQDAARALDVLNFTPLNNRPIRIMYSHRDPSIRKSGQGN 120

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IFIKNLD++IDHKALHDTFS+FGNILSCK+ATD SGQSKG+GFVQF+N+ESAQ AI+KLN
Sbjct: 121 IFIKNLDRAIDHKALHDTFSTFGNILSCKVATDSSGQSKGYGFVQFDNEESAQKAIEKLN 180

Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 239
           GML+NDKQV+VG FLRKQERE+ A K KFNNVFVKNL ESTTD++LK  FGE+GTITSAV
Sbjct: 181 GMLLNDKQVYVGPFLRKQERESAADKAKFNNVFVKNLSESTTDDELKNTFGEFGTITSAV 240

Query: 240 VMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFE 299
           VMRDGDGKSKCFGFVNFENADDAA+AVEALNGK FDD+EWYVGKAQKKSERE ELK +FE
Sbjct: 241 VMRDGDGKSKCFGFVNFENADDAARAVEALNGKNFDDKEWYVGKAQKKSERENELKQRFE 300

Query: 300 QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 359
           Q+MKE  DK+QG NLY+KNL DSI DEKLKELFS FGTITSCKVMRDP+G+S+GSGFVAF
Sbjct: 301 QSMKEAADKYQGANLYVKNLDDSIGDEKLKELFSPFGTITSCKVMRDPNGLSRGSGFVAF 360

Query: 360 STPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPM 419
           STPEEASRAL EMNGKM+VSKPLYV +AQRKE+RRARLQAQF+QMRPV M PSV PR+PM
Sbjct: 361 STPEEASRALLEMNGKMVVSKPLYVTLAQRKEDRRARLQAQFAQMRPVGMPPSVGPRVPM 420

Query: 420 YPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQ 479
           YPPG  G+GQQ  Y Q PPAIIP Q GFGYQQQL+PGMRP  AP+PNFFVP+V QGQQGQ
Sbjct: 421 YPPGGPGIGQQLFYSQGPPAIIPSQPGFGYQQQLMPGMRPGAAPVPNFFVPMVQQGQQGQ 480

Query: 480 RPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMG 539
           RPGGRR    VQQ+QQP+P+MP QM PRG  YRYP GR + D P    AG M  VP D+G
Sbjct: 481 RPGGRRPGA-VQQSQQPVPMMPQQMLPRGRVYRYPPGRGIPDVPIPGVAGGMFSVPYDVG 539

Query: 540 AGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLE 599
            G+P RDAS+ Q +P+ AL+TALANASPEQQRT+LGE+LYPLVEQLE D AAKVTGMLLE
Sbjct: 540 -GMPLRDASISQQIPVGALATALANASPEQQRTMLGENLYPLVEQLEPDNAAKVTGMLLE 598

Query: 600 MDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 652
           MDQTEVLHLLESPEALKAKVAEAM+VLR+VAQQQA   ADQLASLSLN+NLVS
Sbjct: 599 MDQTEVLHLLESPEALKAKVAEAMDVLRNVAQQQAGGTADQLASLSLNDNLVS 651

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499763|ref|XP_003518706.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score = 1008 bits (2605), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 508/650 (78%), Positives = 569/650 (87%), Gaps = 4/650 (0%)

Query: 1   MAQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVR 60
           MAQ+QV  Q  +        GA+GNQF+TTSLYVGDLD NVTD+QLYDLF+Q+GQV+SVR
Sbjct: 1   MAQVQVPPQNAIP--GPNGGGAAGNQFVTTSLYVGDLDPNVTDAQLYDLFNQLGQVVSVR 58

Query: 61  VCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNI 120
           VCRDL++RRSLGYGYVN++NP DAARALDVLNFTPLNN+ IRIMYSHRDPSIRKSG GNI
Sbjct: 59  VCRDLTSRRSLGYGYVNFSNPQDAARALDVLNFTPLNNRPIRIMYSHRDPSIRKSGQGNI 118

Query: 121 FIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNG 180
           FIKNLD++IDHKALHDTFS+FGNILSCK+ATD SGQSKG+GFVQF+N+ESAQ AI+KLNG
Sbjct: 119 FIKNLDRAIDHKALHDTFSTFGNILSCKVATDSSGQSKGYGFVQFDNEESAQKAIEKLNG 178

Query: 181 MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 240
           ML+NDKQV+VG FLRKQERE+ A K KFNNVFVKNL ESTTD++LK +FGE+GTITSAVV
Sbjct: 179 MLLNDKQVYVGPFLRKQERESTADKAKFNNVFVKNLSESTTDDELKNVFGEFGTITSAVV 238

Query: 241 MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 300
           MRDGDGKSKCFGFVNFENADDAA+AVEALNGKKFDD+EWYVGKAQKKSERE ELK +FEQ
Sbjct: 239 MRDGDGKSKCFGFVNFENADDAARAVEALNGKKFDDKEWYVGKAQKKSERENELKQRFEQ 298

Query: 301 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 360
           +MKE  DK+QG NLY+KNL DS+ D+KLKELFS FGTITSCKVMRDP+GIS+GSGFVAFS
Sbjct: 299 SMKEAADKYQGANLYVKNLDDSLGDDKLKELFSPFGTITSCKVMRDPNGISRGSGFVAFS 358

Query: 361 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 420
           TP+EASRAL EMNGKM+VSKPLYV +AQRKE+RRARLQAQF+QMRPV M PSV PR+PMY
Sbjct: 359 TPDEASRALLEMNGKMVVSKPLYVTLAQRKEDRRARLQAQFAQMRPVGMPPSVGPRVPMY 418

Query: 421 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 480
           PPG  G+GQQ  Y Q PPAIIP Q GFGYQQQLVPGMRP  AP+PNFFVP+V QGQQGQR
Sbjct: 419 PPGGPGIGQQIFYAQGPPAIIPSQPGFGYQQQLVPGMRPGAAPVPNFFVPMVQQGQQGQR 478

Query: 481 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 540
             G R  G VQQ+QQP+P+MP QM PRG  YRYP GR M D      AG M  VP D+G 
Sbjct: 479 -PGGRRTGAVQQSQQPVPMMPQQMLPRGRVYRYPPGRGMPDVSMPGVAGGMFSVPYDVG- 536

Query: 541 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 600
           G+P RDAS+ Q +P+ AL+TALANASPEQQRT+LGE+LYPLVEQLE D AAKVTGMLLEM
Sbjct: 537 GMPLRDASISQQIPVGALATALANASPEQQRTMLGENLYPLVEQLEPDNAAKVTGMLLEM 596

Query: 601 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENL 650
           DQTEVLHLLESPEALKAKVAEAM+VLR+VAQQQA   ADQLASLSLN+NL
Sbjct: 597 DQTEVLHLLESPEALKAKVAEAMDVLRNVAQQQAGGTADQLASLSLNDNL 646

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552218|ref|XP_003544466.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score = 1008 bits (2605), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 528/655 (80%), Positives = 587/655 (89%), Gaps = 6/655 (0%)

Query: 1   MAQIQVQHQAQMSGP--NGVA-AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVL 57
           MAQIQVQHQ+ +S P  NGVA A  + NQF+TTSLYVGDL+ NV D+QLYDLF+QV QV+
Sbjct: 1   MAQIQVQHQSPVSAPPPNGVANAPNNPNQFVTTSLYVGDLEQNVNDAQLYDLFNQVVQVV 60

Query: 58  SVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGT 117
           SVRVCRDL+TRRSLGYGYVN++NP DAARALDVLNFTPLNN+ IRIMYSHRDPS+RKSGT
Sbjct: 61  SVRVCRDLTTRRSLGYGYVNFSNPQDAARALDVLNFTPLNNRPIRIMYSHRDPSLRKSGT 120

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
            NIFIKNLDK+IDHKALHDTFSSFG ILSCKIATD SG SKG+GFVQF+++ESAQNAIDK
Sbjct: 121 ANIFIKNLDKAIDHKALHDTFSSFGLILSCKIATDASGLSKGYGFVQFDSEESAQNAIDK 180

Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 237
           LNGMLINDKQV+VGHFLRKQ+RE    KTKFNNV+VKNL ESTTDE+L K FGEYGTITS
Sbjct: 181 LNGMLINDKQVYVGHFLRKQDRENALSKTKFNNVYVKNLSESTTDEELMKFFGEYGTITS 240

Query: 238 AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQ 297
           AV+MRD DGKS+CFGFVNFEN DDAAKAVE LNGKK DD+EWYVGKAQKKSEREQELKG+
Sbjct: 241 AVIMRDADGKSRCFGFVNFENPDDAAKAVEGLNGKKVDDKEWYVGKAQKKSEREQELKGR 300

Query: 298 FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFV 357
           FEQ++KE+ DK+QG+NLY+KNL D+I DEKLKE+F+E+GTITSCKVMRDP+GI +GSGFV
Sbjct: 301 FEQSIKESADKYQGVNLYLKNLDDTISDEKLKEMFAEYGTITSCKVMRDPTGIGRGSGFV 360

Query: 358 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRM 417
           AFSTPEEASRAL EMNGKMI  KPLYVA+AQRKE+RRARLQAQFSQMRPVA+ PSV PRM
Sbjct: 361 AFSTPEEASRALGEMNGKMIAGKPLYVALAQRKEDRRARLQAQFSQMRPVAITPSVAPRM 420

Query: 418 PMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQ 477
           P+YPPG  GLGQQFLYGQ PPA++PPQAGFGYQQQLVPGMRP G PMP+FFVP+V QGQQ
Sbjct: 421 PLYPPGAPGLGQQFLYGQGPPAMMPPQAGFGYQQQLVPGMRPGGGPMPSFFVPMVQQGQQ 480

Query: 478 GQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVD 537
           GQRPGGRRG GPVQQ QQP+P+M  QM PRG  YRYP GRNMQD P    AG M+ VP D
Sbjct: 481 GQRPGGRRGTGPVQQPQQPMPMMQQQMLPRGRVYRYPPGRNMQDVPLQGVAGGMMSVPYD 540

Query: 538 MGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGML 597
           MG G+P RDA VGQPMPI AL+TALANA PEQQRT+LGE+LYPLV+QLE DAAAKVTGML
Sbjct: 541 MG-GLPIRDA-VGQPMPIQALATALANAPPEQQRTMLGEALYPLVDQLEHDAAAKVTGML 598

Query: 598 LEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 652
           LEMDQ EVLHL+ESP+ALKAKVAEAM+VLR+VAQQQ  NPADQLASLSLN+NLVS
Sbjct: 599 LEMDQPEVLHLIESPDALKAKVAEAMDVLRNVAQQQT-NPADQLASLSLNDNLVS 652

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|386780450|dbj|BAM15222.1| poly(A)-binding protein [Nicotiana tabacum]

 Score = 1006 bits (2602), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 518/660 (78%), Positives = 583/660 (88%), Gaps = 11/660 (1%)

Query: 1   MAQIQVQHQA--------QMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQ 52
           MAQIQVQHQ+          +   G AA A+     +TSLYVGDL+FNVTDSQLYDLF+Q
Sbjct: 1   MAQIQVQHQSPVAGGNGVVAAAVGGAAAVATPGGLTSTSLYVGDLEFNVTDSQLYDLFNQ 60

Query: 53  VGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSI 112
           VGQV+SVRVCRDLSTRRSLGYGYVNY+NP DA+RA+++LNFTP+N KSIR+MYSHRDP++
Sbjct: 61  VGQVVSVRVCRDLSTRRSLGYGYVNYSNPNDASRAMEMLNFTPVNGKSIRVMYSHRDPTL 120

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
           RKSG+ NIFIKNLDKSID+KALHDTFSSFGNILSCKIATD +GQSKG+GFVQ++N+ESAQ
Sbjct: 121 RKSGSANIFIKNLDKSIDNKALHDTFSSFGNILSCKIATDSNGQSKGYGFVQYDNEESAQ 180

Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEY 232
            AIDKLNGML+NDKQV+VGHFLRKQERE+    TKF NV+VKNL ESTTD++LKK+FGE+
Sbjct: 181 GAIDKLNGMLMNDKQVYVGHFLRKQERESTTGMTKFQNVYVKNLSESTTDDELKKVFGEF 240

Query: 233 GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
           G ITSAVVMRD DGKSKCFGF+NFE A+DAAKAVE+LNGKKFDD+EWYVGKAQKKSEREQ
Sbjct: 241 GNITSAVVMRDADGKSKCFGFINFETAEDAAKAVESLNGKKFDDKEWYVGKAQKKSEREQ 300

Query: 293 ELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISK 352
           ELK +FEQ  KE VDK+QGLNLY+KNL D+IDDEKLKELFSEFGTITSCKVMRDPSGIS+
Sbjct: 301 ELKSKFEQTAKEAVDKYQGLNLYVKNLDDTIDDEKLKELFSEFGTITSCKVMRDPSGISR 360

Query: 353 GSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 412
           GSGFVAFST EEASRAL+EMNGKMIVSKPLYVA+AQRKEERRA+LQAQFSQ+RPVAM PS
Sbjct: 361 GSGFVAFSTSEEASRALSEMNGKMIVSKPLYVALAQRKEERRAKLQAQFSQLRPVAMPPS 420

Query: 413 VPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVV 472
           + PRMP+YPPG  G+GQQ  YGQ PPA+IPPQAGFGYQQQLVPGMRP GAPMPNFF+P+V
Sbjct: 421 LAPRMPIYPPGAPGIGQQLFYGQGPPAMIPPQAGFGYQQQLVPGMRPGGAPMPNFFMPLV 480

Query: 473 SQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSML 532
            QGQQGQRPGGRRGAGPVQQTQQP+P+M  QM PRG  YRYP GRN  + P     G ML
Sbjct: 481 QQGQQGQRPGGRRGAGPVQQTQQPMPLMQQQMLPRGRMYRYPPGRNGPEGPMPGVPGGML 540

Query: 533 PVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAK 592
            VP DMG  +P RD+++GQPMPI+ L++ALANA PEQQRT+LGESLYPLV+QLE + AAK
Sbjct: 541 SVPYDMGGMLP-RDSAMGQPMPISTLASALANAPPEQQRTMLGESLYPLVDQLEHEHAAK 599

Query: 593 VTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 652
           VTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLR+V  QQ  NPADQLASLSLN+NLVS
Sbjct: 600 VTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRNV--QQTTNPADQLASLSLNDNLVS 657

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P42731	PABP2_ARATH	No assigned EC number	0.6788	0.9493	0.9841	yes	no
Q6CDH3	PABP_YARLI	No assigned EC number	0.4253	0.8481	0.8791	yes	no
Q5R8F7	PABP1_PONAB	No assigned EC number	0.4662	0.9110	0.9339	yes	no
P31209	PABP_SCHPO	No assigned EC number	0.4532	0.8788	0.8774	yes	no
P61286	PABP1_BOVIN	No assigned EC number	0.4678	0.9110	0.9339	yes	no
P0CP46	PABP_CRYNJ	No assigned EC number	0.4528	0.8773	0.8499	yes	no
A3LXL0	PABP_PICST	No assigned EC number	0.4429	0.8389	0.8655	yes	no
Q5B630	PABP_EMENI	No assigned EC number	0.4295	0.9141	0.8142	yes	no
Q9EPH8	PABP1_RAT	No assigned EC number	0.4684	0.9156	0.9386	yes	no
Q54BM2	PAP1A_DICDI	No assigned EC number	0.4555	0.8435	0.9734	yes	no
Q6BI95	PABP_DEBHA	No assigned EC number	0.4256	0.8527	0.8867	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	652
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.0
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-60
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-49
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-48
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-45
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-44
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-34
pfam00658	72	pfam00658, PABP, Poly-adenylate binding protein, u	2e-32
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-29
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-28
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-28
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-28
smart00517	64	smart00517, PolyA, C-terminal domain of Poly(A)-bi	9e-28
smart00360	73	smart00360, RRM, RNA recognition motif	2e-26
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-26
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-26
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-26
smart00360	73	smart00360, RRM, RNA recognition motif	2e-23
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-23
smart00360	73	smart00360, RRM, RNA recognition motif	1e-22
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-22
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-22
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-22
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-22
smart00360	73	smart00360, RRM, RNA recognition motif	2e-21
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-21
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-20
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-20
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-20
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	8e-20
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-19
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-19
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-19
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-19
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-18
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-18
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-18
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-18
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-18
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	6e-18
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-17
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-17
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-17
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-17
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-17
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-17
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	9e-17
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-16
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-16
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-16
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-16
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-16
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-16
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-16
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-16
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-15
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-15
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-15
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-15
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-15
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	5e-15
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-15
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	5e-15
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-15
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-15
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-15
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-14
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-14
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-14
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-14
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-14
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-14
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-14
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-14
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-14
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-14
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-14
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-14
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	6e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-14
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	7e-14
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	9e-14
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-13
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-13
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-13
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-13
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-13
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-13
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-13
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-13
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-13
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-13
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-13
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-13
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-13
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	4e-13
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-13
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	5e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-13
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-13
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	6e-13
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	7e-13
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-13
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	7e-13
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	7e-13
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	8e-13
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	8e-13
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	9e-13
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-12
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-12
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-12
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-12
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-12
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-12
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-12
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-12
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-12
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-12
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-12
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-12
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-12
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-12
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-12
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-12
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-12
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	3e-12
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-12
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-12
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-12
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-12
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-12
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-12
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-12
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-12
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	5e-12
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-12
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-12
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-12
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	5e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-12
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	6e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	7e-12
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	7e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-12
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	8e-12
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-12
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	9e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-11
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-11
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-11
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-11
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-11
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-11
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-11
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-11
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-11
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-11
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-11
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-11
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-11
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-11
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-11
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-11
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	3e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-11
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	4e-11
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-11
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-11
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	4e-11
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	5e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-11
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	5e-11
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	5e-11
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-11
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-11
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	7e-11
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	8e-11
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	8e-11
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	8e-11
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	8e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	9e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-11
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	9e-11
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-10
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-10
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-10
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-10
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-10
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-10
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-10
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-10
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-10
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	2e-10
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-10
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	2e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-10
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-10
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-10
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-10
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-10
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	3e-10
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-10
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-10
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-10
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-10
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	4e-10
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	5e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-10
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	6e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	6e-10
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-10
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	6e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-10
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	7e-10
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	7e-10
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	7e-10
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	8e-10
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	8e-10
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	8e-10
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	8e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	9e-10
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	9e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-09
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-09
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	1e-09
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-09
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-09
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-09
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-09
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	1e-09
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-09
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-09
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-09
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-09
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-09
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-09
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-09
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-09
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-09
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-09
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	3e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-09
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-09
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-09
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	3e-09
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	3e-09
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-09
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-09
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	3e-09
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	3e-09
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-09
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-09
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-09
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	4e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-09
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-09
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-09
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	6e-09
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	6e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	6e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	6e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	6e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	6e-09
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	6e-09
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	6e-09
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	7e-09
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	7e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-09
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-09
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	7e-09
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	8e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	8e-09
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	8e-09
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	9e-09
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	9e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	9e-09
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	9e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-08
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	1e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-08
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	1e-08
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-08
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-08
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	1e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-08
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-08
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-08
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-08
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-08
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-08
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	2e-08
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-08
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-08
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	2e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-08
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	2e-08
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-08
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	3e-08
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-08
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	4e-08
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-08
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-08
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	4e-08
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-08
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	5e-08
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	5e-08
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-08
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-08
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	5e-08
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	5e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	6e-08
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	6e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	6e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	7e-08
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	7e-08
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	7e-08
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	7e-08
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	7e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	8e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	8e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	8e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	8e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	8e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	8e-08
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	8e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	8e-08
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	8e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	9e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	9e-08
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	9e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	9e-08
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	9e-08
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	9e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	9e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	1e-07
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-07
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-07
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	1e-07
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-07
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-07
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-07
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	1e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-07
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	1e-07
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	1e-07
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	1e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-07
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-07
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-07
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-07
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-07
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	2e-07
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-07
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-07
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-07
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-07
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	2e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-07
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	3e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-07
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	3e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	3e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-07
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	3e-07
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-07
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-07
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-07
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	3e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-07
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	4e-07
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	4e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-07
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	4e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	4e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-07
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	4e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	5e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	5e-07
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	5e-07
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	5e-07
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	5e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	6e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	6e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	6e-07
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	6e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	6e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	6e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-07
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	6e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	6e-07
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-07
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	7e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	7e-07
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	7e-07
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	7e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	8e-07
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	8e-07
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	8e-07
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	9e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	9e-07
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	9e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	9e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-06
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-06
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	1e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	1e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-06
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-06
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	1e-06
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	1e-06
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	1e-06
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	1e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	1e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-06
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-06
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-06
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-06
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-06
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	2e-06
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	2e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-06
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	2e-06
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	2e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-06
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-06
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-06
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	2e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	3e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-06
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	3e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-06
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	3e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	3e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	3e-06
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	3e-06
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	3e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	3e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-06
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	4e-06
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	4e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	4e-06
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	4e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	4e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	4e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-06
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	4e-06
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	4e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	5e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	5e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	5e-06
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	5e-06
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	5e-06
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	5e-06
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	5e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-06
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	6e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	6e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	6e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	6e-06
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	6e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	7e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	7e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	7e-06
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	7e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	7e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	7e-06
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	7e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	8e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	8e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	9e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	9e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	9e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	9e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	9e-06
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	9e-06
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	9e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-05
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	1e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	1e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	1e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	1e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	1e-05
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	1e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	1e-05
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	1e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	1e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-05
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	2e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-05
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-05
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	2e-05
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-05
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	2e-05
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	2e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	2e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-05
cd12602	76	cd12602, RRM2_SF2_plant_like, RNA recognition moti	2e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	2e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	3e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	3e-05
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	3e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	3e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	3e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	3e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	3e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	3e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	3e-05
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	3e-05
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	3e-05
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	3e-05
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	3e-05
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	3e-05
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	3e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	4e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	4e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-05
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	4e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	4e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	4e-05
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	4e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	4e-05
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	4e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	5e-05
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	5e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	5e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-05
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	5e-05
cd12425	76	cd12425, RRM4_PTBP1_like, RNA recognition motif 4	5e-05
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	5e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	5e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-05
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	6e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	6e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	6e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	6e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	6e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	7e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	7e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-05
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	7e-05
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	7e-05
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	7e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	7e-05
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	7e-05
cd12349	74	cd12349, RRM2_SHARP, RNA recognition motif 2 in SM	7e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	8e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	8e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	8e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	8e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	8e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	8e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	8e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	8e-05
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	8e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	8e-05
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	8e-05
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	8e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	9e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	9e-05
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	9e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	9e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	9e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	9e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	9e-05
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	9e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	9e-05
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	9e-05
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	1e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	1e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-04
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	1e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	1e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	1e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	1e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	1e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	1e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-04
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	1e-04
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	1e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	1e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	1e-04
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	1e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	2e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	2e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	2e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-04
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-04
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	2e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-04
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	2e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	2e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	2e-04
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-04
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	2e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-04
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	2e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	3e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	3e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	3e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	3e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	3e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	3e-04
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	3e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	3e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	3e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	3e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	3e-04
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	3e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	4e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-04
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	4e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	4e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-04
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	4e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	4e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	4e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	4e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	4e-04
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	4e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	4e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	4e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	4e-04
cd12435	71	cd12435, RRM_GW182_like, RNA recognition motif in	4e-04
cd12289	93	cd12289, RRM_LARP6, RNA recognition motif in La-re	4e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	5e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	5e-04
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	5e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	5e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	5e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	5e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	5e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	5e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	5e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	5e-04
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	5e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	5e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	5e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	5e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	5e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	5e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	5e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	6e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	6e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	6e-04
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	6e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	6e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	6e-04
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	6e-04
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	6e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	7e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	7e-04
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	7e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	7e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	7e-04
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	7e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	7e-04
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	7e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	8e-04
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	8e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	8e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	8e-04
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	8e-04
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	8e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	9e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	9e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	9e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	9e-04
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	9e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.001
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.001
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.001
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.001
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.001
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.001
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.001
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.001
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.001
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.001
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.001
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.001
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.001
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.001
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.001
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.001
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.001
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	0.001
cd12388	70	cd12388, RRM1_RAVER, RNA recognition motif 1 in ri	0.001
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.001
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.001
cd12441	73	cd12441, RRM_Nup53_like, RNA recognition motif in	0.001
pfam08777	102	pfam08777, RRM_3, RNA binding motif	0.001
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.001
cd12625	77	cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in	0.001
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	0.002
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	0.002
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	0.002
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.002
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.002
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.002
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	0.002
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.002
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.002
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.002
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	0.002
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.002
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	0.002
cd12541	76	cd12541, RRM2_La, RNA recognition motif 2 in La au	0.002
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	0.002
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	0.002
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.003
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.003
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.003
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.003
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	0.003
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.003
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	0.003
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.003
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.003
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.003
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.003
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.003
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.003
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.003
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.003
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	0.003
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.003
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	0.003
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.003
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.003
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.003
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.003
cd12443	73	cd12443, RRM_MCM3A_like, RNA recognition motif in	0.003
cd12540	105	cd12540, RRM_U2AFBPL, RNA recognition motif in U2	0.003
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.004
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	0.004
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.004
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.004
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.004
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.004
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	0.004
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.004
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.004
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.004
cd12289	93	cd12289, RRM_LARP6, RNA recognition motif in La-re	0.004
cd12465	88	cd12465, RRM_UHMK1, RNA recognition motif found in	0.004
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.004
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.004

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

 Score =  705 bits (1822), Expect = 0.0
 Identities = 311/602 (51%), Positives = 403/602 (66%), Gaps = 46/602 (7%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           SLYVGDLD +VT+++LYDLF   G VLSVRVCRD  TRRSLGYGYVN+ NPADA RAL+ 
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 91  LNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA 150
           +NF  L  K IRIM+S RDPS+R+SG GNIF+KNLDKS+D+KAL DTFS FGNILSCK+A
Sbjct: 62  MNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVA 121

Query: 151 TDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
           TD +G+S+G+GFV FE +ESA+ AI K+NGML+NDK+V+VG F++K ERE  A   KF N
Sbjct: 122 TDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE-AAPLKKFTN 180

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++VKNLD S  ++ L+++F ++G ITSA VM+DG G+S+ F FVNFE  +DAAKAVE +N
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 271 GKKFDDREW----YVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
           GKK    +     YVG+AQK++ERE EL+ +FE+  +E   K QG+NLY+KNL D++ DE
Sbjct: 241 GKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDE 300

Query: 327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 386
           KL+ELFSE G ITS KVM D  G+S+G GFV FS PEEA+RA+ EM+G+M+  KPLYVA+
Sbjct: 301 KLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL 360

Query: 387 AQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQA- 445
           AQRKE+RRA LQ QF Q++P         ++PM  P    +GQ   YGQ P      Q  
Sbjct: 361 AQRKEQRRAHLQDQFMQLQPRM------RQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPL 414

Query: 446 GFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMP 505
           G+     +   M P G   PN   P+ +           R A   Q   Q  P+ P   P
Sbjct: 415 GWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPS------RNA---QNAAQKPPMQPVMYP 465

Query: 506 PRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANA 565
           P   +                     LP+  D+    P+  ++  Q      L+  LA+A
Sbjct: 466 PNYQS---------------------LPLSQDL----PQPQSTASQGGQNKKLAQVLASA 500

Query: 566 SPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV 625
           +P+ Q+ +LGE L+PLVE +E   AAK+TGMLLEMD +E+LHLLESPE LK+KV EA+EV
Sbjct: 501 TPQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELLHLLESPELLKSKVDEALEV 560

Query: 626 LR 627
           L+
Sbjct: 561 LK 562

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

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

 Score =  211 bits (540), Expect = 1e-60
 Identities = 101/292 (34%), Positives = 162/292 (55%), Gaps = 20/292 (6%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +++V +LD +V +  L+D FS+ G +LS +V  D    +S GYG+V++     A  A+
Sbjct: 88  VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAI 146

Query: 89  DVLNFTPLNNKSI---RIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNIL 145
             +N   LN+K +   R +  H   +       N+++KNLD S++   L + F+ FG I 
Sbjct: 147 QKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEIT 206

Query: 146 SCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLI----NDKQVFVGHF-------- 193
           S  +  DGSG+S+GF FV FE  E A  A++++NG  I      K+++VG          
Sbjct: 207 SAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREA 266

Query: 194 ----LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK 249
                 ++ ++   +K +  N++VKNLD++ TDE L+++F E G ITSA VM D  G S+
Sbjct: 267 ELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSR 326

Query: 250 CFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQA 301
            FGFV F N ++A +AV  ++G+    +  YV  AQ+K +R   L+ QF Q 
Sbjct: 327 GFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQL 378

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

 Score =  166 bits (422), Expect = 2e-49
 Identities = 57/77 (74%), Positives = 69/77 (89%)

Query: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           G GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+ATD +G SKG+GFV FE +E+A  AI
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAI 60

Query: 176 DKLNGMLINDKQVFVGH 192
           +K+NGML+NDK+VFVG 
Sbjct: 61  EKVNGMLLNDKKVFVGP 77

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

 Score =  162 bits (411), Expect = 7e-48
 Identities = 55/79 (69%), Positives = 66/79 (83%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G+NLY+KNL DSIDDE+L+E FS FGTITS KVM D  G SKG GFV FS+PEEA++A+ 
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

Query: 371 EMNGKMIVSKPLYVAVAQR 389
           EMNG++I  KPLYVA+AQR
Sbjct: 61  EMNGRIIGGKPLYVALAQR 79

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

 Score =  156 bits (396), Expect = 1e-45
 Identities = 54/80 (67%), Positives = 63/80 (78%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           SLYVGDL  +VT++ LY++FS  G VLS+RVCRDL TRRSLGY YVN+ NPADA RALD 
Sbjct: 1   SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 91  LNFTPLNNKSIRIMYSHRDP 110
           LNF  +  K IRIM+S RDP
Sbjct: 61  LNFDVIKGKPIRIMWSQRDP 80

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

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

 Score =  153 bits (389), Expect = 1e-44
 Identities = 51/80 (63%), Positives = 63/80 (78%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           F NV+VKNL E   DE LK++FG+YG ITSA VM+D +GKSK FGFVNFEN + A KAVE
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVE 60

Query: 268 ALNGKKFDDREWYVGKAQKK 287
            LNGK+ + ++ YVG+AQKK
Sbjct: 61  ELNGKEVNGKKLYVGRAQKK 80

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

 Score =  124 bits (313), Expect = 4e-34
 Identities = 45/78 (57%), Positives = 57/78 (73%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N+Y+KNLG+ +DDEKLKELF ++G ITS KVM+D  G SKG GFV F   E A +A+ E+
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 373 NGKMIVSKPLYVAVAQRK 390
           NGK +  K LYV  AQ+K
Sbjct: 63  NGKEVNGKKLYVGRAQKK 80

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|201378 pfam00658, PABP, Poly-adenylate binding protein, unique domain

 Score =  118 bits (299), Expect = 2e-32
 Identities = 41/69 (59%), Positives = 55/69 (79%)

Query: 558 LSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKA 617
            ++ALA A P++Q+ +LGE LYPL++ +  + A K+TGMLLEMD +E+LHLLES EALKA
Sbjct: 4   TASALAAAPPQEQKQMLGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEALKA 63

Query: 618 KVAEAMEVL 626
           KV EA+ VL
Sbjct: 64  KVDEALAVL 72

The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family. Length = 72

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

 Score =  109 bits (275), Expect = 6e-29
 Identities = 38/77 (49%), Positives = 52/77 (67%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N++VKNLD+S  DE L++ F  +GTITSA VM D  G+SK FGFV F + ++A KAV  +
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 270 NGKKFDDREWYVGKAQK 286
           NG+    +  YV  AQ+
Sbjct: 63  NGRIIGGKPLYVALAQR 79

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

 Score =  108 bits (272), Expect = 2e-28
 Identities = 36/73 (49%), Positives = 49/73 (67%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N++IKNL  SID++ L + FS FG I SCKV  D +G SKG GFV F T E A RA+ ++
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 373 NGKMIVSKPLYVA 385
           NG ++  K ++V 
Sbjct: 64  NGMLLNDKKVFVG 76

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

 Score =  114 bits (286), Expect = 4e-28
 Identities = 67/306 (21%), Positives = 127/306 (41%), Gaps = 15/306 (4%)

Query: 101 IRIMYSHRDPSIRKS-GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKG 159
                     S  +S    +I    L + +  +       +    L+ ++ +        
Sbjct: 1   KESKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEIS 60

Query: 160 FGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTK------FNNVFV 213
               +       +   ++      + ++ +   F  +  R + + K++       N +FV
Sbjct: 61  PPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFV 120

Query: 214 KNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGK 272
            NL    T+EDL+++F ++G +    ++RD + GKS+ F FV FE+ + A KA+E LNGK
Sbjct: 121 GNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK 180

Query: 273 KFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKF------QGLNLYIKNLGDSIDDE 326
           + + R   V KAQ  S+   EL    + +  + + +       +  NLY+ NL     +E
Sbjct: 181 ELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEE 240

Query: 327 KLKELFSEFGTITSCKVMRDPSG-ISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 385
           +L +LF   G I    +     G I K   FV     ++A  + +  N K I+ +    A
Sbjct: 241 ELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGRGPRKA 300

Query: 386 VAQRKE 391
            +Q + 
Sbjct: 301 FSQPRL 306

Length = 306

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

 Score =  115 bits (288), Expect = 7e-28
 Identities = 57/152 (37%), Positives = 91/152 (59%), Gaps = 3/152 (1%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L   +T  ++  LF+ +G++ S ++ RD  T +SLGYG+VNY  P DA +A++
Sbjct: 4   TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            LN   L NK+I++ Y+   PS       N+++  L K++    L   FS FG I++ +I
Sbjct: 64  SLNGLRLQNKTIKVSYAR--PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRI 121

Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
            +D  +G SKG GF++F+ ++ A  AI  LNG
Sbjct: 122 LSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG 153

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|197769 smart00517, PolyA, C-terminal domain of Poly(A)-binding protein

 Score =  105 bits (265), Expect = 9e-28
 Identities = 40/63 (63%), Positives = 51/63 (80%)

Query: 566 SPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV 625
            P++Q+  LGE LYP V+ LE + A K+TGMLLEMD +E+LHLLESPE L+AKV EA+EV
Sbjct: 1   PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRAKVDEALEV 60

Query: 626 LRS 628
           L+S
Sbjct: 61  LKS 63

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly). Length = 64

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

 Score =  102 bits (257), Expect = 2e-26
 Identities = 35/73 (47%), Positives = 51/73 (69%), Gaps = 1/73 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
            +FV NL   TT+E+L+++F ++G + S  ++RD + GKSK F FV FE+ +DA KA+EA
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 269 LNGKKFDDREWYV 281
           LNGK+ D R   V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score =  102 bits (256), Expect = 3e-26
 Identities = 35/78 (44%), Positives = 54/78 (69%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N+++KNL + +D + L + F  +G I S K+  D  G+SKGFGFV FEN E+AQ A+++L
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 179 NGMLINDKQVFVGHFLRK 196
           NG  +N K+++VG   +K
Sbjct: 63  NGKEVNGKKLYVGRAQKK 80

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score =  101 bits (253), Expect = 5e-26
 Identities = 36/70 (51%), Positives = 48/70 (68%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL   TT+EDLK +F ++G I S  ++RD  G+SK F FV FE+ +DA KA+EALN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 271 GKKFDDREWY 280
           GK+   RE  
Sbjct: 61  GKELGGRELR 70

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

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

 Score =  100 bits (251), Expect = 9e-26
 Identities = 38/71 (53%), Positives = 52/71 (73%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL   TT+EDL+++F ++G I S  ++RD DGKSK F FV FE+ +DA KA+EALN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 271 GKKFDDREWYV 281
           GK+ D R+  V
Sbjct: 61  GKELDGRKLKV 71

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

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

 Score = 93.8 bits (234), Expect = 2e-23
 Identities = 31/73 (42%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L++ NL     +E+L+ELFS+FG + S +++RD  +G SKG  FV F + E+A +AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 372 MNGKMIVSKPLYV 384
           +NGK +  +PL V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 93.0 bits (232), Expect = 4e-23
 Identities = 30/74 (40%), Positives = 47/74 (63%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+F+KNLD+S  ++ L   F  +G I S  V  D +G SK +GFV+FE  + A +A+E +
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 270 NGKKFDDREWYVGK 283
           NG   +D++ +VG 
Sbjct: 64  NGMLLNDKKVFVGP 77

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|214636 smart00360, RRM, RNA recognition motif

 Score = 91.5 bits (228), Expect = 1e-22
 Identities = 26/73 (35%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +F+ NL      + L + FS FG + S ++  D  +G+SKGF FV+FE++E A+ A++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 178 LNGMLINDKQVFV 190
           LNG  ++ + + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 90.3 bits (225), Expect = 2e-22
 Identities = 28/69 (40%), Positives = 44/69 (63%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NL      + L D FS FG I S +I  D +G+SKGF FV+FE++E A+ A++ LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 180 GMLINDKQV 188
           G  +  +++
Sbjct: 61  GKELGGREL 69

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

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

 Score = 90.8 bits (226), Expect = 2e-22
 Identities = 32/71 (45%), Positives = 46/71 (64%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL     +E L+ELFS+FG I S +++RD  G SKG  FV F +PE+A +AL  +N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 374 GKMIVSKPLYV 384
           GK +  + L V
Sbjct: 61  GKELDGRKLKV 71

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

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

 Score = 90.1 bits (224), Expect = 4e-22
 Identities = 28/71 (39%), Positives = 44/71 (61%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NL      + L + FS FG I S +I  D  G+SKGF FV+FE+ E A+ A++ LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 180 GMLINDKQVFV 190
           G  ++ +++ V
Sbjct: 61  GKELDGRKLKV 71

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

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

 Score = 89.6 bits (223), Expect = 6e-22
 Identities = 35/73 (47%), Positives = 49/73 (67%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N+++KNLD SID + L + FS FG I S K+ TD  G+SKGFGFV F + E A  A+ ++
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 179 NGMLINDKQVFVG 191
           NG +I  K ++V 
Sbjct: 63  NGRIIGGKPLYVA 75

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|214636 smart00360, RRM, RNA recognition motif

 Score = 88.4 bits (220), Expect = 2e-21
 Identities = 27/73 (36%), Positives = 49/73 (67%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+VG+L  + T+ +L +LFS+ G+V SVR+ RD  T +S G+ +V + +  DA +AL+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 91  LNFTPLNNKSIRI 103
           LN   L+ + +++
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 87.4 bits (217), Expect = 4e-21
 Identities = 33/80 (41%), Positives = 53/80 (66%), Gaps = 2/80 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNIL-SCKIATD-GSGQSKGFGFVQFENKESAQNAID 176
           N+FI NLD  +D K L+DTFS+FG IL + KI  D  +G SKGF F+ +++ E++  AI+
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 177 KLNGMLINDKQVFVGHFLRK 196
            +NG  + ++ + V +  +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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 94.3 bits (234), Expect = 7e-21
 Identities = 56/184 (30%), Positives = 93/184 (50%), Gaps = 9/184 (4%)

Query: 6   VQHQAQMSGPNGVAAGASGNQFLT------TSLYVGDLDFNVTDSQLYDLFSQVGQVLSV 59
           + + A M+  N + +  SG           T+L V  L  ++TD +LY LF  +G + + 
Sbjct: 78  MGNMANMASTNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTC 137

Query: 60  RVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           R+ RD  T  S GY +V++ + AD+ RA+  LN   + NK +++ Y+   P        N
Sbjct: 138 RIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYAR--PGGESIKDTN 195

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++ NL ++I    L   F  +G I+   I  D  +G  +G  FV+F  +E AQ AI  L
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255

Query: 179 NGML 182
           N ++
Sbjct: 256 NNVI 259

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 85.7 bits (213), Expect = 1e-20
 Identities = 30/70 (42%), Positives = 44/70 (62%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL     +E LK+LFS+FG I S +++RD +G SKG  FV F   E+A +AL  +N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 374 GKMIVSKPLY 383
           GK +  + L 
Sbjct: 61  GKELGGRELR 70

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

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

 Score = 85.4 bits (212), Expect = 2e-20
 Identities = 32/78 (41%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV+NL   TTDE L++ F E G I    V++D G  K + FG+V F   +DA +A+E  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 270 NGKKFDDREWYVGKAQKK 287
              KF  R+ +V  A+KK
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

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

 Score = 84.6 bits (210), Expect = 3e-20
 Identities = 35/78 (44%), Positives = 52/78 (66%), Gaps = 1/78 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N++V NL  + T+EDLK +FG++G +TSA V+ D + G+S+ FGFV  E A++A  A+E 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 269 LNGKKFDDREWYVGKAQK 286
           LNG  F  R   V +A+ 
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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

>gnl|CDD|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 = 83.8 bits (208), Expect = 8e-20
 Identities = 28/80 (35%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           G  L++  L     +++L+ LFS+FG +    +M+DP +G S+G GFV F + E+A  A+
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 370 AEMNGKMIVSKPLYVAVAQR 389
            ++NGK +  + + V  A+R
Sbjct: 61  RDLNGKELEGRVIKVEKAKR 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 83.0 bits (206), Expect = 1e-19
 Identities = 28/71 (39%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L  + T+  L DLFS+ G + S+R+ RD  T RS G+ +V + +  DA +AL+ L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 92  NFTPLNNKSIR 102
           N   L  + +R
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 88.5 bits (218), Expect = 4e-19
 Identities = 45/242 (18%), Positives = 89/242 (36%), Gaps = 15/242 (6%)

Query: 193 FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG 252
               +   +     K  ++    L E    E+   +        +  V            
Sbjct: 3   SKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPP 62

Query: 253 FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGL 312
                 + +  +  E    ++ D    Y  + +++  R  E              K +  
Sbjct: 63  SKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPK------SRQKSKEENN 116

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L++ NL   + +E L+ELF +FG +   +++RD  +G S+G  FV F + E A +A+ E
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 372 MNGKMIVSKPLYV----AVAQRKEERR----ARLQAQFSQMRPVAMGPSVPPRMPMYPPG 423
           +NGK +  +PL V      +Q + E      A    + S+ + + +  S    +   P  
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLK 236

Query: 424 PS 425
            +
Sbjct: 237 TA 238

Length = 306

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

 Score = 88.8 bits (220), Expect = 5e-19
 Identities = 54/167 (32%), Positives = 89/167 (53%), Gaps = 20/167 (11%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T E+++ +F   G I S  ++RD   G+S  +GFVN+   +DA KAV +
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG +  ++   V  A+  S                  D  +G NLY+  L  ++   +L
Sbjct: 65  LNGLRLQNKTIKVSYARPSS------------------DSIKGANLYVSGLPKTMTQHEL 106

Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 374
           + +FS FG I + +++ D  +G+SKG GF+ F   +EA RA+  +NG
Sbjct: 107 ESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG 153

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

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

 Score = 88.5 bits (219), Expect = 7e-19
 Identities = 51/157 (32%), Positives = 88/157 (56%), Gaps = 8/157 (5%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++  + +   F+S G I SCK+  D   GQS G+GFV +   E A+ A++ 
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT-IT 236
           LNG+ + +K + V  + R     + +IK    N++V  L ++ T  +L+ IF  +G  IT
Sbjct: 65  LNGLRLQNKTIKVS-YARPS---SDSIKGA--NLYVSGLPKTMTQHELESIFSPFGQIIT 118

Query: 237 SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 273
           S ++  +  G SK  GF+ F+  D+A +A++ LNG  
Sbjct: 119 SRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTT 155

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

 Score = 80.2 bits (198), Expect = 1e-18
 Identities = 33/77 (42%), Positives = 52/77 (67%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  ++  LFS +G++ S ++ RD  T +SLGYG+VNY +P DA +A++
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   L NK+I++ Y+
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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 79.7 bits (197), Expect = 2e-18
 Identities = 26/72 (36%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L  + T+  L +LFS+ G++ SVR+ RD    +S G+ +V + +P DA +AL+ L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 92  NFTPLNNKSIRI 103
           N   L+ + +++
Sbjct: 60  NGKELDGRKLKV 71

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

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 88.4 bits (219), Expect = 2e-18
 Identities = 69/280 (24%), Positives = 111/280 (39%), Gaps = 24/280 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           VFV  L     + DL + F + G +     ++D    +SK   +V F + +   KA+ AL
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-AL 150

Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
            G+    R   V  +Q +  R  +       A  +  D    L LY+ NL  +I +++L+
Sbjct: 151 TGQMLLGRPIIVQSSQAEKNRAAKA------ATHQPGDIPNFLKLYVGNLHFNITEQELR 204

Query: 330 ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
           ++F  FG I   ++ RDP +G SKG GF+ F   EEA  AL  MNG  +  +P+ V  AQ
Sbjct: 205 QIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ 264

Query: 389 RKEERRARLQAQFSQMRPVAMGPSV--PPRMPMYPPGP----------SGLGQQFLYGQA 436
                           +   MG ++    R  +                G G +    Q 
Sbjct: 265 DSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQK 324

Query: 437 --PPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQ 474
                II P     Y    +  M    + +P+    + + 
Sbjct: 325 LQRDGIIDPNIPSRYATGALAIM-ARNSFVPSTNNNLATT 363

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

 Score = 85.8 bits (211), Expect = 3e-18
 Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 23/175 (13%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +L+VG+L ++VT+  L +LF + G V  VR+ RD  T +S G+ +V + +   A +A+
Sbjct: 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKSG----------------------TGNIFIKNLD 126
           + LN   L  + +R+  +      R                         + N+++ NL 
Sbjct: 175 EELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLP 234

Query: 127 KSIDHKALHDTFSSFGNILSCKIATDGSG-QSKGFGFVQFENKESAQNAIDKLNG 180
                + L D F S G+I+   +     G   K   FV  E  + A  +  + N 
Sbjct: 235 LKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNK 289

Length = 306

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 87.3 bits (216), Expect = 3e-18
 Identities = 58/219 (26%), Positives = 100/219 (45%), Gaps = 15/219 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+  L      + L++ FS  G +   +   D  S +SKG  +V+F + ES   A+  L
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-AL 150

Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKT------KFNNVFVKNLDESTTDEDLKKIFGEY 232
            G ++  + + V     ++ R   A          F  ++V NL  + T+++L++IF  +
Sbjct: 151 TGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPF 210

Query: 233 GTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSERE 291
           G I    + RD + G+SK FGF+ F +A++A +A+E +NG +   R   VG AQ  +   
Sbjct: 211 GDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLL 270

Query: 292 QELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 330
                       E +DK Q +   +         EKL  
Sbjct: 271 DAANTF------EDIDKQQQMGKNLNTEEREQLMEKLDR 303

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

 Score = 78.9 bits (195), Expect = 5e-18
 Identities = 32/83 (38%), Positives = 54/83 (65%), Gaps = 2/83 (2%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           G NL+I NL   +D++ L + FS FG I  + K+MRDP +G SKG  F+++ + E +  A
Sbjct: 1   GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

Query: 369 LAEMNGKMIVSKPLYVAVAQRKE 391
           +  MNG+ + ++P+ V+ A +K+
Sbjct: 61  IEAMNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 78.4 bits (194), Expect = 6e-18
 Identities = 25/74 (33%), Positives = 41/74 (55%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +KNL   + +++L+E F   G +T  KVMR   G S+  GFV F + E+A +A+   N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 374 GKMIVSKPLYVAVA 387
              I +  + V +A
Sbjct: 63  KTFIDTSKISVELA 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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 28/67 (41%), Positives = 39/67 (58%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V+NL    T+ DLKK+F  +G +    + R  DGK K F FV F +  DA KA++ +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 271 GKKFDDR 277
           GKK   R
Sbjct: 62  GKKIKGR 68

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 84.3 bits (208), Expect = 2e-17
 Identities = 68/248 (27%), Positives = 111/248 (44%), Gaps = 37/248 (14%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 109 NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN 168

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG    ++   V  A+   E           ++K+T       NLY+ NL  +I D++L
Sbjct: 169 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 210

Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA 385
             +F ++G I    ++RD  +G  +G  FV F+  EEA  A++ +N  +    S+PL V 
Sbjct: 211 DTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR 270

Query: 386 VAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQA 445
           +A+  E  +A+     SQM    M             G  G G   + G +      P A
Sbjct: 271 LAE--EHGKAKAHHYMSQMGHGNM-------------GNMGHGNMGMAGGSGMNPPNPPA 315

Query: 446 GFGYQQQL 453
             G    +
Sbjct: 316 FMGMNNMV 323

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

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

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 27/65 (41%), Positives = 40/65 (61%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + VKNL +  T++ L++ F   G +T   VMR  DGKS+ FGFV F++ +DA +AV+  N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 271 GKKFD 275
               D
Sbjct: 63  KTFID 67

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|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 = 76.9 bits (190), Expect = 2e-17
 Identities = 30/72 (41%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI +L      + L+  F+ FGN++S K+  D  +GQSK FGFV ++N ESAQ AI  +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 179 NGMLINDKQVFV 190
           NG  +  K++ 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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 83.5 bits (206), Expect = 3e-17
 Identities = 52/160 (32%), Positives = 84/160 (52%), Gaps = 9/160 (5%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESA 171
             SGT N+ +  L + +  + L+  F + G I +C+I  D  +G S G+ FV F ++  +
Sbjct: 104 NNSGT-NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADS 162

Query: 172 QNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGE 231
           Q AI  LNG+ + +K++ V +     E        K  N++V NL  + TD+ L  IFG+
Sbjct: 163 QRAIKNLNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGK 216

Query: 232 YGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
           YG I    ++RD   G  +   FV F   ++A +A+ ALN
Sbjct: 217 YGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256

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|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 = 75.7 bits (187), Expect = 5e-17
 Identities = 30/79 (37%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
           N +FV  L   TT+++L+ +F ++G +   ++M+D   G+S+ FGFV FE+ +DA  A+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 268 ALNGKKFDDREWYVGKAQK 286
            LNGK+ + R   V KA++
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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 75.3 bits (186), Expect = 6e-17
 Identities = 32/77 (41%), Positives = 49/77 (63%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NLY+ NL  ++ +E LK+LF +FG +TS +V+ D  +G S+G GFV   T EEA+ A+ +
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG     + L V  A+
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

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

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

 Score = 75.5 bits (186), Expect = 6e-17
 Identities = 30/76 (39%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
            L++ NL  S+DDE LK  F +FGT+   +V+ D  +G S+G G+V F +PE+A +A+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 372 MNGKMIVSKPLYVAVA 387
           M+GK +  +P+ 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 75.0 bits (185), Expect = 9e-17
 Identities = 30/72 (41%), Positives = 43/72 (59%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG+L +NVT+  L DLF Q G+V S RV  D  T RS G+G+V      +A  A++ L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 92  NFTPLNNKSIRI 103
           N T    +++ +
Sbjct: 62  NGTDFGGRTLTV 73

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

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 7/68 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V+NL  STT+E L+++F EYG +     ++D       + FV+FE  DDA KA+E +N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 271 GKKFDDRE 278
           GK+ +   
Sbjct: 57  GKELEGSP 64

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|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 = 25/71 (35%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           ++++ +L   ID E L+  F+ FG I+  +V++D  +G SKG GFV+F   E+A  A+  
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 372 MNGKMIVSKPL 382
           MNG+ +  + +
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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 73.7 bits (182), Expect = 2e-16
 Identities = 25/67 (37%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V+NL  S T+EDL++ F  YG +    ++R+ D + + F FV F + +DA  A++ LN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 271 GKKFDDR 277
           G   D R
Sbjct: 60  GLVLDGR 66

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

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 81.1 bits (200), Expect = 3e-16
 Identities = 47/184 (25%), Positives = 87/184 (47%), Gaps = 12/184 (6%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +++V  L     +  LY+ FS+VG+V  V+  +D ++RRS G  YV + +  ++      
Sbjct: 91  TVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYD-VESVIKALA 149

Query: 91  LNFTPLNNKSIRIMYSHRDPSIRKSGTGN----------IFIKNLDKSIDHKALHDTFSS 140
           L    L  + I +  S  + +       +          +++ NL  +I  + L   F  
Sbjct: 150 LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEP 209

Query: 141 FGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           FG+I   ++  D  +G+SKGFGF+QF + E A+ A++ +NG  +  + + VG+       
Sbjct: 210 FGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYL 269

Query: 200 ETVA 203
              A
Sbjct: 270 LDAA 273

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

 Score = 73.7 bits (182), Expect = 3e-16
 Identities = 24/64 (37%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNG 271
           V NL E   ++DL+++F  +G I+   + +D + G+S+ F FV F   +DA +A+E LNG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 272 KKFD 275
             +D
Sbjct: 64  FGYD 67

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

 Score = 73.2 bits (180), Expect = 4e-16
 Identities = 33/76 (43%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
            +FV NL  S  DE LK  F ++GT+  A V+ D + G+S+ FG+V+FE+ +DA KA+EA
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 269 LNGKKFDDREWYVGKA 284
           ++GK+ D R   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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 73.0 bits (180), Expect = 4e-16
 Identities = 28/72 (38%), Positives = 45/72 (62%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +YVG+LD  VT+  L++LF Q G V++V + +D  T+   GYG+V + +  DA  A+ ++
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 92  NFTPLNNKSIRI 103
           N   L  K IR+
Sbjct: 61  NMIKLYGKPIRV 72

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

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

 Score = 72.4 bits (178), Expect = 6e-16
 Identities = 24/71 (33%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +F+ NL  S+D + L   F  FG ++  ++ TD  +G+S+GFG+V FE+ E A+ AI+ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 178 LNGMLINDKQV 188
           ++G  ++ + +
Sbjct: 61  MDGKELDGRPI 71

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|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 = 71.4 bits (175), Expect = 2e-15
 Identities = 32/77 (41%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 269
           +F+  L   T ++ L+++F +YG I+  VV++D + + S+ FGFV FEN DDA  A+ A+
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 270 NGKKFDDREWYVGKAQK 286
           NGK  D R+  V +A K
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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 71.2 bits (175), Expect = 2e-15
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL  S   +DL++ F E G +    + +D DG+SK FG V F   + A KA+E  +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KS 60

Query: 271 GKKFDDREWYVGKAQKK 287
           G++   RE  V  A ++
Sbjct: 61  GEELLGREIRVDLATER 77

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

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

 Score = 71.2 bits (175), Expect = 2e-15
 Identities = 28/76 (36%), Positives = 47/76 (61%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  ++T  +L  LF  +G + S ++ RD  T +SLGYG+V+Y +  DA +A++
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 90  VLNFTPLNNKSIRIMY 105
            LN   + NK +++ Y
Sbjct: 61  TLNGFEIRNKRLKVSY 76

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

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

 Score = 70.5 bits (173), Expect = 3e-15
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           +IF+ +L   ID + L   F+ FG I   ++  D  +G+SKG+GFV F  KE A+NAI  
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 178 LNGMLINDKQV 188
           +NG  +  + +
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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 70.3 bits (173), Expect = 4e-15
 Identities = 28/70 (40%), Positives = 47/70 (67%), Gaps = 1/70 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +++ +LG+ + DE L   FS++ +    KV+RD  +G SKG GFV+FS P +  +A+ EM
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 373 NGKMIVSKPL 382
           NGK + ++P+
Sbjct: 69  NGKYVGNRPI 78

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

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

 Score = 70.0 bits (172), Expect = 5e-15
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+V NL    T  +L+  F +YG + S  V R+  G    F FV FE+  DA  AV AL+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPG----FAFVEFEDPRDAEDAVRALD 57

Query: 271 GKKFDDREWYVGKA 284
           G++       V  +
Sbjct: 58  GRRICGNRVRVELS 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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 70.1 bits (172), Expect = 5e-15
 Identities = 29/77 (37%), Positives = 44/77 (57%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L +  L   +TD +   LF  VG V + ++ RD  T  S G+G+V+Y +  DA RA+ 
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   L NK I++ Y+
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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 69.6 bits (171), Expect = 5e-15
 Identities = 32/68 (47%), Positives = 43/68 (63%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV+NL  S T +DLK +F E G +  A V  D DG+SK FG V FE+ +DA +A+E  N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 271 GKKFDDRE 278
           G   + RE
Sbjct: 61  GYDLEGRE 68

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|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 = 69.9 bits (172), Expect = 6e-15
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID 176
             +F+  L      K L   FS FG +    +  D  +G+S+GFGFV FE+ E A  AI 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 177 KLNGMLINDKQVFVGHFLR 195
            LNG  +  + + V    R
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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 69.6 bits (171), Expect = 7e-15
 Identities = 29/62 (46%), Positives = 38/62 (61%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF++NL  S+  + L D F   GN+L   + TD  G+SKGFG V FE+ E AQ AI+  N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 180 GM 181
           G 
Sbjct: 61  GY 62

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|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 = 69.2 bits (170), Expect = 8e-15
 Identities = 26/62 (41%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+ +L    TD+DL ++F  +G + SA V  D + G+SKCFGFV+++N + A  A++A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 270 NG 271
           NG
Sbjct: 61  NG 62

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

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

 Score = 68.9 bits (169), Expect = 1e-14
 Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL  S + + L+E F E G +   ++ +D  G SKG G V F+T E A +AL E +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EKS 60

Query: 374 GKMIVSKPLYVAVAQRK 390
           G+ ++ + + V +A  +
Sbjct: 61  GEELLGREIRVDLATER 77

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

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

 Score = 69.3 bits (170), Expect = 1e-14
 Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           NL +  L   +  E+L+ LF   G I SCK++RD  +G S G GFV +    +A +A+  
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 372 MNGKMIVSKPLYVAVA 387
           +NG  I +K L V+ A
Sbjct: 62  LNGFEIRNKRLKVSYA 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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 77.0 bits (189), Expect = 1e-14
 Identities = 99/475 (20%), Positives = 160/475 (33%), Gaps = 84/475 (17%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  + + +    L   F   G I   ++  D SGQ++G+ FV F  KE A+ A+  LN
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120

Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 239
              I           R      V I      +FV  + ++   E+   I  E+  +T  V
Sbjct: 121 NYEI-----------RPGRLLGVCISVDNCRLFVGGIPKNKKREE---ILEEFSKVTEGV 166

Query: 240 V------MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQE 293
           V            K++ F FV +E+   AA A   L   +   + W    A   +E E+E
Sbjct: 167 VDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRI--QLWGHVIAVDWAEPEEE 224

Query: 294 LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGIS 351
           +       +K          LY++NL  +  +E +++ FSEF  G +   K +RD     
Sbjct: 225 VDEDVMAKVKI---------LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD----- 270

Query: 352 KGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR-KEERRARLQAQFSQMRPVAMG 410
               FV F   E+A +A+ E+NGK +    + V +A+   ++   R              
Sbjct: 271 --YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQA 328

Query: 411 PSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVP 470
                   +Y P    L  +  Y   P                        AP  +F   
Sbjct: 329 ARQSLGQ-VYDPASRSLAYEDYYYHPPY-----------------------APSLHFPRM 364

Query: 471 VVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHA------YRYPLGRNMQDFPF 524
                 +G+     R AG                PP G+       Y Y   R   +  +
Sbjct: 365 PGPIRGRGRGGAPSRAAG------------GRGYPPYGYEAYYGDYYGYHDYRGKYEDKY 412

Query: 525 DMGAGSMLPVPVDMGAGIPRRDASVGQPMP-ITALSTALANASPEQQRTLLGESL 578
                 M   P++   G P          P     + A   A  +  R L    +
Sbjct: 413 YGYDPGMELTPMNPVRGKPGGRGGRPAIPPPRGRKNGAPPPAIGQDGRQLFLYKI 467

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. Length = 578

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

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+++NL     DE+L+E FSE G I  C V++D  S   +G G+V F+  E+A RAL E 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 373 NGKMIVSKPLYVAVAQRK 390
                  + ++V  A++K
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

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

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L ++NL     +  LK+LFS FG +    + R P G  KG  FV F++  +A +A+  +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 374 GKMIVSKPLYVAV 386
           GK I  +P  VAV
Sbjct: 62  GKKIKGRP--VAV 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 24/70 (34%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY++NL  S+ +E L+E FS +G +   +++R+     +G  FV F++PE+A  AL ++N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 374 GKMIVSKPLY 383
           G ++  + L 
Sbjct: 60  GLVLDGRTLR 69

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

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

 Score = 68.5 bits (168), Expect = 2e-14
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L +KNL   I ++KL++LF  FGTIT  ++     G  +  GFV + T EEA +AL   N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 374 GKMIVSKPLYV 384
              I +  + V
Sbjct: 63  NSFIDTSKITV 73

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 68.6 bits (168), Expect = 2e-14
 Identities = 25/71 (35%), Positives = 38/71 (53%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NLD     + LK++F   G +  A +  D +GKS+  G V FE+  +A +A+   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 271 GKKFDDREWYV 281
           G+   DR   V
Sbjct: 61  GQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 28/72 (38%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           LY+ NL  +I ++ L+ +F  FG I   ++ RDP +G SKG GF+ F+  E+A +AL ++
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 373 NGKMIVSKPLYV 384
           NG  +  +P+ 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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NLD S+    L   FS  G I   ++  +  G+SKG+ +V+FEN+ES Q A+ KL+
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-KLD 60

Query: 180 GMLINDKQVFV 190
             LI  + +FV
Sbjct: 61  RELIKGRPMFV 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 67.8 bits (166), Expect = 3e-14
 Identities = 23/72 (31%), Positives = 39/72 (54%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VGDL   +    L   F+  G++   RV +D+ T +S GYG+V++    DA  A+  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 92  NFTPLNNKSIRI 103
           N   L  ++IR 
Sbjct: 62  NGQWLGGRAIRT 73

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

 Score = 68.0 bits (167), Expect = 3e-14
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVV------MRDGDGKSKCFGFVNFENADDAAK 264
           +FVKNL+  TT+E LKK F + G + S  +         G   S  +GFV F++ + A K
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 265 AVEALNGKKFDDR 277
           A++ L G   D  
Sbjct: 63  ALKRLQGTVLDGH 75

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|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 = 67.6 bits (166), Expect = 3e-14
 Identities = 24/74 (32%), Positives = 46/74 (62%)

Query: 33  YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN 92
           +VG++ ++ T+ QL ++FS+VG V+S R+  D  T +  GYG+  + +   AA A+  LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 93  FTPLNNKSIRIMYS 106
               N +++R+ ++
Sbjct: 62  GYEFNGRALRVDFA 75

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

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 67.8 bits (165), Expect = 4e-14
 Identities = 34/77 (44%), Positives = 49/77 (63%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +L  LFS +G+V S ++ RD     SLGYG+VNY N  DA RA++
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   L +K+I++ Y+
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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 67.4 bits (165), Expect = 5e-14
 Identities = 28/76 (36%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  ++++ LFS  G I SCK++RD  +G S G GFV +  PE+A +A+  
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 372 MNGKMIVSKPLYVAVA 387
           +NG  + +K + V+ A
Sbjct: 63  LNGLRLQNKTIKVSYA 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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 66.8 bits (164), Expect = 5e-14
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA-- 268
           F+  L   TT+E L++ F +YG +   V+M+D   G+S+ FGFV F +     K + A  
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61

Query: 269 --LNGKKFD 275
             L+G++ D
Sbjct: 62  HVLDGREID 70

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

 Score = 66.9 bits (164), Expect = 6e-14
 Identities = 29/72 (40%), Positives = 46/72 (63%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG+L FN+T+  L  +F   G++  V++ RD  T RS GYG++ +A+  DA +AL+ L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 92  NFTPLNNKSIRI 103
           N   L  + I++
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|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 = 66.9 bits (164), Expect = 7e-14
 Identities = 24/74 (32%), Positives = 39/74 (52%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             L+V  L    T+ +L  LFS+ G+V  V + +D  T  S G+G+V + +  DA  A+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 90  VLNFTPLNNKSIRI 103
            LN   L  + I++
Sbjct: 62  DLNGKELEGRVIKV 75

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

 Score = 66.7 bits (163), Expect = 7e-14
 Identities = 21/69 (30%), Positives = 41/69 (59%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + +FV  L  S T E+L+K+F ++G + S  ++ +  GK K   +V +EN   A++AV  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 269 LNGKKFDDR 277
           ++G +  ++
Sbjct: 63  MDGTEIKEK 71

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

 Score = 66.0 bits (162), Expect = 9e-14
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           VFV NL     +E+L+K F + G + +  ++RD   G  K FG+V F+  D  A A+  L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 270 NGKKFDDRE 278
           NG K   R+
Sbjct: 61  NGIKLKGRK 69

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|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 = 66.4 bits (162), Expect = 1e-13
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F+  +  L  +FS+ GQ+  V V +D  T+RS G+G+V + NP DA  A+  +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 92  NFTPLNNKSIRI 103
           N   ++ + IR+
Sbjct: 63  NGKSVDGRQIRV 74

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

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

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
           N +FV  L+  TTDEDL+ IF  +G I S  V+RD   G S  + F+ FE  +D  +A  
Sbjct: 4   NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 268 ALNGKKFDDREWYV 281
            ++    DDR  +V
Sbjct: 64  KMDNVLIDDRRIHV 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+++ NL  ++  + L D F  FG + S ++ TD  +G+S+GFGFV+ E  E A  AI+K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 178 LNGMLINDKQVFV 190
           LNG     + + V
Sbjct: 61  LNGTDFGGRTLTV 73

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|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 = 65.0 bits (159), Expect = 2e-13
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+I +L +   D+ L +LF+ FG + S KV  D  +G SK  GFV++  PE A  A+  M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 373 NGKMIVSKPLYV 384
           NG  +  K L V
Sbjct: 61  NGFQVGGKRLKV 72

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

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

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L +  T E+L+ +F   G I S  ++RD   G+S  +GFV++ + +DA KA+  
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 269 LNG 271
           LNG
Sbjct: 62  LNG 64

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

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

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 23/71 (32%), Positives = 41/71 (57%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  L  S+  + L   F   G + S ++ T+ SG+ KG  +V++EN+ SA  A+ K++
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 180 GMLINDKQVFV 190
           G  I +K + V
Sbjct: 65  GTEIKEKTISV 75

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

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

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF+  +      + L D FS FG++   KI TD +G SKG+GFV FE +E A+  +   N
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGN 64

Query: 180 GMLINDKQVFVGHFLRK 196
            +    K++ +G  +RK
Sbjct: 65  -LNFRGKKLNIGPAIRK 80

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

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 9/83 (10%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N +FV  +   TT+E+L+  F  +G++    ++ D  G SK +GFV FE  +DA K +  
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 269 ----LNGKKFDDREWYVGKAQKK 287
                 GKK +     +G A +K
Sbjct: 63  GNLNFRGKKLN-----IGPAIRK 80

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

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 24/61 (39%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           ++I+NL     +E+LKELFS+FG +   ++++D  +G SKG+ FV F T E A + L   
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 373 N 373
           +
Sbjct: 63  D 63

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

 Score = 65.3 bits (160), Expect = 2e-13
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 124 NLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGML 182
            L      + L + FS +G I   ++  D  +G+S+GFGFV FE+ E A+ A ++LNGM 
Sbjct: 6   GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 183 INDKQVFV 190
           I+ +++ V
Sbjct: 66  IDGRRIRV 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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 64.9 bits (159), Expect = 3e-13
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           LY+ +L   + +  L E+FS  G + S +V RD  +  S G  +V F  P +A RAL  +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 373 NGKMIVSKPLYVAVAQR 389
           N  +I  KP+ +  +QR
Sbjct: 62  NFDVIKGKPIRIMWSQR 78

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

 Score = 65.1 bits (159), Expect = 3e-13
 Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           NL I  L  ++ DE+ + LF   G + +CK++RD  +G S G GFV + + E+A RA+  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 372 MNGKMIVSKPLYVAVA 387
           +NG  + +K + VA A
Sbjct: 62  LNGLQLQNKRIKVAYA 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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 64.9 bits (159), Expect = 3e-13
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIAT------DGSGQSKGFGFVQFENKESAQN 173
           +F+KNL+     + L   F   G + S  IA        G   S G+GFV+F++KE+AQ 
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 174 AIDKLNGMLINDKQV 188
           A+ +L G +++   +
Sbjct: 63  ALKRLQGTVLDGHAL 77

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

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

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 27/71 (38%), Positives = 40/71 (56%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           ++++NL  S+  + LK+LF E G +    V  D  G SKG G V F +PE+A RA+   N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 374 GKMIVSKPLYV 384
           G  +  + L V
Sbjct: 61  GYDLEGRELEV 71

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

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

 Score = 64.6 bits (158), Expect = 4e-13
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 372
           L + NL     DE+ +EL S FG +  C ++   S G SKG GFV +++   A +A  ++
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 373 NGKMIVSKPLYV 384
           +GK I  + L 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 64.6 bits (158), Expect = 4e-13
 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
            ++++ +L   + D  L+E F   + ++   KV+ DP +G SKG GFV F   +E  RAL
Sbjct: 2   HSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL 61

Query: 370 AEMNGKMIVSKPLYVAVA 387
            EMNG    S+P+ V+ A
Sbjct: 62  TEMNGVYCSSRPMRVSPA 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 64.3 bits (157), Expect = 5e-13
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           ++FV +L      E L+  F  +G I+ A V++D   GKSK +GFV+F   +DA  A+++
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 269 LNGKKFDDRE 278
           +NG+    R 
Sbjct: 61  MNGQWLGGRA 70

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

 Score = 63.8 bits (156), Expect = 5e-13
 Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           NV+++ L  +TTDEDL+K+   +G I S   + D    K K +GFV+F++ + A KA+E 
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 269 LNGKKFD 275
           LNG+   
Sbjct: 62  LNGRGVQ 68

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 63.7 bits (156), Expect = 6e-13
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYV +L  +VT+  L + FS  G+V  VR+ R+    R  G+ +V +A+P DA  AL  L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 92  NFTPLNNKSIR 102
           N   L+ +++R
Sbjct: 59  NGLVLDGRTLR 69

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

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

 Score = 64.2 bits (157), Expect = 6e-13
 Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           VF   L   TT+ DL+++F  YG I    V+ D   G+S+ FGFV FE+ +DA +A E L
Sbjct: 4   VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 270 NGKKFDDRE 278
           NG + D R 
Sbjct: 62  NGMEIDGRR 70

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

 Score = 63.8 bits (156), Expect = 6e-13
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 179 NGMLINDKQVFV 190
           N   +  + + 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 64.1 bits (156), Expect = 7e-13
 Identities = 28/78 (35%), Positives = 40/78 (51%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+V +L F+VT   L D FS V  +    V  D  T  S GYG+V +A   DA  AL  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 91  LNFTPLNNKSIRIMYSHR 108
           L    L+ + +R+  + R
Sbjct: 61  LKNKKLHGRILRLDIAER 78

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

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

 Score = 63.8 bits (156), Expect = 7e-13
 Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 4/76 (5%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSG----QSKGFGFVQFENKESAQNA 174
            ++I NLD  +    L   FS +G I         SG    Q +G+ FV FE KE A+ A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 175 IDKLNGMLINDKQVFV 190
           +  LNG     K++ V
Sbjct: 61  LKSLNGKTALGKKLVV 76

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

 Score = 63.9 bits (156), Expect = 7e-13
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
            +FV NL     +  L ++F  +G +T+  V+RD    K K +GFV   N ++A  A+ +
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 269 LNGKKFDDR 277
           LNG +   R
Sbjct: 63  LNGYRLGGR 71

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

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

 Score = 64.0 bits (155), Expect = 7e-13
 Identities = 31/77 (40%), Positives = 49/77 (63%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +   LF  +G++ S ++ RD  T +SLGYG+VNY +P DA +A++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   L  K+I++ Y+
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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 63.7 bits (155), Expect = 8e-13
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +++VGDL   VTD+ L+  FS        RV  D+ + RS GYG+V++ +  DA  A++ 
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 91  LNFTPLNNKSIRI 103
           +N   L ++ IR 
Sbjct: 61  MNGKWLGSRPIRC 73

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

 Score = 63.9 bits (156), Expect = 8e-13
 Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L++ +L   +DD +L E FS+ + +    KV+ D +G S+G GFV FS   E  RAL EM
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 373 NGKMIV-SKPLYVAVA 387
            G   +  KP+ V++A
Sbjct: 64  QGASGLGGKPIRVSLA 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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 64.0 bits (155), Expect = 9e-13
 Identities = 32/77 (41%), Positives = 50/77 (64%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +L  LF  +G++ S ++ RD  T +SLGYG+VNY +P DA +A++
Sbjct: 5   TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   L  K+I++ Y+
Sbjct: 65  TLNGLRLQTKTIKVSYA 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 24/72 (33%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T++YV +L  ++ D +L +LF + G++ S +V +D    +S G+G+VN+ N   A +A++
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVE 60

Query: 90  VLNFTPLNNKSI 101
            LN   +N K +
Sbjct: 61  ELNGKEVNGKKL 72

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

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 23/65 (35%), Positives = 35/65 (53%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           I +KNL K +    L + F S G +   K+     G+S+ FGFV F+++E AQ A+   N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 180 GMLIN 184
              I+
Sbjct: 63  KTFID 67

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 = 63.0 bits (154), Expect = 1e-12
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 7/74 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY++NL  S  +E+L+ELFSE+G +   K ++D         FV F   ++A +A+ EMN
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 374 GKMIVSKPLYVAVA 387
           GK +   P+ V++A
Sbjct: 57  GKELEGSPIEVSLA 70

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

 Score = 63.5 bits (155), Expect = 1e-12
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L + +  + L   F + G I SCKI  D  +GQS G+GFV + ++  AQ AI+ 
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 178 LNGMLINDKQVFV 190
           LNG  I +K++ V
Sbjct: 62  LNGFEIRNKRLKV 74

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

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 5/69 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 371
           L+I  L     +E L+E FS++G +  C +M+DP +G S+G GFV F+ P    + LA  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 372 ---MNGKMI 377
              ++G+ I
Sbjct: 61  PHVLDGREI 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 63.5 bits (155), Expect = 1e-12
 Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQNAIDK 177
           N+++  L K++  + L   FS +G I++ +I  D   G S+G GF++F+ +  A+ AI  
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 178 LNG 180
           LNG
Sbjct: 62  LNG 64

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

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

 Score = 63.6 bits (154), Expect = 1e-12
 Identities = 31/77 (40%), Positives = 49/77 (63%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +   LF  +G++ S ++ RD  T +SLGYG+VNY +P DA +A++
Sbjct: 4   TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   L  K+I++ Y+
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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 25/78 (32%), Positives = 45/78 (57%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+V +L ++ TD QL + FS+VG +    V +D  +++  G+GYV +A   DA RAL+ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 91  LNFTPLNNKSIRIMYSHR 108
              T    + I + ++ +
Sbjct: 61  KKKTKFGGRKIHVEFAKK 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 62.4 bits (152), Expect = 2e-12
 Identities = 27/75 (36%), Positives = 46/75 (61%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L ++V D  L   F + G V+  RV  D  T RS G+GYV++ +P DA +A++ +
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 92  NFTPLNNKSIRIMYS 106
           +   L+ + I + +S
Sbjct: 62  DGKELDGRPINVDFS 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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           S++VG+L F++ + +L   F   G V +VR+ RD  T    G+GYV +      A AL  
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK- 59

Query: 91  LNFTPLNNKSIRIM 104
           LN   L  + IR+ 
Sbjct: 60  LNGIKLKGRKIRVK 73

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

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

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQ-VLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           S++VGDL  +VTD  L + F      V   +V  D  T RS GYG+V + +  +  RAL 
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 90  VLNFTPLNNKSIRI 103
            +N    +++ +R+
Sbjct: 63  EMNGVYCSSRPMRV 76

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

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVV-----MRDGDGKSKCFGFVNFENADDAAKA 265
           ++V+NLD    ++DL+ IF ++G + S  +      + G   +  F FV F++A  A  A
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGR-LNNGFAFVTFKDASSAENA 61

Query: 266 VEALNGKKFDDREWYV 281
           ++ LNG +   R+  V
Sbjct: 62  LQ-LNGTELGGRKISV 76

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

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

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L + NL   + +E L+ELF   G +   K+  D SG S+G+  V F   E+A RA+ + N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 374 GKMIVSKPLYVAV 386
           G ++  +P+ V +
Sbjct: 63  GVLLDGQPMQVEL 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|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 = 62.6 bits (153), Expect = 2e-12
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            +++ NL   +  + L  TFS FG I   ++  D     KG+ FV+F+  E+A  AI  +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 179 NGMLINDKQV 188
           NG  IN + V
Sbjct: 57  NGTSINGQTV 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 63.1 bits (154), Expect = 2e-12
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVM--RDPSGISKG--SGFVAFSTPEEASRA 368
           NLY+ NL   + +E L + F  FG + S K+M  R      +    GFVAF    +A RA
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 369 LAEMNGKMIVSKPLYVA 385
           L E++GK ++   L + 
Sbjct: 63  LDELDGKDVMGYELKLG 79

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

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVM--RDGDGKSK---CFGFVNFENADDAAK 264
           N++V NL+   T+E L + FG +G + S  +M  R  + + +   C GFV F N  DA +
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC-GFVAFMNRADAER 61

Query: 265 AVEALNGKKFDDREWYVG 282
           A++ L+GK     E  +G
Sbjct: 62  ALDELDGKDVMGYELKLG 79

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

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+ NL  ++ ++ L ELFS+ G I SCK++R+         FV +     A+ AL  MN
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 374 GKMIVSKPLYV 384
           G++I+ + + V
Sbjct: 59  GRLILGQEIKV 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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N++I NL   +D + L      +G ++S +I  D  GQS+G GF + E++E  ++ I K 
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 179 NGMLI 183
           NG  +
Sbjct: 62  NGKYL 66

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|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 = 62.3 bits (152), Expect = 2e-12
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           FV+NL  +TT+E+L+++F  +G I+   + +     +SK F FV+F   + A KA   L+
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 271 GKKFDDR 277
           G  F  R
Sbjct: 63  GSIFQGR 69

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

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

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV  L   TT+E L+++F  YG I    ++RD   G SK + FV +E+  DA +A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 270 NGKKFDDREWYVGKAQKKSEREQELKG 296
           +    D  E +V       ERE+ L G
Sbjct: 66  HKLVIDGSEIFV-----DFERERTLPG 87

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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 62.0 bits (151), Expect = 3e-12
 Identities = 24/71 (33%), Positives = 40/71 (56%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++ NL   +  +KLKE+F   G +    +  D  G S+G G V F  P EA +A++  N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 374 GKMIVSKPLYV 384
           G+M+  +P+ V
Sbjct: 61  GQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 62.0 bits (151), Expect = 3e-12
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++V +L  +  +S L+ LFS  G V +V+V RDL+T +  GYG+V   N  +A  A+  L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 92  NFTPLNNKSIRI 103
           N   L  + +++
Sbjct: 64  NGYRLGGRVLQV 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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 62.1 bits (151), Expect = 3e-12
 Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           N+++ +L   + D  L   FS F + +  +VM D  SG S+G GFV+F + ++A  A+ E
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 372 MNGKMIVSKPL 382
           MNGK + S+P+
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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 26/65 (40%), Positives = 43/65 (66%), Gaps = 7/65 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL ++TT E+L+ +F +YGT+T   V+++       +GFV+ E  +DA  A++ALN
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 271 GKKFD 275
           G +F 
Sbjct: 55  GYEFM 59

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

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 26/70 (37%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ NL    D  ++++ F  +G I S ++ TD  SG+ KGFG+V+F ++E+AQ A+D L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 179 NGMLINDKQV 188
            G  +  + V
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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 61.5 bits (150), Expect = 4e-12
 Identities = 25/71 (35%), Positives = 34/71 (47%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + ++NL        L   FS FG +    I     G+ KGF FVQF +K  A+ AI  +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 180 GMLINDKQVFV 190
           G  I  + V V
Sbjct: 62  GKKIKGRPVAV 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|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 = 61.5 bits (150), Expect = 4e-12
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          L++  L    TD  LY LF+  G V+S +V  D +T +S  +G+V+Y NP  A  A+  +
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 92 N 92
          N
Sbjct: 61 N 61

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

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           VF++NL    T+E+LK++F ++G +  A +++D   G SK   FV F+  + A K +EA 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 270 NGKKFDD 276
           +  +   
Sbjct: 63  DNAEDSG 69

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

 Score = 61.6 bits (150), Expect = 4e-12
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           G  +++ NL    D+  L +LFS FG +T+ KV+RD  +   KG GFV  +  EEA  A+
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 370 AEMNGKMIVSKPLYV 384
           A +NG  +  + L V
Sbjct: 61  ASLNGYRLGGRVLQV 75

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

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

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG+L F  T+ Q+Y+LFS+ G +  + +  D  T+   G+ +V Y    DA  A+  L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 92  NFTPLNNKSIRI 103
           N T L+++ IR+
Sbjct: 61  NGTKLDDRIIRV 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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 61.2 bits (149), Expect = 5e-12
 Identities = 26/71 (36%), Positives = 38/71 (53%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF+ NLD  +  K L + F   G ++   I  D  G+S+G G VQFE+   A  AI   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 180 GMLINDKQVFV 190
           G ++ D+ + V
Sbjct: 61  GQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 27/61 (44%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALN 270
           +V NL  + T++DL+ IF  +G I    + RD + G+SK +GF+ F +A+DA KA+E LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 271 G 271
           G
Sbjct: 62  G 62

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

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

 Score = 61.4 bits (149), Expect = 5e-12
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+++NL  S+  E L + FS+   I    V+ DP +G S+G GFV F+  E+A  ALA++
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 373 NGKMIVSKPLYVAVAQRK 390
             K +  + L + +A+R+
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

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

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 371
           NLY+  L  ++  ++L+ LFS +G I + +++ D   G+S+G GF+ F    EA RA+  
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 372 MNGK 375
           +NG 
Sbjct: 62  LNGT 65

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

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

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           +FV  L   TTD+ L+K F ++G I  AVV+ D   GKS+ +GFV F++ + A +A +  
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 270 NGKKFDDR 277
           N    D R
Sbjct: 63  N-PIIDGR 69

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|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 = 61.4 bits (150), Expect = 5e-12
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 372
           L++  L  +  +E ++ LF E+G I    ++RD   G SKG  FV FS+ EEA +A+  +
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 373 NGKMI---VSKPLYV 384
           +GK+     S+PL 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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L++GDL+  + ++ +Y  F++ G+V SV++ R+  T +S GYG+V +A    A +AL  
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 91  LNFTPLNNKSIR 102
           LN  P+ N   R
Sbjct: 61  LNGKPIPNTQQR 72

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

 Score = 61.4 bits (149), Expect = 6e-12
 Identities = 30/79 (37%), Positives = 47/79 (59%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N +FV  +D  T + DL+K F +YGT+    ++ D  G SK +GFV FE  +DA K ++ 
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQE 62

Query: 269 LNGKKFDDREWYVGKAQKK 287
            N   F D++  +G+A +K
Sbjct: 63  ANRLCFRDKKLNIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 61.4 bits (149), Expect = 6e-12
 Identities = 28/77 (36%), Positives = 43/77 (55%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF+  +D   +   L   FS +G +   KI  D +G SKG+GFV FE +E AQ  + + N
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEAN 64

Query: 180 GMLINDKQVFVGHFLRK 196
            +   DK++ +G  +RK
Sbjct: 65  RLCFRDKKLNIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|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 = 61.1 bits (149), Expect = 6e-12
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGE-YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           + VKNL  S T+ +LK+ F +  G IT   ++R  DGKS+   F+ ++  ++A KA +  
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 270 NG 271
           N 
Sbjct: 63  NN 64

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

 Score = 61.1 bits (149), Expect = 7e-12
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQNAIDKL 178
           + + NL      +   +  S FG +  C +    S G+SKG+GFV++ +K SA  A ++L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 179 NGMLINDKQVFV 190
           +G  I  +++ 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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 61.2 bits (149), Expect = 7e-12
 Identities = 21/65 (32%), Positives = 38/65 (58%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           NLYI NL   +D++ L+ +   +G + S +++RD  G S+G GF    + E+    +++ 
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 373 NGKMI 377
           NGK +
Sbjct: 62  NGKYL 66

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|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 = 60.7 bits (148), Expect = 8e-12
 Identities = 31/75 (41%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           VFV N+    T+E L +IF E G + S  ++ D D GK K +GF  FE+ + AA A+  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 270 NGKKFDDREWYVGKA 284
           NG +F+ R   V  A
Sbjct: 61  NGYEFNGRALRVDFA 75

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

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

 Score = 61.1 bits (149), Expect = 8e-12
 Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 1/54 (1%)

Query: 138 FSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           FS FG I SC++  D  +G S  + F++FE KE  + A  K++ +LI+D+++ V
Sbjct: 24  FSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHV 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 66.5 bits (162), Expect = 9e-12
 Identities = 64/281 (22%), Positives = 111/281 (39%), Gaps = 18/281 (6%)

Query: 20  AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
           A  S +     +LYV  L   +T  +L  +FS  GQ+++ R+  D  T  S G G++ + 
Sbjct: 80  ARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFD 139

Query: 80  NPADAARALDVLNFTPLNNKS--IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDT 137
              +A RA+  LN T  +  +  I + +++ +PS   S      +  L+   + +     
Sbjct: 140 KRDEADRAIKTLNGTTPSGCTEPITVKFAN-NPS---SSNSKGLLSQLEAVQNPQTTRVP 195

Query: 138 FSSFGNILSCKIATDGS-------GQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
            S+             +       G        Q +    AQ    +       D Q   
Sbjct: 196 LSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAG 255

Query: 191 GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSK 249
                    +  A       +FV NL   T +  L ++FG +G + +  ++RD    + K
Sbjct: 256 ----LAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCK 311

Query: 250 CFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSER 290
            +GFV+  N D+AA A+ +LNG    +R   V     K+ R
Sbjct: 312 GYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAYR 352

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

 Score = 60.8 bits (148), Expect = 9e-12
 Identities = 28/70 (40%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
           V+V NL  S T+ DL KIF +YG +    +++D +  KSK   F+ F + +DA K V+AL
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 270 NGKKFDDREW 279
           N K+   R  
Sbjct: 64  NNKELFGRTL 73

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

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

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 19/69 (27%), Positives = 43/69 (62%), Gaps = 1/69 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++++NL  S+  + L + FS +G +   ++  +   + +GF FV+F + E A+ A+ KLN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 180 GMLINDKQV 188
           G++++ + +
Sbjct: 60  GLVLDGRTL 68

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

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

 Score = 60.6 bits (148), Expect = 1e-11
 Identities = 26/60 (43%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNG 180
           + NL +  D   L + F  FG I    +A D  +GQS+GF FV F  +E A+ AI+KLNG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 60.7 bits (148), Expect = 1e-11
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 8/73 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV +L    TDE L + F +Y +   A V+RD   GKSK +GFV+F + +D  KA++ +
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 270 NGKKFDDREWYVG 282
           NGK       YVG
Sbjct: 69  NGK-------YVG 74

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

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 6/70 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR--DPSG----ISKGSGFVAFSTPEEASR 367
           L++KNL     +E LK+ F + G + S  + +  DP G    +S G GFV F + E A +
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 368 ALAEMNGKMI 377
           AL  + G ++
Sbjct: 63  ALKRLQGTVL 72

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

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

 Score = 60.2 bits (146), Expect = 1e-11
 Identities = 23/71 (32%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           NIF+ +L   +    L   FS+F +    ++  D  SG+S+G+GFV F +++ A+NAI++
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 178 LNGMLINDKQV 188
           +NG  +  + +
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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 60.5 bits (147), Expect = 1e-11
 Identities = 25/72 (34%), Positives = 43/72 (59%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L F+  +  +Y+ F + G++ SVR+  D  + R  G+GYV +++   A  ALD L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 92  NFTPLNNKSIRI 103
             T L  + +R+
Sbjct: 61  GGTDLLGRPVRL 72

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

>gnl|CDD|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 = 60.3 bits (147), Expect = 1e-11
 Identities = 28/64 (43%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV  L ++ T+ED++ +F EYG I    ++RD D G+SK   FV F + ++A KA+EAL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 270 NGKK 273
           +GK 
Sbjct: 62  HGKV 65

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|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 = 60.4 bits (147), Expect = 1e-11
 Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEF-GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L +KNL  S+ + +LKE FS+  G IT  K++R   G S+   F+ + T EEA +A    
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 373 NGKMI 377
           N   I
Sbjct: 63  NNTYI 67

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

 Score = 67.0 bits (163), Expect = 1e-11
 Identities = 96/479 (20%), Positives = 172/479 (35%), Gaps = 81/479 (16%)

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTK---------FNNVFVKNL 216
           E K+  Q A  K   M  + KQV +      Q+++    + +            V+V ++
Sbjct: 58  EQKDDIQKA--KKYAMEQSIKQVLLKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSI 115

Query: 217 DESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFD 275
                ++ +++ F  +G I S  +  D   GK K F FV +E  + A  A+E +NG+   
Sbjct: 116 SFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG 175

Query: 276 DREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-LYIKNLGDSIDDEKLKELFSE 334
            R   VG+             Q +  +    ++ +  N +Y+ ++   + +  +K +F  
Sbjct: 176 GRNIKVGRPSNM--------PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEA 227

Query: 335 FGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 393
           FG I  C++ R P+G   KG GF+ ++  +  S A+A MN        L+          
Sbjct: 228 FGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN--------LF---------- 269

Query: 394 RARLQAQFSQMRPVAMGPSVPPRMPMYPPG-PSGLGQQFLYGQAPPAIIPPQAGFGYQQQ 452
              L  Q+     + +G  V P   +  P   S +         P A     A    +  
Sbjct: 270 --DLGGQY-----LRVGKCVTPPDALLQPATVSAI---------PAAAAVAAAAATAKIM 313

Query: 453 LVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYR 512
               +  A    P    P           G +      ++  + +P +P   P       
Sbjct: 314 AAEAVAGAAVLGPRAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPPLPQAAPAV----- 368

Query: 513 YPLGRNMQDFPFDMGAGSMLPVPV-DMGAGIPRRDASVGQPMPITALSTALANASPEQQR 571
                 ++  P +      +P PV   G  IP   A  G   P     + LA+   + +R
Sbjct: 369 ------VKPGPME------IPTPVPPPGLAIPSLVAPPGLVAPTEINPSFLASPRKKMKR 416

Query: 572 TLLGESLYPLVEQL------ERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME 624
             L  +   L + L      + D  ++   ML  M +      LE  +  K K  E ++
Sbjct: 417 EKLPVTFGALDDTLAWKEPSKEDQTSEDGKMLAIMGEAAAALALEPKKKKKEKEGEELQ 475

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

 Score = 59.9 bits (146), Expect = 2e-11
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++ +LD ++ +  LYD FS  G +LS +V  D +   S GYG+V++     A RA++ +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAIEKV 63

Query: 92  NFTPLNNKSI 101
           N   LN+K +
Sbjct: 64  NGMLLNDKKV 73

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

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

 Score = 59.9 bits (146), Expect = 2e-11
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
           +V +L    T+  L +IF   G + S  V RD    +S  + +VNF+N  DA +A++ LN
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

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

 Score = 59.7 bits (145), Expect = 2e-11
 Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++    +   FSS G I SCK+  D  +GQS G+GFV + + E A+ AI+ 
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 178 LNGMLINDKQVFV 190
           LNG+ + +K + V
Sbjct: 63  LNGLRLQNKTIKV 75

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

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

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NL  S +   L + F   G ++  +IA D  G+SKGFG V+F  +E AQ A++K +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK-S 60

Query: 180 GMLINDKQVFV 190
           G  +  +++ V
Sbjct: 61  GEELLGREIRV 71

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 7/68 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VFV NLD S  +++L+K+F + G IT   ++++  GKSK + +V FEN +      EAL 
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEE---SVQEAL- 57

Query: 271 GKKFDDRE 278
            K   DRE
Sbjct: 58  -KL--DRE 62

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|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 = 59.9 bits (146), Expect = 2e-11
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ N+      + L + FS  G ++S ++ TD  +G+ KG+GF +FE+ E+A +AI  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 179 NGMLINDKQVFVGH 192
           NG   N + + V  
Sbjct: 61  NGYEFNGRALRVDF 74

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

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

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 23/72 (31%), Positives = 40/72 (55%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG L   V +  L+  F   G +  +++  D  T++  G+ +V +  P DAA A+D +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 92  NFTPLNNKSIRI 103
           N + L  ++IR+
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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 22/68 (32%), Positives = 36/68 (52%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NL    T+EDL+++FG  G +    +  D  G+S+    V FE  +DA +A++  N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 271 GKKFDDRE 278
           G   D + 
Sbjct: 63  GVLLDGQP 70

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|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 = 59.9 bits (145), Expect = 2e-11
 Identities = 31/73 (42%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N+FI +L +      L   F  FGN++S K+  D  + QSK FGFV F+N  SAQ AI  
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 178 LNGMLINDKQVFV 190
           +NG  I  K++ V
Sbjct: 66  MNGFQIGMKRLKV 78

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

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

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           S++VG L  +VT  +L + FS+ G++L V + +  +   +  + ++ +     AARA++ 
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVES 62

Query: 91  LNFTPLNNKSIRIMY 105
            N + L NK++ + Y
Sbjct: 63  ENHSMLKNKTMHVQY 77

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

 Score = 59.7 bits (145), Expect = 2e-11
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            +FV NL+ + T+E+L++ F  YG +    + R   G+   + FV F N D A +A  A+
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 270 NGKKFDDREWYVGKAQKK 287
           +G+       Y+G+ Q K
Sbjct: 64  SGQ-------YIGRNQIK 74

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

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

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L++  L  +++ + LKE+FS +GT+    +  D    + +G  +V F +PE+A +A+  M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 373 NGKMI 377
           +G  I
Sbjct: 61  DGGQI 65

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

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 2/81 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRDGD-GKSKCFGFVNFENADDAAKAVE 267
           N+F+ NLD    ++ L   F  +G I     +MRD D G SK F F+++++ + +  A+E
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 268 ALNGKKFDDREWYVGKAQKKS 288
           A+NG+   +R   V  A KK 
Sbjct: 63  AMNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F++NL      + L + FS  G I  C +  D GS + +GFG+V F  +E A+ A+++ 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 179 NGMLINDKQVFV 190
                  +++ V
Sbjct: 62  KKTKFGGRKIHV 73

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

 Score = 59.5 bits (145), Expect = 3e-11
 Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 1/60 (1%)

Query: 316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 374
           + NL +  D++ L+ELF  FG I+   + +D  +G S+G  FV F T E+A RA+ ++NG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 23/63 (36%), Positives = 37/63 (58%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           VKNL +   ++ L+K+F  +GTIT   +    DGK + FGFV ++  ++A KA++  N  
Sbjct: 5   VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNS 64

Query: 273 KFD 275
             D
Sbjct: 65  FID 67

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 59.5 bits (145), Expect = 3e-11
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 6/77 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI+NL      + L + FS FG +   +I  D  +G SKG  FV+F+ KESAQ  ++  
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 179 N-----GMLINDKQVFV 190
           +     G+ ++ +++ V
Sbjct: 63  DNAEDSGLSLDGRRLIV 79

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|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 23/61 (37%), Positives = 34/61 (55%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L + NL   + D+ +KELF+EFG +    V  D SG S G+  V F    +A +A+ + N
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYN 62

Query: 374 G 374
           G
Sbjct: 63  G 63

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 59.2 bits (144), Expect = 4e-11
 Identities = 26/78 (33%), Positives = 46/78 (58%), Gaps = 5/78 (6%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVL-SVRVCRDLSTRRSLGYGYVNYAN--PADAARAL 88
           L++G+LD  V +  LYD FS  G +L + ++ RD  T  S G+ +++Y +   +DA  A+
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDA--AI 61

Query: 89  DVLNFTPLNNKSIRIMYS 106
           + +N   L N+ I + Y+
Sbjct: 62  EAMNGQYLCNRPITVSYA 79

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

>gnl|CDD|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 = 58.8 bits (143), Expect = 4e-11
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 372
           L+++NL  +  +E+L+ELF  FG I+   +  D     SKG  FV+F  PE A +A +E+
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 373 NGKMIVSKPLYV 384
           +G +   + L+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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  L       +L   FS FG I    + TD  +G+S+G+GFV F++KESA+ A    
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 179 N 179
           N
Sbjct: 63  N 63

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

>gnl|CDD|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 = 58.8 bits (143), Expect = 4e-11
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSF-GNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           + +KNL  S+    L + FS   G I   K+     G+S+   F+ ++ +E AQ A D  
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 179 NGMLINDKQVFV 190
           N   IN  ++ V
Sbjct: 63  NNTYINTSKISV 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 25/73 (34%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           I++ ++   +    +   F +FG I SC +A D  +G+ KG+GF+++EN +SAQ+AI  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 179 NGMLINDKQVFVG 191
           N   +  +Q+ VG
Sbjct: 63  NLFDLGGQQLRVG 75

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

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNG 271
           V NL   TT +DL+++F +YG +    + RD    +S+ F FV F +  DA  A++A++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 272 KKFDDRE 278
           K+ D RE
Sbjct: 63  KELDGRE 69

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

 Score = 59.2 bits (144), Expect = 4e-11
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 314 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L++  L     D   L++LFS+ G  T C++   P+G  +G  FV ++T E+A  A   +
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 373 NGKMIVSKPLYVA 385
           NG  +   P+ V+
Sbjct: 65  NGHSLQGSPIRVS 77

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

 Score = 65.1 bits (158), Expect = 5e-11
 Identities = 38/158 (24%), Positives = 81/158 (51%), Gaps = 7/158 (4%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++ ++   +    +   F  FG I S  ++ D  +G+ KGF FV++E  E+AQ A++++
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYG 233
           NG ++  + + VG      + + +         KFN ++V ++    ++ D+K +F  +G
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229

Query: 234 TITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEALN 270
            I    + R   G   K +GF+ + N    ++A+ ++N
Sbjct: 230 EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN 267

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

 Score = 58.3 bits (142), Expect = 5e-11
 Identities = 18/72 (25%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           + +  L ++++   L + FS++G +    +  D      +G+ +V+FE+ E A+ AI  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 179 NGMLINDKQVFV 190
           +G  I+ ++V V
Sbjct: 61  DGGQIDGQEVTV 72

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

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

 Score = 58.6 bits (142), Expect = 5e-11
 Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV+NL  S  ++DL+K+F ++G ++   V  D   GKSK F +V F + +DA KA + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 270 NGKKFDDR 277
           +GK F  R
Sbjct: 65  DGKVFQGR 72

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 59.0 bits (142), Expect = 5e-11
 Identities = 26/69 (37%), Positives = 42/69 (60%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G GF    + E+    ++  
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 373 NGKMIVSKP 381
           NGK I + P
Sbjct: 62  NGKFIKTPP 70

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

 Score = 58.6 bits (142), Expect = 6e-11
 Identities = 26/61 (42%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVE 267
             +FV  L+  T+D  L++ F  YG +T  VVM D + K S+ FGF+ F +AD+A +A+E
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 268 A 268
           A
Sbjct: 63  A 63

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

 Score = 58.1 bits (141), Expect = 7e-11
 Identities = 29/76 (38%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS----GFVAFSTPEEASRA 368
            L+I NL   + +  L +LFS++G I     +   SG  KG      FV F T EEA +A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 369 LAEMNGKMIVSKPLYV 384
           L  +NGK  + K L V
Sbjct: 61  LKSLNGKTALGKKLVV 76

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|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 = 58.3 bits (142), Expect = 7e-11
 Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 121 FIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLN 179
           F+  L K+   + +   F  +GNI    I  D  +GQSKG  FV+F ++E AQ AI+ L+
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62

Query: 180 GM 181
           G 
Sbjct: 63  GK 64

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 58.3 bits (141), Expect = 7e-11
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++  L    ++  ++ +F+ FG+I  C V+RD +G S+G  FV F++ + A  A+  M+
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

Query: 374 GKMIV---SKPLYVAVA 387
               +   S PL V  A
Sbjct: 64  HSQTMEGCSSPLVVKFA 80

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

 Score = 58.1 bits (141), Expect = 8e-11
 Identities = 22/71 (30%), Positives = 36/71 (50%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + +KNL K I    L   F +FG I   ++     G+ + FGFV ++ +E AQ A+   N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 180 GMLINDKQVFV 190
              I+  ++ V
Sbjct: 63  NSFIDTSKITV 73

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 57.9 bits (140), Expect = 8e-11
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+FV +L    TD  L   F  + + + A VM D   G+S+ +GFV+F +  DA  A+  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 269 LNGKKFDDR 277
           +NGK    R
Sbjct: 61  MNGKWLGSR 69

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

 Score = 58.3 bits (141), Expect = 8e-11
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 314 LYIKNLGDSIDDEKLKELF-SEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           +++ +L   +++  L  LF S F +  S K+M DP +G+S+G GFV FS   +  RAL E
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 372 MNGKMIVSKPLYVAVA 387
           M G     +P+ ++ 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 58.4 bits (142), Expect = 8e-11
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 266
           F  +FV  L+  TT+  L++ F EYG I    ++RD   GK + + F+ FE+  D   A 
Sbjct: 1   FKTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 267 EALNGKKFDDR 277
           +  +GKK D R
Sbjct: 61  KYADGKKIDGR 71

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

 Score = 57.7 bits (140), Expect = 9e-11
 Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++ NL  +I    L   F  FG I   ++  D  +G+SKG+GF+QF + E A+ A+++L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 179 NGMLINDKQVFVG 191
           NG  +  + + VG
Sbjct: 61  NGFELAGRPIKVG 73

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

 Score = 58.0 bits (141), Expect = 9e-11
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           +++  L     D+ L++ FS+FG I    V+ D  +G S+G GFV F   E A RA  + 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 373 NGKMIVSKPLYVAVA 387
           N  +I  +   V +A
Sbjct: 63  N-PIIDGRKANVNLA 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 58.1 bits (141), Expect = 9e-11
 Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 3/71 (4%)

Query: 320 GDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV 378
           G S+ ++ L+E F+ FG I    V++D  +  SKG  +V F+    A+RA+ EMNGK + 
Sbjct: 11  GKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLG 70

Query: 379 S--KPLYVAVA 387
              KPL V +A
Sbjct: 71  GDTKPLKVLIA 81

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

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

 Score = 57.8 bits (140), Expect = 1e-10
 Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T ++++ +F   G I S  ++RD   G+S  +GFVN+ + +DA KA+  
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 269 LNG 271
           LNG
Sbjct: 63  LNG 65

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

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

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y+ NLG      +L++ F ++G + S  V R+P G      FV F  P +A  A+  ++
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGF----AFVEFEDPRDAEDAVRALD 57

Query: 374 GKMIVSKPLYVAVAQR 389
           G+ I    + V +++ 
Sbjct: 58  GRRICGNRVRVELSRG 73

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

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

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 22/63 (34%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+ +  L ++ TDE+ + +F   G + +  ++RD   G S  FGFV++++A+DA +A+  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 269 LNG 271
           LNG
Sbjct: 62  LNG 64

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

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 63.9 bits (155), Expect = 1e-10
 Identities = 68/294 (23%), Positives = 130/294 (44%), Gaps = 43/294 (14%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             ++VG +  ++ + +L  LF + G +  +R+  D S +   GY +V +    +A  A+ 
Sbjct: 59  CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNR-GYAFVTFCGKEEAKEAVK 117

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGN-IFIKNLDKSIDHKALHDTFSSFGNILSCK 148
           +     LNN  IR     R   +  S     +F+  + K+   + + + FS     +   
Sbjct: 118 L-----LNNYEIR---PGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDV 169

Query: 149 I---ATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVA-- 203
           I   +     +++GF FV++E+  +A  A  K    L+  +    GH +     E     
Sbjct: 170 IVYHSAADKKKNRGFAFVEYESHRAAAMARRK----LMPGRIQLWGHVIAVDWAEPEEEV 225

Query: 204 ---IKTKFNNVFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFEN 258
              +  K   ++V+NL  +TT+E ++K F E+  G +     +RD       + FV+FE+
Sbjct: 226 DEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD-------YAFVHFED 278

Query: 259 ADDAAKAVEALNGKKFD------------DREWYVGKAQKKSEREQELKGQFEQ 300
            +DA KA++ LNGK+ +            D++ YV   +    R +E +   + 
Sbjct: 279 REDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQS 332

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. Length = 578

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

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 37  LDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL 96
           L    T+  L ++FS+ G +  V+V  D  T RS G+G+V + +  DA  A + LN   +
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 97  NNKSIRIMYS 106
           + + IR+ YS
Sbjct: 67  DGRRIRVDYS 76

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

 Score = 57.7 bits (140), Expect = 1e-10
 Identities = 24/75 (32%), Positives = 39/75 (52%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L VG+L    TD Q  +L S  G V    +    ST  S GYG+V YA+ A A +A + L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 92  NFTPLNNKSIRIMYS 106
           +   +  + +++ ++
Sbjct: 62  DGKQIGGRKLQVDWA 76

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|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 = 57.2 bits (139), Expect = 1e-10
 Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            +Y+ NL   + +E+L+  FS FG I   +V +D     KG  FV F T E A+ A+  +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 373 NGKMI 377
           NG  I
Sbjct: 57  NGTSI 61

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + V N+     D DL+++FG++G I    ++ +  G SK FGFV F N+ DA +A E 
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREK 59

Query: 269 LNGKKFDDREWYVGKA 284
           L+G   + R+  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|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 = 57.4 bits (139), Expect = 1e-10
 Identities = 23/63 (36%), Positives = 35/63 (55%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++  L     ++ ++ LF  FGTI  C ++R P G SKG  FV FS+  EA  A+  ++
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 374 GKM 376
           G  
Sbjct: 64  GSQ 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 = 57.3 bits (139), Expect = 1e-10
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV--- 266
           +FV  L E  T+EDL++ F +YG + S  ++ D + GK + F FV F++ D   K V   
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 267 -EALNGKKFD 275
              +NG + +
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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 213 VKNLDESTTDEDLKKIFGEYG--TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           ++ LD  TT+ED+ +         I    ++RD   G S+ F FV F + +DA + ++AL
Sbjct: 7   LRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDAL 66

Query: 270 NGK---KFDDRE 278
           N       D R 
Sbjct: 67  NNLDPFVIDGRV 78

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

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV  L    T+E+ K+ F ++G +  A +M+D D G+S+ FGFV F++ + A + V + 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 270 NGKKFDDREWYVGKA 284
              +   ++  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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N++I+ L  +   + L      FG I+S K   D  + + KG+GFV F++ E+A  AI+ 
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 178 LNGM 181
           LNG 
Sbjct: 62  LNGR 65

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

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+  L      + L + FS +G+I   ++  D  +G SKG+ FV++E++  A  A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 179 NGMLINDKQVFV 190
           + ++I+  ++FV
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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 56.4 bits (137), Expect = 2e-10
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           + V  L  +   + LK+IF  YGT+    + +       + + +V FE+ +DA KA++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 270 NGKKFDDRE 278
           +G + D +E
Sbjct: 61  DGGQIDGQE 69

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 57.3 bits (138), Expect = 2e-10
 Identities = 25/62 (40%), Positives = 40/62 (64%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +F+ NLD + T+ DL++ F  +G IT   + R G G++  +GF+ FEN D A +A  A++
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 271 GK 272
           GK
Sbjct: 70  GK 71

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

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+VG+LD  VT+  LY+LF Q G +  V++ +D +  +   + +V + +      A+ +
Sbjct: 3   TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQL 61

Query: 91  LNFTPLNNKSIRI 103
           LN   L  + +RI
Sbjct: 62  LNGIRLFGRELRI 74

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 57.0 bits (137), Expect = 2e-10
 Identities = 26/69 (37%), Positives = 41/69 (59%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G GF    + E+    +   
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 373 NGKMIVSKP 381
           NGK I + P
Sbjct: 62  NGKYIKTPP 70

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

 Score = 56.4 bits (136), Expect = 3e-10
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQFENKESAQNAID 176
           G +FI  L    + ++L   FS +G I    +  D   Q S+GFGFV FEN + A++A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 177 KLNGMLINDKQVFVGH 192
            +NG  ++ +Q+ V  
Sbjct: 61  AMNGKSVDGRQIRVDQ 76

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

 Score = 56.7 bits (137), Expect = 3e-10
 Identities = 23/74 (31%), Positives = 44/74 (59%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++  L  S+  E+L++LF + G + S +++ + SG  KG  +V +     AS+A+ +M+
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 374 GKMIVSKPLYVAVA 387
           G  I  K + VA++
Sbjct: 65  GTEIKEKTISVAIS 78

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

 Score = 56.4 bits (136), Expect = 3e-10
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV+NL  S T EDL   F +   I  AVV+ D + G+S+ +GFV F   +DA +A+  L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 270 NGKKFDDR 277
             KK   R
Sbjct: 62  KNKKLHGR 69

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

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIA----TDGSGQSKGFGFVQFENKESAQNAI 175
           I+++NLD  +D   L   FS FG + S +I           + GF FV F++  SA+NA+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 176 DKLNGMLINDKQVFV 190
            +LNG  +  +++ 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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L++ +L   +D+  +   F+E G +TS K++R+  +G S G GFV F+T E A +AL  +
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 373 NGKMI 377
           NGK I
Sbjct: 62  NGKPI 66

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

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

 Score = 56.4 bits (137), Expect = 3e-10
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
           L ++ L     +E + +  S      I   +++RD  +G S+G  FV F + E+A++ + 
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 371 EMNGKM 376
            +N   
Sbjct: 65  ALNNLD 70

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

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 56.8 bits (138), Expect = 3e-10
 Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 314 LYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           LYI NL + I  ++LK     LFS+FG +      +      +G  FV F   E A+ AL
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLK--MRGQAFVVFKDVESATNAL 59

Query: 370 AEMNGKMIVSKPLYVAVA 387
             + G     KP+ +  A
Sbjct: 60  RALQGFPFYDKPMRIQYA 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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
            +G  LY+   G  + +E LK+ FS FG I +  + ++     K  GFV F   E A RA
Sbjct: 2   RKGNTLYVH--GYGLTEEILKKAFSPFGNIINISMEKE-----KNCGFVTFEKMESADRA 54

Query: 369 LAEMNGKMIVSKPLYVAVAQR 389
           +AE+NG  +    L V++A++
Sbjct: 55  IAELNGTTVQGVQLKVSLARK 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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 63.0 bits (153), Expect = 3e-10
 Identities = 64/322 (19%), Positives = 118/322 (36%), Gaps = 83/322 (25%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQV------------GQVLSVRVCRDLSTRRSLGYGYVNYA 79
           LYVG +     +  + D F+ +              V SV + ++ +      + ++ + 
Sbjct: 178 LYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKN------FAFLEFR 231

Query: 80  NPADAARALDVLNFTPLNNKSIRIMYSH--------------RDPSIRKSGTGN------ 119
              +A  A+  L+    +N  ++I   H              ++P               
Sbjct: 232 TVEEATFAM-ALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTT 290

Query: 120 -------IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESA 171
                  I+I NL   +    + +   SFG++ +  +  D  +G SKG+ F ++++    
Sbjct: 291 VLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVT 350

Query: 172 QNAIDKLNGMLINDKQVFV--GHFLRKQ----ERETVAIKTKF----------------- 208
             AI  LNG    D ++ V        Q        +A  T                   
Sbjct: 351 DVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTK 410

Query: 209 -----NNVFVKNL--DESTTD--EDLKKIFGEYGTITSAVVMRDGDGKSKCFG----FVN 255
                N V   +L  DE   +  ED+K  F +YG + + V+ R    ++   G    F+ 
Sbjct: 411 VVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLE 470

Query: 256 FENADDAAKAVEALNGKKFDDR 277
           + +   A KA+E +NG+KF+DR
Sbjct: 471 YADVRSAEKAMEGMNGRKFNDR 492

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 56.0 bits (136), Expect = 3e-10
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 328 LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA 387
           L +LFS FG +   K+++       G  FV FST E A +A+  +NG +   +PL V  +
Sbjct: 1   LYKLFSPFGNVEKIKLLKK----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 55.6 bits (135), Expect = 3e-10
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           L+  FS FGN+   K+      +  GF FV+F  +E+A+ A+  LNG+L   + + V
Sbjct: 1   LYKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

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

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  + +    + +HD F+ FG I +  +  D  +G  KG+  +++E K+ AQ AI+ L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 179 NGMLINDKQVFV 190
           NG  +  + + V
Sbjct: 69  NGKELLGQTISV 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 56.0 bits (136), Expect = 4e-10
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
          ++ V +L  +  +  L +LF   G +  V + +D  T +S G+ +V +    DA RA++ 
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 91 LN 92
          LN
Sbjct: 61 LN 62

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

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 27/68 (39%), Positives = 41/68 (60%), Gaps = 3/68 (4%)

Query: 324 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPL 382
            +E+L++ FS FG++   K++ D +G+SKG GFV F T E+A + LA   G +    K L
Sbjct: 15  TEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM--GNLNFRGKKL 72

Query: 383 YVAVAQRK 390
            +  A RK
Sbjct: 73  NIGPAIRK 80

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

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 22/67 (32%), Positives = 37/67 (55%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + + NL   +  + L + F   G +   KI  D SG+S+G   V FE +E A+ AI + N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 180 GMLINDK 186
           G+L++ +
Sbjct: 63  GVLLDGQ 69

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

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 120 IFIKNLDKS-IDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ NL+   +  + L + FS +G IL   +        KG+GFVQF+N+E A+ A+   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 179 NGMLIN 184
           NG  I 
Sbjct: 56  NGREIA 61

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

 Score = 56.3 bits (135), Expect = 4e-10
 Identities = 30/81 (37%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV NL     +  L ++FG +G +T+  V+RD    K K FGFV   N D+AA A+ +L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           NG +  DR   V     K+ +
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

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

 Score = 56.2 bits (135), Expect = 5e-10
 Identities = 31/84 (36%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
           G  ++I NLG   D+  L ++F  FG +T+ KV+RD  +   KG GFV  +  EEA+ A+
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 370 AEMNGKMIVSKPLYVAVAQRKEER 393
           A +NG  +  K L V+    K  +
Sbjct: 61  ASLNGYRLGDKILQVSFKTSKSHK 84

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

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

 Score = 55.3 bits (134), Expect = 6e-10
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI  L      ++L + FS +G ++ C I  D  +G+S+GFGFV F +  S    +   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 179 NGMLINDKQV 188
              +++ +++
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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 55.2 bits (134), Expect = 6e-10
 Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
           ++ NL   I++E+L++ F + G + + +++RD  +GI KG G+V F T +  + AL    
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62

Query: 374 GKM 376
            K+
Sbjct: 63  IKL 65

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 55.9 bits (135), Expect = 6e-10
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGT----ITSAVVMRDGDGKSKCFG--FVNFENADDAAK 264
           V++ NL  S+++EDL++   ++      I S  V      + +  G  +  F + + A K
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 265 AVEALNGKKFDDREWYV 281
            V+ LNGK F +R+ +V
Sbjct: 62  VVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|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 = 55.6 bits (134), Expect = 6e-10
 Identities = 26/72 (36%), Positives = 43/72 (59%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG++ +  T+ QL D+FS+VG V+S R+  D  T +  GYG+  Y +   A  A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 92  NFTPLNNKSIRI 103
           N   LN + +R+
Sbjct: 61  NGYELNGRQLRV 72

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

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 55.6 bits (134), Expect = 6e-10
 Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 209 NNVFVKNLDESTTD-EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
             + ++NL  S      LKKIFG YG +  A + R   GK   F FV  +   +A  A+E
Sbjct: 1   PKLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALE 60

Query: 268 ALNGKKFDDR----EWYVGK 283
             NG + D R    +W V K
Sbjct: 61  NTNGLEIDGRPVAVDWAVQK 80

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 55.9 bits (134), Expect = 6e-10
 Identities = 24/69 (34%), Positives = 42/69 (60%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           NLYI NL  S+D+++L+ +   FG + S +++RD +G+S+G GF    + E+    +   
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 373 NGKMIVSKP 381
           NGK + + P
Sbjct: 63  NGKYLKTPP 71

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|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 = 55.3 bits (134), Expect = 7e-10
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T++YVG+L   +T+ +L   FS  G +  VRV +D       GY +V +     AA A+ 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIV 54

Query: 90  VLNFTPLNNKSIR 102
            +N T +N ++++
Sbjct: 55  AVNGTSINGQTVK 67

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|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 = 55.3 bits (134), Expect = 7e-10
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            V+V NL    T+E+L++ F  +G I    V +D     K + FV F+  + AA A+ A+
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 270 NGKKFDDR 277
           NG   + +
Sbjct: 57  NGTSINGQ 64

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

 Score = 55.7 bits (135), Expect = 7e-10
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKS-IDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+  L K+  D   L   FS  G    C++A   +GQ +GF FV++   E A+ A   L
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 179 NGMLINDKQVFV 190
           NG  +    + V
Sbjct: 65  NGHSLQGSPIRV 76

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

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

 Score = 55.7 bits (135), Expect = 7e-10
 Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 225 LKKIFGE--YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD 275
           L+KIF +   G I    +  D  GK+K + FV F   ++A +AV+ALNG K D
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 55.4 bits (133), Expect = 7e-10
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+FI +L +      L  TF  FGN++S K+  D  +  SK FGFV ++N +SAQ AI  
Sbjct: 6   NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 178 LNGMLINDKQVFV 190
           +NG  I  K++ V
Sbjct: 66  MNGFQIGTKRLKV 78

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

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

 Score = 55.1 bits (133), Expect = 8e-10
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV NL     ++ + + FGEYG I+S  +      G+ K FG+V F + + A  A++AL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 270 NGKKFDDR 277
            G     R
Sbjct: 61  GGTDLLGR 68

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

 Score = 55.4 bits (134), Expect = 8e-10
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV  L    T E+L + F  +G I    +++  +  +  F F+ FE    AA+AVE+ N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESEN 64

Query: 271 GKKFDDREWYV 281
                ++  +V
Sbjct: 65  HSMLKNKTMHV 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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 55.0 bits (132), Expect = 8e-10
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NLD     + LK++F   GT+  A +  D DGKS+  G V FE   +A +A+   N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 271 GKKFDDREWYV 281
           G+   DR  +V
Sbjct: 63  GQFLFDRPMHV 73

This subgroup corresponds to the RRM2 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 = 76

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

 Score = 55.5 bits (133), Expect = 8e-10
 Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV NL   + +  L ++FG +G + +  V+RD    K K FGFV   N D+AA A+ +L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           NG +  DR   V     K+ +
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

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

>gnl|CDD|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 = 55.2 bits (133), Expect = 9e-10
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           L+I  L    +++ L+++FS++G I+   V++D  +  S+G GFV F  P++A  A+  M
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 373 NGKMIVSKPLYVAVAQR 389
           NGK +  + + V  A +
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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 54.9 bits (133), Expect = 9e-10
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           N+YI+ L  +  DE L++L   FG I S K + D  +   KG GFV F +PE A +A+  
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 372 MNGK 375
           +NG+
Sbjct: 62  LNGR 65

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

 Score = 55.0 bits (133), Expect = 9e-10
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            IF+ NL    D   L   FS FG + + K+  D  + + KG+GFV   N E A +AI  
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 178 LNGMLINDK--QV 188
           LNG  +  +  QV
Sbjct: 63  LNGYRLGGRVLQV 75

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

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

 Score = 54.7 bits (132), Expect = 1e-09
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N+ I  L +++  +     F + G + +CKI  D  +G S GFGFV +++ E AQ AI  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 178 LNGMLINDKQVFVGH 192
           LNG+ + +K++ V +
Sbjct: 62  LNGLQLQNKRIKVAY 76

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

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          T++Y+  L  N TD  L  L    G+++S +   D  T +  GYG+V++ +P  A +A++
Sbjct: 1  TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 90 VLN 92
           LN
Sbjct: 61 GLN 63

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

 Score = 55.1 bits (132), Expect = 1e-09
 Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  E+LK LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 66  LNGLRLQTKTIKVSYAR 82

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

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

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 21/73 (28%), Positives = 47/73 (64%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           +++YV +L F++T++ L+ +FS+ G+V+ V + +D  TR+S G  ++ + +  DA + + 
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 90  VLNFTPLNNKSIR 102
            LN   L  ++++
Sbjct: 62  ALNNKELFGRTLK 74

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|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 = 54.9 bits (132), Expect = 1e-09
 Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+F+ +L +   D +L ++F  +G + SA V  D    +SKCFGFV+F+N   A  A++A
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 269 LNG 271
           +NG
Sbjct: 66  MNG 68

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

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T L V +LDF V+D  + +LF++ G +    V  D S  RSLG   V +   ADA +A+ 
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSG-RSLGTADVVFERRADALKAMK 59

Query: 90  VLNFTPLNNKSIRI 103
             N  PL+ + ++I
Sbjct: 60  QYNGVPLDGRPMKI 73

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 26/67 (38%), Positives = 37/67 (55%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NLD   +D+D+K++F E+G +  A V  D  G+S     V FE   DA KA++  N
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYN 62

Query: 271 GKKFDDR 277
           G   D R
Sbjct: 63  GVPLDGR 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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 54.6 bits (131), Expect = 1e-09
 Identities = 27/63 (42%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 268
           N+F+ +L +  TD DL + F  +G + SA V  D     SKCFGFV+++N D A  A++A
Sbjct: 6   NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 269 LNG 271
           +NG
Sbjct: 66  MNG 68

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|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 = 54.8 bits (132), Expect = 1e-09
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 8/72 (11%)

Query: 211 VFVKNLDESTT-DEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV   D  TT +ED++K+F  +G +     +R      K F FV FE+++DA KA+EAL
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVR-CDIR------KTFAFVEFEDSEDATKALEAL 54

Query: 270 NGKKFDDREWYV 281
           +G + D     V
Sbjct: 55  HGSRIDGSVLTV 66

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|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 = 55.3 bits (134), Expect = 1e-09
 Identities = 24/59 (40%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 223 EDLKKIFGEYGTITSAVVMRDGDGKSKCFG----FVNFENADDAAKAVEALNGKKFDDR 277
           ED+K+  G+YG + S V+ R         G    FV F + +DA KA  AL G+KFD R
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGR 84

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 55.3 bits (134), Expect = 1e-09
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 16/74 (21%)

Query: 213 VKNLDESTTDEDLKKIF---------GEYGTITSAVVMRD-------GDGKSKCFGFVNF 256
           ++NL +S  ++ LK++F          +   I    +MRD       G GKSK +GFV F
Sbjct: 5   IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 257 ENADDAAKAVEALN 270
            N + A KA+ ALN
Sbjct: 65  TNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV N+DE T+ E+L+ +F  YG + S  VMR        F FV+      A +A+E LN
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-------FAFVHLRGEAAADRAIEELN 55

Query: 271 GKKFDDREWYV 281
           G++   R+  V
Sbjct: 56  GRELHGRKLVV 66

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 54.5 bits (132), Expect = 1e-09
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +++V  L   V +  LY+ FS+ G+V  VR+ RD ++RRS G  YV + +      AL  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG- 59

Query: 91  LNFTPLNNKSIRIM 104
           L    L  + I + 
Sbjct: 60  LTGQRLLGQPIMVQ 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 56.6 bits (136), Expect = 1e-09
 Identities = 28/93 (30%), Positives = 51/93 (54%)

Query: 26  QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAA 85
           + ++T L++G L +   D+ L D F+  G V+  +V  D  T RS G+G+VN+ +   A 
Sbjct: 31  RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAAT 90

Query: 86  RALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
            A+  ++   LN + IR+  ++  PS  ++  G
Sbjct: 91  AAISEMDGKELNGRHIRVNPANDRPSAPRAYGG 123

Length = 144

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

 Score = 54.6 bits (131), Expect = 1e-09
 Identities = 27/78 (34%), Positives = 49/78 (62%), Gaps = 3/78 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NLY+  L  ++  ++L++LFS++G I + +++RD  +G+S+G GF+ F    EA  A+  
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 372 MNGKMIV--SKPLYVAVA 387
           +NG+     S+P+ V  A
Sbjct: 62  LNGQKPEGASEPITVKFA 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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
           L+I  L     D+ LK  FS++G IT C VM+DP +  S+G GFV F++  E   A+ 
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMN 59

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

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 325 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMI 377
           DE L+ +FS FG I SC+V+RD  +G S    F+ F T E+   A  +M+  +I
Sbjct: 17  DEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLI 70

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

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITS----CKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +Y++NL   +D++ L+ +FS+FG + S     K       ++ G  FV F     A  AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 370 AEMNGKMIVSKPLYVA 385
            ++NG  +  + + V+
Sbjct: 63  -QLNGTELGGRKISVS 77

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

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 54.4 bits (131), Expect = 2e-09
 Identities = 26/68 (38%), Positives = 40/68 (58%)

Query: 323 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL 382
            ++  L++ FS++GT+   K++ D +G+SKG GFV F T E+A + L E N      K L
Sbjct: 14  TNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEANRLCFRDKKL 73

Query: 383 YVAVAQRK 390
            +  A RK
Sbjct: 74  NIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 54.3 bits (131), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 5/72 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA- 268
           +F+  L   TTD+ LK  F ++G IT  VVM+D + K S+ FGFV F +A +   A+ A 
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61

Query: 269 ---LNGKKFDDR 277
              ++G++ + +
Sbjct: 62  PHKVDGREVEPK 73

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

 Score = 54.4 bits (131), Expect = 2e-09
 Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           +YI +L     +++LK+ FS+FGT+ + +V R   +G SK  GF+ F  PE A+ A   M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 373 NGKMIVSKPLYVAV 386
           N  +++ K L 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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 5/71 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL + I +E+ KELFS++G ++   + ++     KG GF+   T   A +A AE++
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 374 GKMIVSKPLYV 384
           G M   + L V
Sbjct: 59  GIMRKGRQLRV 69

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

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ NL  ++  K L + FS FG + SC +  D  +G SKG+GFV F +++  +NA+ K 
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61

Query: 179 NGML 182
             +L
Sbjct: 62  KHIL 65

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

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 371
           NLY+ NL   + +++L+++F  +G I  C ++RD S G+ +G  FV +   EEA  A++ 
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 372 MNGKMI--VSKPLYVAVA 387
           +NG +    + PL V  A
Sbjct: 62  LNGTIPPGSTMPLSVRYA 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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 22/61 (36%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          LYV +LD ++ D +L + FS  G + S +V  D    RS G+G+V +++P +A +A+  +
Sbjct: 4  LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAVTEM 62

Query: 92 N 92
          N
Sbjct: 63 N 63

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

 Score = 59.1 bits (143), Expect = 3e-09
 Identities = 56/257 (21%), Positives = 97/257 (37%), Gaps = 24/257 (9%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG+L FN+T+ +L  +F   G +  V++ RD  T RS G+G++ + +  +A  AL+V+
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIAT 151
           N   L  + I++   +   S       N F     +    K L+            +   
Sbjct: 249 NGFELAGRPIKV--GYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDG 306

Query: 152 DGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV--------FVGHFLRKQERETVA 203
           DG     G G      ++  ++ I   N                 FV           + 
Sbjct: 307 DGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLV 366

Query: 204 IKTKFNNV------FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFE 257
           +   F+        F   + +   +E  K      G +   V  ++  GK     ++ F 
Sbjct: 367 LSNMFDPATEEEPNFDNEILDDVKEECSKY----GGVVHIYVDTKNSAGKI----YLKFS 418

Query: 258 NADDAAKAVEALNGKKF 274
           + D A  A +ALNG+ F
Sbjct: 419 SVDAALAAFQALNGRYF 435

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

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VGDL   VTD  L   FS+       +V RD  T +S GYG+V++++P D  +A+  +
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 92  NFTPLNNKSIRI 103
           N   + N+ I++
Sbjct: 69  NGKYVGNRPIKL 80

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

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

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 19/58 (32%), Positives = 36/58 (62%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          L++G L ++ T+  L + FS+ G+V+   + +D  T RS G+G+V +A+P+   + L 
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

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

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

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK----CFGFVNFENADDAAKA 265
            +++ NLD   T+  L K+F +YG I     +    G  K     + FV FE  ++A KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 266 VEALNGKKF 274
           +++LNGK  
Sbjct: 61  LKSLNGKTA 69

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

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++ NLD+++    L + FS  G I SCK+  +       + FV++ +  SA  A+  +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 180 GMLINDKQVFVG 191
           G LI  +++ V 
Sbjct: 59  GRLILGQEIKVN 70

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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 20/73 (27%), Positives = 40/73 (54%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+V +L F  T+ +L +LF   G++  V +  D  T+RS G+ +V++  P  A +A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 92  NFTPLNNKSIRIM 104
           + +    + + ++
Sbjct: 62  DGSIFQGRLLHVL 74

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

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L++ NL    D++ + E F E+G I+S ++  DP SG  KG G+V FS+ E A  AL  +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 373 NGKMIVSKPL 382
            G  ++ +P+
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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 53.6 bits (129), Expect = 3e-09
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           Q   L++  L     D  L+  F+ +G +T C VM DP +  S+G GF+ FS+ +EA  A
Sbjct: 1   QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 369 LAEM 372
           +   
Sbjct: 61  MEAQ 64

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 53.2 bits (128), Expect = 3e-09
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F+   +A RA  +++
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLH 61

Query: 374 GKMIVSKPLYVAVA 387
           G ++  + + V  A
Sbjct: 62  GTVVEGRKIEVNNA 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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 53.9 bits (129), Expect = 3e-09
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +F+ NL +   +  L ++FG +G +T+  V+RD    K K FGFV   N ++AA A+ +L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           NG +  D+   V     KS +
Sbjct: 64  NGYRLGDKILQVSFKTSKSHK 84

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

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

 Score = 55.8 bits (134), Expect = 3e-09
 Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 6/100 (6%)

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIAT 151
           N +   N  +  M      S+R   T  +FI  L    D  +L D F+ FG+++  K+  
Sbjct: 14  NISSNGNVPVTSMLG----SLRLMST-KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIV 68

Query: 152 D-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           D  +G+S+GFGFV F ++ +A  AI +++G  +N + + V
Sbjct: 69  DRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV 108

Length = 144

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

 Score = 53.7 bits (129), Expect = 3e-09
 Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQNAIDK 177
           N+++ NL + +    L   F ++GNI+ C +  D S G  +G  FV+++ +E AQ AI  
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 178 LNGML 182
           LNG +
Sbjct: 62  LNGTI 66

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

 Score = 53.9 bits (129), Expect = 3e-09
 Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV NL     +  L ++FG +G +T+  V+RD    K K FGFV   N D+AA A+ +L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 270 NGKKFDDR 277
           NG +  DR
Sbjct: 64  NGYRLGDR 71

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 53.7 bits (130), Expect = 3e-09
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 9/78 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-------SGISKGSGFVAFSTPEEAS 366
           LY+KNL   + +E L  +F  F  + S    ++         G  KG  FV F + E A+
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 367 RALAEMNGKMIVSKPLYV 384
           +AL  +NG ++  KP+ +
Sbjct: 62  KALNLVNGYVLKGKPMVI 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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 53.5 bits (128), Expect = 3e-09
 Identities = 27/73 (36%), Positives = 40/73 (54%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + VFV NLD     + LK++F   G +  A ++ D DGKS+  G V FE   +A +A+  
Sbjct: 1   STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISM 60

Query: 269 LNGKKFDDREWYV 281
            NG+   DR  +V
Sbjct: 61  FNGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 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. 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). . Length = 76

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V V  L E  + +DLK    + G +T A V RD +G     G V F + +D  +A+  L+
Sbjct: 3   VVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEG----EGVVEFTSQEDMERALRKLD 58

Query: 271 GKKFDDRE 278
           G +F  R 
Sbjct: 59  GTEFRGRR 66

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCR-----DLSTRRSLGYGYVNYANPADA 84
           T+L+V +L+F  T+  L   F + G V SV + +           S+GYG+V + +   A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 85  ARALDVLNFTPLNNKSIRIMYS 106
            +AL  L  T L+  ++ +  S
Sbjct: 61  QKALKRLQGTVLDGHALELKLS 82

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

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
            V NL    TDE  +++   +G +    ++     G+SK +GFV + +   A KA   L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 271 GKKFDDREWYV 281
           GK+   R+  V
Sbjct: 63  GKQIGGRKLQV 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|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 = 53.4 bits (129), Expect = 4e-09
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IFI  L   +    + +   SFG + +  +  D  +G SKG+ F ++ +      AI  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 179 NGMLINDKQVFV 190
           NGM + DK++ V
Sbjct: 63  NGMQLGDKKLTV 74

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

 Score = 53.2 bits (128), Expect = 4e-09
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV NL   TT+++L+  FG  G I    +M   D GK K F FV+FE  + A  A++  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK-- 58

Query: 270 NGKKFDDREWYVGKAQ 285
            GK  + R   V   +
Sbjct: 59  -GKHLNGRALRVEYGE 73

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

 Score = 53.2 bits (128), Expect = 4e-09
 Identities = 19/50 (38%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 323 IDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
             ++ LK+ FS FG +   +V +DP +G SKG GFV F+  E+  + L++
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

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

 Score = 53.1 bits (128), Expect = 4e-09
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           IF+ N+D     + L + F S G I    I  D  +GQ KGF +++F +K S +NA+  L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60

Query: 179 NGMLINDKQVFV 190
           N      +Q+ V
Sbjct: 61  NESEFRGRQIKV 72

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

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++++         A+ + FS +G +   K+          F FV+FE+ ESA  A D ++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVH 54

Query: 180 GMLINDKQVFV 190
           G ++N+  ++V
Sbjct: 55  GKVLNNNPLYV 65

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

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

 Score = 52.9 bits (128), Expect = 5e-09
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ NL   I+ + L   F   G++ + +I  D  +G  KGFG+V F+ K+S   A+ KL
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 179 NGMLINDKQVFV 190
           NG+ +  +++ V
Sbjct: 61  NGIKLKGRKIRV 72

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

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

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +Y+ ++   + ++ +K +F  FG I SC +  DP +G  KG GF+ +  P+ A  A+A M
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 373 NG 374
           N 
Sbjct: 63  NL 64

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

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

 Score = 53.0 bits (127), Expect = 5e-09
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 4/71 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFEN---ADDAAKAV 266
           +F+  L+  TTD+ L++ FG++G +T   VMRD   G+S+ FGF+ F+     ++  K  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 267 EALNGKKFDDR 277
             L+GK  D +
Sbjct: 61  HILDGKIIDPK 71

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

 Score = 52.8 bits (127), Expect = 5e-09
 Identities = 29/60 (48%), Positives = 36/60 (60%), Gaps = 5/60 (8%)

Query: 326 EKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALA----EMNGKMIVSK 380
           E L+E FS+FG I  C VMRDP+   S+G GFV FS P    + LA    E++GK I  K
Sbjct: 13  EGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKIDPK 72

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|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 = 52.7 bits (127), Expect = 5e-09
 Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  LD ++    L   F  FG I+  KI        KG GFVQF ++ +A+ AI +L 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP-----GKGCGFVQFVHRAAAEAAIQQLQ 58

Query: 180 GMLI 183
           G +I
Sbjct: 59  GTII 62

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

 Score = 58.7 bits (142), Expect = 6e-09
 Identities = 28/84 (33%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 25  NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
            +    +LYV +LD  VTD +L +LFS+ G++ S +V  D     S G+G+V ++NP +A
Sbjct: 281 MKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEA 339

Query: 85  ARALDVLNFTPLNNKSIRIMYSHR 108
            RA+  ++   L  K + +  + R
Sbjct: 340 NRAVTEMHGRMLGGKPLYVALAQR 363

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 52.9 bits (127), Expect = 6e-09
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  L K  +   +   F+ FG+I  C +  D +GQS+G  FV F +++ A NAI  ++
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 52.7 bits (126), Expect = 6e-09
 Identities = 25/71 (35%), Positives = 42/71 (59%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++ NL   +  +KLKE+FS  GT+    +  D  G S+G G V F  P EA +A++  N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 374 GKMIVSKPLYV 384
           G+ +  +P++V
Sbjct: 63  GQFLFDRPMHV 73

This subgroup corresponds to the RRM2 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 = 76

>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 = 52.6 bits (126), Expect = 6e-09
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 4/71 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 371
           ++I  L     D+ L+E F +FG +T C VMRD  +G S+G GF+ F  P+  +  + + 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 372 --MNGKMIVSK 380
             ++GK+I  K
Sbjct: 61  HILDGKIIDPK 71

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

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+      S    D+K++F   G +    ++       +   F+ FEN + A  A+E LN
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR---TVQPHAFITFENLEAAQLAIETLN 58

Query: 271 GKKFDDRE 278
           G   D   
Sbjct: 59  GASVDGNC 66

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

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 3/71 (4%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++      S     +   F + G +    + +      +   F+ FEN E+AQ AI+ LN
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR---TVQPHAFITFENLEAAQLAIETLN 58

Query: 180 GMLINDKQVFV 190
           G  ++   + V
Sbjct: 59  GASVDGNCIKV 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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N++V  L  +T   DLK++F +YG +  A +V       ++CFGFV   + ++AAK ++ 
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 269 LNGKKFDDREWYV 281
           L+  +   R   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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 52.7 bits (126), Expect = 6e-09
 Identities = 26/71 (36%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF++NL      K L D F+  G++L   I  + +G+SKG G V+FE+ E A+ A   +N
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMN 60

Query: 180 GMLINDKQVFV 190
           G  +N +++ V
Sbjct: 61  GYKLNGREIDV 71

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

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA- 268
           +FV  L  +TT++D+KK F ++G +  A++M D    + + FGFV FE+ D   K  E  
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 269 ---LNGKK 273
              +N K 
Sbjct: 62  FHEINNKM 69

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 52.8 bits (126), Expect = 7e-09
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV +   ++A RA+  
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + SK + V+ A+
Sbjct: 63  LNGLRLQSKTIKVSYAR 79

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

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

 Score = 52.8 bits (126), Expect = 7e-09
 Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T E+LK +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 269 LNGKKFDDREWYVGKAQ 285
           LNG +   +   V  A+
Sbjct: 66  LNGLRLQTKTIKVSYAR 82

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

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

 Score = 52.7 bits (127), Expect = 7e-09
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 4/79 (5%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI----ATDGSGQSKGFGFVQFENKESAQ 172
           T N+++ NL+  +  + L   F  FG + S KI      +   +++  GFV F N+  A+
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 173 NAIDKLNGMLINDKQVFVG 191
            A+D+L+G  +   ++ +G
Sbjct: 61  RALDELDGKDVMGYELKLG 79

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

 Score = 52.3 bits (126), Expect = 7e-09
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NLD + T++ L ++F + G I S  ++R+       + FV + +   AA A++ +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 271 GKKFDDREWYVGKA 284
           G+    +E  V  A
Sbjct: 59  GRLILGQEIKVNWA 72

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

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

 Score = 52.8 bits (126), Expect = 7e-09
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
           G  +++ NL    D+  L +LF  FG +T+ KV+RD  +   KG GFV  +  +EA+ A+
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 370 AEMNGKMIVSKPLYVAVAQRKEER 393
           A +NG  +  + L V+    K+ +
Sbjct: 61  ASLNGYRLGDRVLQVSFKTSKQHK 84

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

 Score = 52.6 bits (126), Expect = 7e-09
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 5/73 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID-- 176
           +F+  L      K L + FS FG ++ C I  D  +G+S+GFGFV F++  S +  +D  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 177 --KLNGMLINDKQ 187
             KL+G +I+ K+
Sbjct: 61  EHKLDGRVIDPKR 73

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

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

 Score = 52.7 bits (127), Expect = 8e-09
 Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 33  YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN 92
           +VG +  + T+ +L D FS+ G V  V++  D     S GYG+V +    DA + L + N
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMGN 64

Query: 93  FTPLNNKSIRIMYSHRDPSIRK 114
                 K + I      P+IRK
Sbjct: 65  L-NFRGKKLNI-----GPAIRK 80

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

 Score = 52.4 bits (125), Expect = 8e-09
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++  + L   F S G I SCK+  D  +GQS G+GFV + + + A+ AI+ 
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 178 LNGMLINDKQVFVGH 192
           LNG+ +  K + V +
Sbjct: 66  LNGLRLQTKTIKVSY 80

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

 Score = 52.0 bits (125), Expect = 8e-09
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY++       +  ++E+FS +G +   K++           FV F + E A RA   ++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVH 54

Query: 374 GKMIVSKPLYV 384
           GK++ + PLYV
Sbjct: 55  GKVLNNNPLYV 65

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

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

 Score = 52.3 bits (126), Expect = 9e-09
 Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N++V  L ++ T ++L+ +F  YG I ++ ++ D   G S+  GF+ F+   +A +A++A
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 269 LNGKK 273
           LNG  
Sbjct: 62  LNGTI 66

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

 Score = 52.4 bits (125), Expect = 9e-09
 Identities = 28/77 (36%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  E+ K LF   G I SCK++RD  +G S G GFV +  P +A +A+  
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 65  LNGLKLQTKTIKVSYAR 81

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

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

 Score = 52.3 bits (126), Expect = 9e-09
 Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
           N ++V ++    +++D+K +F  +G I S  +  D + GK K +GF+ +EN   A  A+ 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 268 ALNGKKFD 275
           ++N   FD
Sbjct: 61  SMNL--FD 66

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

 Score = 52.4 bits (125), Expect = 9e-09
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           ++F+ +L   I    +   F+ FG I   ++  D  +G+SKG+GFV F NK  A+NAI +
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 178 LNGMLINDKQV 188
           + G  +  +Q+
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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 22/71 (30%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++ NL  S+ +++L++LFS+ G IT  +++++  G SKG  +V F   E    AL  ++
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK-LD 60

Query: 374 GKMIVSKPLYV 384
            ++I  +P++V
Sbjct: 61  RELIKGRPMFV 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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 6/70 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL--- 369
           LY+  L + +D++ L   F  FG I   ++  D  +   +G  FV F  PE+A+ A+   
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 370 --AEMNGKMI 377
             +E+ G+ I
Sbjct: 61  NESELFGRTI 70

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

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQV-GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL- 88
           SL+VGDL  +V D QLY+ FS+        +V  D     S GYG+V +++ ++  RAL 
Sbjct: 3   SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALT 61

Query: 89  DVLNFTPLNNKSIRI 103
           ++   + L  K IR+
Sbjct: 62  EMQGASGLGGKPIRV 76

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL D+   E+L+ LF ++GT+T C V+++        GFV     E+A  A+  +N
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 374 GKMIVSKPLYV 384
           G   + K + V
Sbjct: 55  GYEFMGKRINV 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF+  L   +  + L++ FS  G IL   +    +  +  F F++FE +++A  A++  N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESEN 64

Query: 180 GMLINDKQVFV 190
             ++ +K + V
Sbjct: 65  HSMLKNKTMHV 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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 52.4 bits (125), Expect = 1e-08
 Identities = 24/65 (36%), Positives = 36/65 (55%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N++I NL  S+D + L +    FG ++S +I  D SG S+G GF + E+ E  +  I   
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 179 NGMLI 183
           NG  I
Sbjct: 62  NGKFI 66

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAV 266
            + +F+    +S T++DL++ F  +G I    V++D   K SK   +V F  A  AA+A+
Sbjct: 3   NSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 267 EALNGKKFDDRE 278
           E +NGK      
Sbjct: 62  EEMNGKCLGGDT 73

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

>gnl|CDD|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 = 52.1 bits (125), Expect = 1e-08
 Identities = 22/60 (36%), Positives = 36/60 (60%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
           FV  L +  T++D++++F  +GTI    ++R  DG SK   FV F +  +A  A+ AL+G
Sbjct: 5   FVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64

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 = 51.9 bits (125), Expect = 1e-08
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+  L + +  + L + FS +GN+ S +I TD  +G+ +GF FV F++ +     + + 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 179 NGMLINDKQVFV 190
               IN  +V V
Sbjct: 62  YHT-INGHRVEV 72

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

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 5/83 (6%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
           T +L +  LD   T+  +    S +    +  VR+ RD  T  S G+ +V + +  DA +
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 87  ALDVLNFTP---LNNKSIRIMYS 106
            +D LN      ++ + +R+ Y+
Sbjct: 62  WMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 225 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           L K+F  +G +    +++   G    F FV F   + A KAV+ LNG  F  R
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPG----FAFVEFSTEEAAEKAVQYLNGVLFGGR 49

(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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 46  LYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY 105
           LY LFS  G V  +++ +        G+ +V ++    A +A+  LN      + +R+ Y
Sbjct: 1   LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 106 S 106
           S
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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 22/65 (33%), Positives = 44/65 (67%), Gaps = 1/65 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N++V  L ++ T ++L+++F +YG I ++ ++RD   G S+  GF+ F+   +A +A++ 
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 269 LNGKK 273
           LNG+K
Sbjct: 62  LNGQK 66

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 24/71 (33%), Positives = 43/71 (60%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++ NL   +  +KLKE+FS  G +    ++ D  G S+G G V F  P EA +A++  N
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62

Query: 374 GKMIVSKPLYV 384
           G+++  +P++V
Sbjct: 63  GQLLFDRPMHV 73

This subgroup corresponds to the RRM2 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. 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). . Length = 76

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           ++V+NL    + E+L  +FG+YG I     +R G   +++   FV +E+  DA  A + L
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAI---RQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 270 NGKKFDDR 277
           +G    +R
Sbjct: 62  SGFNVANR 69

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

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 23/67 (34%), Positives = 39/67 (58%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL+    +E L ++F + G +T   + +D +GK K FGFV F++++    A+  LN
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 271 GKKFDDR 277
           G +   R
Sbjct: 64  GIRLYGR 70

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

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID-- 176
           +FI  L      K L +  S FG +L C I TD  +G+S+GFGFV F++  S    ++  
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 177 --KLNGMLINDKQ 187
             KL+G LI+ K+
Sbjct: 62  EHKLDGKLIDPKR 74

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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 22/64 (34%), Positives = 35/64 (54%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  L+K    K + + FS +G +    +  D   QS+G  FV++ +KE AQ AI  LN
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 180 GMLI 183
           G+  
Sbjct: 62  GVYT 65

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FVK L E TT+E LK+ F   G+I + +V     G SK FGFV+F + +DA  A EA+ 
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60

Query: 271 GKKFD 275
             + D
Sbjct: 61  DGEID 65

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

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 121 FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLN 179
           ++ +L   +    L++ FS  G +LS ++  D  + +S G+ +V F+N   A+ A+D LN
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 180 GMLINDK 186
             +I  K
Sbjct: 63  FDVIKGK 69

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

 Score = 56.5 bits (136), Expect = 2e-08
 Identities = 34/108 (31%), Positives = 57/108 (52%), Gaps = 9/108 (8%)

Query: 7   QHQAQMSGP-------NGVAAGASGNQFLTTS--LYVGDLDFNVTDSQLYDLFSQVGQVL 57
           QH AQ + P        G+AAGA           ++V +L  +  ++ L+ LF   G V 
Sbjct: 238 QHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQ 297

Query: 58  SVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY 105
           +V++ RDL+T +  GYG+V+  N  +AA A+  LN   L N+ +++ +
Sbjct: 298 NVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSF 345

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++ NL      + L D F  +G + S  +A        GF FV+FE+   A++A+  L+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR----NPPGFAFVEFEDPRDAEDAVRALD 57

Query: 180 GMLINDKQVFVGH 192
           G  I   +V V  
Sbjct: 58  GRRICGNRVRVEL 70

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

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 8/68 (11%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           GL+LY         +  L+E+FS +G I   +V+ D  +G S+G GFV F + E+A  A 
Sbjct: 6   GLSLYT-------TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAK 58

Query: 370 AEMNGKMI 377
             +NG  I
Sbjct: 59  ERLNGMEI 66

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

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

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSS-FGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ +L   +D   L++ FS  + +    K+  D +G S+G+GFV+F ++   + A+ ++
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 179 NG 180
            G
Sbjct: 64  QG 65

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

 Score = 51.7 bits (123), Expect = 2e-08
 Identities = 30/80 (37%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T E+ K +FG  G I S  ++RD   G+S  +GFVN+ + +DA KA+  
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 269 LNGKKFDDREWYVGKAQKKS 288
           LNG K   +   V  A+  S
Sbjct: 65  LNGLKLQTKTIKVSYARPSS 84

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

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L V +L ++VT+  L +LF +VG+V  V++  D  + RS G   V +    DA RA+   
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQF 61

Query: 92  NFTPLNNKSIRI 103
           N   L+ + +++
Sbjct: 62  NGVLLDGQPMQV 73

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

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

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 24/68 (35%), Positives = 38/68 (55%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NLD   T+E L ++F + G +    + +D +GK K F FV F++      A++ LN
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 271 GKKFDDRE 278
           G +   RE
Sbjct: 64  GIRLFGRE 71

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

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           +++  + +   +E + + F+EFG I +  +  D  +G  KG   + + T +EA  A+  +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 373 NGKMIVSKPLYV 384
           NGK ++ + + V
Sbjct: 69  NGKELLGQTISV 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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 30/76 (39%), Positives = 40/76 (52%), Gaps = 16/76 (21%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGT---------ITSCKVMRD-------PSGISKGSGFV 357
           L I+NL  S+D++KLKELF +  +         I   K+MRD         G SKG GFV
Sbjct: 3   LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFV 62

Query: 358 AFSTPEEASRALAEMN 373
            F+  E A +AL  +N
Sbjct: 63  EFTNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 51.1 bits (122), Expect = 2e-08
 Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+++  L K++  K L   FS +G I++ +I  D  +G S+G GF++F+ +  A+ AI  
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 178 LNG 180
           LNG
Sbjct: 62  LNG 64

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

>gnl|CDD|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 = 51.1 bits (123), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           ++I  L + + ++++KEL   FG + +  +++D  +G+SKG  F  +  P    +A+A +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 373 NGKMIVSKPLYVAVA 387
           NG  +  K 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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 51.9 bits (124), Expect = 2e-08
 Identities = 21/63 (33%), Positives = 39/63 (61%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+F+ NLD + ++ +L++ F +YG I   V+ R   G+   + F+ F+N D A +A  A+
Sbjct: 10  NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 270 NGK 272
           +G+
Sbjct: 70  SGR 72

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

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 7/68 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV N+  + T ++L+ +F E+G +     ++D       + FV+ E  ++A  A+EALN
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALN 55

Query: 271 GKKFDDRE 278
           GK+   R 
Sbjct: 56  GKEVKGRR 63

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

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

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 11/77 (14%)

Query: 120 IFIKNLDKSIDHKALHDTF-----SSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
           +F+ N+      + + D F        G +LS K   D  +G+ K FGF +FE+ E A  
Sbjct: 3   VFVGNI-----PEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALR 57

Query: 174 AIDKLNGMLINDKQVFV 190
           A+  LNG+ +  K++ V
Sbjct: 58  ALRLLNGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           VFV N+ E  +D+ ++K+  + G + S   V     GK K FGF  FE+ + A +A+  L
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 270 NGKKFDDREWYV 281
           NG +   ++  V
Sbjct: 63  NGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           +F++NL  + T+EDL+K+F +YG ++   +  D    K K F FV +   + A KA   L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 270 NGKKFDDR 277
           +G  F  R
Sbjct: 65  DGTVFQGR 72

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 50.9 bits (122), Expect = 3e-08
 Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRS---LGYGYVNYANPADAARAL 88
           L+V  L F+VT  +L  LF + G V SVR    L T RS    G  YV Y N + A++A+
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVR----LVTNRSGKPKGLAYVEYENESSASQAV 60

Query: 89  DVLNFTPLNNKSIRIMYS 106
             ++ T +  K+I +  S
Sbjct: 61  LKMDGTEIKEKTISVAIS 78

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

 Score = 51.3 bits (122), Expect = 3e-08
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

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

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

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSL---GYGYVNYANPADAARAL 88
           +YV +LDF + +  L  +FS+ G+V S+R+ +    ++     G+ +V + + + A  AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 89  DVLNFTPLNNKSIRI 103
             LN T L  + I +
Sbjct: 63  Q-LNGTELGGRKISV 76

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

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

 Score = 52.7 bits (126), Expect = 3e-08
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L   T D  L+  F  +G +  A V+ D + G+S+ FGFVNF +   A  A+  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 270 NGKKFDDREWYVGKAQKKS 288
           +GK+ + R   V  A  + 
Sbjct: 97  DGKELNGRHIRVNPANDRP 115

Length = 144

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 50.9 bits (122), Expect = 3e-08
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           NV++ N+D+S T+E L+  F +YG I S   +R    +  C  FVNF N  +A KA++ +
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLR----EKNC-AFVNFTNISNAIKAIDGV 59

Query: 270 NGKK 273
               
Sbjct: 60  KSHP 63

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 50.4 bits (120), Expect = 3e-08
 Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID-- 176
           +FI  L      K L D FS FG ++ C +  D  +G+S+GFGFV F+  ES    +D  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 177 --KLNGMLINDKQ 187
             KLNG +I+ K+
Sbjct: 61  EHKLNGKVIDPKR 73

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQNAIDKL 178
           +F++NL  +   + L + F +FG I    +  D    +SKGF FV F   E A  A  +L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 179 NGMLINDKQVFVGHFLR 195
                 D  +F G  L 
Sbjct: 62  ------DGSIFQGRLLH 72

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

 Score = 50.3 bits (121), Expect = 4e-08
 Identities = 23/63 (36%), Positives = 33/63 (52%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          T ++VG L ++ TD  L   FSQ G++    V  D  T +S GYG+V + +   A RA  
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 90 VLN 92
            N
Sbjct: 61 DPN 63

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

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

 Score = 50.5 bits (120), Expect = 4e-08
 Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
           G  +++ NL    D+  L ++F  FG +T+ KV+RD  +   KG GFV  +  +EA+ A+
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 370 AEMNGKMIVSKPLYVAVAQRKEER 393
           A +NG  +  + L V+    K  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

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

 Score = 50.5 bits (120), Expect = 4e-08
 Identities = 28/68 (41%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IFI NL +  D   L   F  FG + + K+  D  + + KGFGFV   N E A  AI  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 179 NGMLINDK 186
           NG  + DK
Sbjct: 64  NGYRLGDK 71

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|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 = 50.2 bits (120), Expect = 4e-08
 Identities = 23/74 (31%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ N+      + L D FS  G ++S ++  D  +G+ KG+GF +++++E+A +A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 179 NGMLINDKQVFVGH 192
           NG  +N +Q+ V +
Sbjct: 61  NGYELNGRQLRVDN 74

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

 Score = 52.3 bits (125), Expect = 4e-08
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEAS 366
           +     L+I  L    DD  L++ F+ FG +   KV+ D  +G S+G GFV F+    A+
Sbjct: 31  RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAAT 90

Query: 367 RALAEMNGKMIVSKPLYVAVAQRK 390
            A++EM+GK +  + + V  A  +
Sbjct: 91  AAISEMDGKELNGRHIRVNPANDR 114

Length = 144

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

 Score = 50.3 bits (120), Expect = 4e-08
 Identities = 24/71 (33%), Positives = 37/71 (52%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL   + +E L ELF + G +T   + +D  G  K  GFV F   E    A+A +N
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 374 GKMIVSKPLYV 384
           G  +  +P+ V
Sbjct: 64  GIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 50.2 bits (120), Expect = 4e-08
 Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG+LD  VT+  L  +F   G V +V++  D    + + YG+V Y    DA  AL  L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 92  NFTPLNNKSIRI 103
           N   + N  IR+
Sbjct: 60  NGRQIENNEIRV 71

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 50.6 bits (121), Expect = 4e-08
 Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP------SGISKGSGFVAFSTPEEASR 367
           L++KNL  S  ++ L + F         +V   P        +S G GFV F T E+A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 368 ALAEMNGKMIVSKPLYVAVAQR 389
           AL  M+G ++    L V  + R
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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 50.0 bits (120), Expect = 4e-08
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 124 NLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNG 180
            + KS+  + LH  F     +  C +  D  +G+SKGF +V + N  SA  A +KLNG
Sbjct: 6   VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 63

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

 Score = 50.0 bits (119), Expect = 5e-08
 Identities = 22/62 (35%), Positives = 34/62 (54%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NL+  +  + L++ F   G +    I  D  G+ K FGFV F++ ES   AI  LN
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 180 GM 181
           G+
Sbjct: 64  GI 65

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 50.4 bits (120), Expect = 5e-08
 Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           L+I  L     DE L+  F ++GT+T C VMRDP +  S+G GFV +S+ EE   A+
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +FV  L  + T+ DL+K F ++GT+T  VVM D + K  + FGF+ FE+ D   + 
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 266 V----EALNGKK 273
           V      +NGKK
Sbjct: 61  VNEHFHDINGKK 72

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + ++V N   S    D++ +F +YG I S         K++ F +V F + + AA AV  
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 269 LNGKKFDDREWYV 281
           LNGK  +  +  V
Sbjct: 61  LNGKLGEGYKLVV 73

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 50.2 bits (121), Expect = 5e-08
 Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGF-GFVQFENKESAQNAIDKLNG 180
           I NL   +    LH  FS +G +   KI      ++ G    VQF++ ESA+NA   LNG
Sbjct: 6   ISNLLYPVTVDVLHQVFSPYGAVE--KILI--FEKNTGVQALVQFDSVESAENAKKALNG 61

Query: 181 MLINDKQ 187
             I D  
Sbjct: 62  RNIYDGC 68

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 49.9 bits (120), Expect = 5e-08
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           VKNL   TT+E+L+++F ++G++   +++      S+    V F    DA KA ++L  K
Sbjct: 5   VKNLPFGTTEEELRELFEKFGSLG-RLLL----PPSRTIALVEFLEPSDARKAFKSLAYK 59

Query: 273 KFDDREWYVGKA 284
           +F     Y+  A
Sbjct: 60  RFKHVPLYLEWA 71

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 49.5 bits (119), Expect = 6e-08
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NL  +   + L   F  +G +  C +        K +GFV  E +E A++AI  LN
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV-------KNYGFVHMEEEEDAEDAIKALN 54

Query: 180 GMLINDKQVFV 190
           G     K++ V
Sbjct: 55  GYEFMGKRINV 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 50.0 bits (120), Expect = 6e-08
 Identities = 22/61 (36%), Positives = 34/61 (55%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NLD  +  + L++ F   G +   KI  D +G+ K F FV F+++ S   AI  LN
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 180 G 180
           G
Sbjct: 64  G 64

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 50.1 bits (120), Expect = 6e-08
 Identities = 19/48 (39%), Positives = 31/48 (64%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
          L++G L +  TD  L + FSQ G++    V +D +T+RS G+G+V +A
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFA 49

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

 Score = 50.1 bits (120), Expect = 6e-08
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
          L V  L +  T+  L D FS  G++L V+V +D  T +S G+G+V +A+  D  + L
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 49.7 bits (119), Expect = 6e-08
 Identities = 21/50 (42%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 219 STTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
           S T+EDL++ F E+G I    +++D   G+SK FG+V F     AA A+E
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 50.1 bits (119), Expect = 6e-08
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           ++F+ +L   I  + +   F+ FG I   ++  D  +G+SKG+GFV F NK  A+NAI  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 178 LNGMLINDKQV 188
           + G  +  +Q+
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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 49.7 bits (118), Expect = 7e-08
 Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 269 LNGKKFDDREWYVGKAQKKS 288
           LNG +   +   V  A+  S
Sbjct: 64  LNGLRLQTKTIKVSYARPSS 83

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

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

 Score = 49.9 bits (119), Expect = 7e-08
 Identities = 30/76 (39%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRA 368
           +G NL+I +L     D +L ++F  FG + S KV  D  +  SK  GFV+F  P  A  A
Sbjct: 3   EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

Query: 369 LAEMNGKMIVSKPLYV 384
           +  MNG  I  K L V
Sbjct: 63  IQAMNGFQIGMKRLKV 78

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

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 50.0 bits (119), Expect = 7e-08
 Identities = 24/65 (36%), Positives = 35/65 (53%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N++I NL  S+D + L      FG ++S +I  D SG S+G GF + E+ E  +  I   
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 179 NGMLI 183
           NG  I
Sbjct: 62  NGKYI 66

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

 Score = 49.6 bits (118), Expect = 7e-08
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +G NL+I +L     D  L + F  FG + S KV  D  + +SK  GFV++  P+ A  A
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

Query: 369 LAEMNGKMIVSKPLYV 384
           +  MNG  I +K L V
Sbjct: 63  IQAMNGFQIGTKRLKV 78

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

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

 Score = 49.5 bits (118), Expect = 7e-08
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF+ N+  +     L   F  FG ++ C          K + FV  E +E A  AI+ LN
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEALN 55

Query: 180 GMLINDKQVFV 190
           G  +  +++ V
Sbjct: 56  GKEVKGRRINV 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 54.6 bits (131), Expect = 8e-08
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  E+++ LF+  G I SCK++RD   G S G GFV +  PE+A +A+  
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 65  LNGLRLQNKTIKVSYAR 81

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

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

 Score = 54.6 bits (131), Expect = 8e-08
 Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           G  +++ NL    D+  L +LF  FG + + K++RD  +   KG GFV+ +  +EA+ A+
Sbjct: 269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI 328

Query: 370 AEMNGKMIVSKPLYVAVAQRKEER 393
             +NG  + ++ L V+    K  R
Sbjct: 329 LSLNGYTLGNRVLQVSFKTNKAYR 352

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

 Score = 49.7 bits (118), Expect = 8e-08
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++  +     F S G I SCK+  D  +GQS G+GFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 178 LNGMLINDKQVFVGH 192
           LNG+ +  K + V +
Sbjct: 64  LNGLRLQTKTIKVSY 78

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

 Score = 49.2 bits (118), Expect = 8e-08
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG+LD  VT+  L +LFSQ+G + S   C+ +    +  Y +V Y +   AA AL  +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKS---CKLIREHGNDPYAFVEYYDHRSAAAALQTM 57

Query: 92  NFTPLNNKSIRI 103
           N   +  + I++
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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 49.5 bits (119), Expect = 8e-08
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 3/69 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKC-FGFVNFENADDAAKAVEA 268
           ++V NL   TT+E + ++F   G I   ++M  D   K+ C F FV +   +DA  AV+ 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKR-IIMGLDRFTKTPCGFCFVEYYTREDAENAVKY 59

Query: 269 LNGKKFDDR 277
           LNG K DDR
Sbjct: 60  LNGTKLDDR 68

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

 Score = 49.5 bits (118), Expect = 8e-08
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N++V NL    T+++L+KIF  YG I    ++RD   G  +   FV ++  ++A  A+ +
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 269 LNGKKFDDR 277
           LNG      
Sbjct: 62  LNGTIPPGS 70

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

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 49.5 bits (119), Expect = 8e-08
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYV +L F ++  +LYDLF + G +  +R+     TR   G  +V Y +  DA  A D L
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETR---GTAFVVYEDIYDAKNACDHL 61

Query: 92  NFTPLNNKSIRIMY 105
           +   + N+ + ++Y
Sbjct: 62  SGFNVANRYLVVLY 75

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

 Score = 49.7 bits (119), Expect = 8e-08
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 9/76 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSC-----KVMRDPSGISKGSGFVAFSTPEEASRA 368
           L+I+NL  +  +E L++LFS++G ++       K+ + P    KG  FV +  PE A +A
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP----KGFAFVTYMIPEHAVKA 60

Query: 369 LAEMNGKMIVSKPLYV 384
            AE++G +   + L++
Sbjct: 61  FAELDGTVFQGRLLHL 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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 49.7 bits (118), Expect = 8e-08
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L+I  +    ++  ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

Query: 374 GKMIV---SKPLYVAVA 387
               +   S P+ V  A
Sbjct: 64  QAQTMEGCSSPIVVKFA 80

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 49.9 bits (120), Expect = 8e-08
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +++  L    T+ D+  +F +YG I    ++RD   GKSK F F+ +E+      AV+ L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 270 NGKKFDDR 277
           NG K   R
Sbjct: 72  NGIKLLGR 79

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

 Score = 49.7 bits (119), Expect = 8e-08
 Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           TSLYV ++        L  LF + G ++ V +  D  TRR  G+ YV + +  DA  AL 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKS 115
            L+ T    + I I ++  D   RK+
Sbjct: 61  YLDRTRFLGREIEIQFAQGD---RKT 83

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

 Score = 49.4 bits (118), Expect = 9e-08
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 7/77 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +F++NL  S+  + L D FS    I    + TD  +G+S+G+GFV F   E AQ A+ KL
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 179 NGMLINDKQVFVGHFLR 195
               ++      G  LR
Sbjct: 62  KNKKLH------GRILR 72

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

 Score = 49.5 bits (119), Expect = 9e-08
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGN--ILSCKIATDG-SGQSKGFGFVQFENKESAQNAID 176
           + ++ LD     + +    S+  +  I   ++  D  +G S+GF FV+F + E A   +D
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 177 KLNGML---INDKQVFV 190
            LN +    I+ + V V
Sbjct: 65  ALNNLDPFVIDGRVVRV 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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 49.4 bits (119), Expect = 9e-08
 Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 45  QLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM 104
            LY LFSQ G VL +   + L  R   G  +V + +   A  AL  L   P  +K +RI 
Sbjct: 19  SLYALFSQFGPVLDIVASKTLKMR---GQAFVVFKDVESATNALRALQGFPFYDKPMRIQ 75

Query: 105 YSH 107
           Y+ 
Sbjct: 76  YAK 78

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 49.9 bits (120), Expect = 9e-08
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           I+I  L   +    +   FS +G I+   +  D  +G+SKGF F+ +E++ S   A+D L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 179 NGMLINDKQVFVGH 192
           NG+ +  + + V H
Sbjct: 72  NGIKLLGRTIRVDH 85

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

 Score = 49.7 bits (119), Expect = 9e-08
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIAT-DGSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+ NL   I    L + F  FGN+L  +I +  G G+   FGFV F++ E+ Q  +   
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 179 NGMLINDKQVFV 190
                 D ++ V
Sbjct: 66  PIYFRGDHRLNV 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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 49.6 bits (119), Expect = 9e-08
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           I++ NLD +     L + FS  G +   ++A D   Q   + FV+F  + S  NA+ KLN
Sbjct: 7   IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE-TQPTRYAFVEFAEQTSVINAL-KLN 64

Query: 180 GMLINDKQVFVGH 192
           G +   + + V H
Sbjct: 65  GAMFGGRPLKVNH 77

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>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 = 49.1 bits (118), Expect = 9e-08
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +YI +L     + +L++ FS+FGT+T  ++ R   +G SKG  FV F +PE A      M
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 373 NGKMIVSKPL 382
           N  ++  + L
Sbjct: 62  NNYLLFERLL 71

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 15/85 (17%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR---------RSLGYGYVNYANPA 82
           L++G+LD  +T+  L  LFS+ G++      +              +  GY +V +    
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKI------KKFDFLFHKSGPLKGQPRGYCFVTFETKE 55

Query: 83  DAARALDVLNFTPLNNKSIRIMYSH 107
           +A +AL  LN      K + + ++H
Sbjct: 56  EAEKALKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGE-YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV +L     D  L + F + Y +   A V+ D +G S+ +GFV F +  +  +A+  +
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 270 NG 271
            G
Sbjct: 64  QG 65

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

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++  +     F S G I SCK+  D  +GQS G+GFV + +   A  AI+ 
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 178 LNGMLINDKQVFVGH 192
           LNG+ +  K + V +
Sbjct: 65  LNGLKLQTKTIKVSY 79

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 18/66 (27%), Positives = 33/66 (50%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+++ NL     ++DL+ +   YG + S  ++RD  G+S+  GF   E+ +     +   
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 270 NGKKFD 275
           NGK   
Sbjct: 62  NGKYLK 67

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 26/63 (41%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+++NL  S  ++ L++LFS+FG ++   V  D  SG SKG  +V F  PE+A +A  E+
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 373 NGK 375
           +GK
Sbjct: 65  DGK 67

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 49.2 bits (117), Expect = 1e-07
 Identities = 26/71 (36%), Positives = 35/71 (49%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF+ NLD  +  K L + FS  G +    I  D  G+S+G G V FE    A  AI   N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 180 GMLINDKQVFV 190
           G  + D+ + V
Sbjct: 63  GQFLFDRPMHV 73

This subgroup corresponds to the RRM2 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 = 76

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

 Score = 49.4 bits (118), Expect = 1e-07
 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA-- 268
           F+  L   TT E L++ F ++G I   +VMRD   K S+ FGFV F +     K +    
Sbjct: 2   FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61

Query: 269 --LNGKKFD 275
             L+GKK D
Sbjct: 62  HELDGKKID 70

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|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 = 48.8 bits (117), Expect = 1e-07
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 5/61 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VFV  LD + T+++L+ +FG +G I   V +  G    K  GFV F +   A  A++ L 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVY-VKIPPG----KGCGFVQFVHRAAAEAAIQQLQ 58

Query: 271 G 271
           G
Sbjct: 59  G 59

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

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           +VFV +L    T +D+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 269 LNGKKFDDRE 278
           + G+    R+
Sbjct: 63  MGGQWLGGRQ 72

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

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 24/77 (31%), Positives = 43/77 (55%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VGDL   +T   +   F+  G++   RV +D++T +S GYG+V++ N  DA  A+  +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 92  NFTPLNNKSIRIMYSHR 108
               L  + IR  ++ R
Sbjct: 64  GGQWLGGRQIRTNWATR 80

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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++++NL   I  + L+D F  +G I   +I      +++G  FV +E+   A+NA D L+
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTK--ETRGTAFVVYEDIYDAKNACDHLS 62

Query: 180 GMLINDKQVFVGHF 193
           G  + ++ + V ++
Sbjct: 63  GFNVANRYLVVLYY 76

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV + + ++   A
Sbjct: 1   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

Query: 266 VEA 268
           + A
Sbjct: 61  MNA 63

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 28/70 (40%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A+  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 269 LNGKKFDDRE 278
           + G+    R+
Sbjct: 63  MGGQWLGGRQ 72

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

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 24/77 (31%), Positives = 43/77 (55%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VGDL   +T   +   F+  G++   RV +D++T +S GYG+V++ N  DA  A+  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 92  NFTPLNNKSIRIMYSHR 108
               L  + IR  ++ R
Sbjct: 64  GGQWLGGRQIRTNWATR 80

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

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           ++V+N+ ++T  +DL+++FG+YG I    +  D    + + F +V FE+  DA  A+  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 270 NGKKFDDREWYVGKAQ 285
           +  +F  RE  +  AQ
Sbjct: 63  DRTRFLGREIEIQFAQ 78

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           L+I  L     D+ L+E F ++GT+T C VMRDP +  S+G GFV +S  EE   A++  
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64

Query: 371 --EMNGKMIVSK 380
             +++G+++  K
Sbjct: 65  PHKVDGRVVEPK 76

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

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           V+V+ L ++ T E LK +F +YGT+    + R    G  K F F+ FE  ++A KA + L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 270 NGKKFDDREW 279
           N       + 
Sbjct: 62  NNPPETATDK 71

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|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 20/58 (34%), Positives = 30/58 (51%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +KNL   + ++ L   FS FG +    +  D  G+S G G V+F  K  AQ AI + +
Sbjct: 4   VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCS 61

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|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 = 48.8 bits (117), Expect = 1e-07
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + ++N+      K L + FS FG + S ++     G  +GF FV+F  K+ AQNA++ L 
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62

Query: 180 G 180
            
Sbjct: 63  S 63

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 25/67 (37%), Positives = 37/67 (55%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NLD   T+E + ++F + G +    + +D DGK K F FVNF++      A+  LN
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 271 GKKFDDR 277
           G K   R
Sbjct: 64  GIKLYGR 70

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

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 24/68 (35%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQ-VLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          SL++GDL+  + ++ +   F+ +G+ VLSV++ R+  T    GY +V +A+ A A R L 
Sbjct: 1  SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 90 VLNFTPLN 97
           LN  P+ 
Sbjct: 61 KLNGKPIP 68

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

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTF-SSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
            + + NL K +    + + F S  G I    ++ +  G+S G   + F+    A  A DK
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 178 LNGMLINDK 186
            NG + +  
Sbjct: 61  FNGRIDDGN 69

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

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 48.9 bits (116), Expect = 2e-07
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T ++L+ +F   G + SA ++RD   G S  +GFVN+ NA DA +A+  
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 269 LNGKKFDDREWYVGKAQ 285
           LNG +   +   V  A+
Sbjct: 63  LNGLRLQSKTIKVSYAR 79

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

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 20/75 (26%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSS-FGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           IF+ +L   +    L +TF + + ++   K+  D  +G+SKG+GFV+F +++    A+ +
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 178 LNGMLINDKQVFVGH 192
           +NG+  + + + V  
Sbjct: 64  MNGVYCSSRPMRVSP 78

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

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
           L L++  L     +E L+E+FS +G I   +++RD  +G SKG  FV +    +A RA  
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 371 EMNGKMIVSKPLYV 384
           + +  +I    ++V
Sbjct: 64  DAHKLVIDGSEIFV 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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 125 LDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLI 183
           L+  +D   ++  F+  G + S KI  +  +G+S G+GFV+F   E+A+ A+  LNG  I
Sbjct: 7   LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPI 66

Query: 184 -NDKQVF 189
            N +Q F
Sbjct: 67  PNTQQRF 73

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

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 34/72 (47%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++ NL  +I +E+L+  F  +G +    + R P G      FV F   + A RA   M
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 373 NGKMIVSKPLYV 384
           +G+ I    + +
Sbjct: 64  SGQYIGRNQIKI 75

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

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

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
           TG +F++NL  S     L   FS FG +    +A D  SG+SKGF +V F + E A  A 
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61

Query: 176 DKLNGMLINDKQVFVGHFL 194
            +L      D +VF G  +
Sbjct: 62  KEL------DGKVFQGRLI 74

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 18/60 (30%), Positives = 35/60 (58%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV  L +   + D++ +F  +G+I    V+RD +G+S+   FV F +   A  A++A++
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+  L+       L   F  +G I   ++  D  +G+ +G+ F++FE++   + A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 179 NGMLINDKQVFV 190
           +G  I+ ++V V
Sbjct: 64  DGKKIDGRRVLV 75

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

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + + N+        L   F  FG IL  +I  +  G SKGFGFV F N   A  A +KL+
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLH 61

Query: 180 GMLINDKQVFVGHF 193
           G ++  +++ V + 
Sbjct: 62  GTVVEGRKIEVNNA 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|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 = 48.3 bits (115), Expect = 2e-07
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           VFV N+    T+E LK IF E G + S  ++ D + GK K +GF  +++ + A  A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 270 NGKKFDDREWYVGKA 284
           NG + + R+  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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 120 IFIKNLDKSI-DHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           + I+NL  SI     L   F  +G +    I     G+  GF FV  + +++A+ A++  
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 179 NGMLINDKQVFVGHFLRKQ 197
           NG+ I+ + V V   ++K 
Sbjct: 63  NGLEIDGRPVAVDWAVQKN 81

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 48.9 bits (116), Expect = 2e-07
 Identities = 22/62 (35%), Positives = 36/62 (58%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N++I NL  S+D + L +    FG+++S +I  D +G S+G GF + E+ E  +  I   
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 179 NG 180
           NG
Sbjct: 63  NG 64

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

 Score = 48.9 bits (116), Expect = 2e-07
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
           G  +++ NL    D+  L +LF  FG + + KV+RD  +   KG GFV  +  +EA+ A+
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 370 AEMNGKMIVSKPLYVAVAQRKEER 393
           A +NG  +  + L V+    K  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

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

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +F+  L   +  + L++ FS  G +   +I  D  S +SKG  +V+F ++ES   A+  L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60

Query: 179 NGMLIN 184
            G  + 
Sbjct: 61  TGQRLL 66

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

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIA-TDGSGQSKGFGFVQFENKESAQNAIDKL 178
           I+I +L      K L   FS FG + + ++A +  +G SK +GF+QF N E A  A   +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 179 NGMLINDK 186
           N  L+  K
Sbjct: 62  NNYLLMGK 69

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

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIAT-DGSGQSKGFGFVQFENKESAQNAI 175
           +F+ NL        L   F   G I   ++ T + SG+ KGF FV FE  E A NA+
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP 81
          +++G L++  TD  L + F Q G+V    V RD +T RS G+G++ +  P
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKP 50

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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++  L     +++++E+FS +G +    +MRD    S+G  FV +S+ E A  A+  +N
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 374 GKMIV---SKPLYVAVA 387
           G   +    +PL V  A
Sbjct: 62  GVYTMRGCDQPLIVRFA 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 372
           +++ N+ + + D+ +++L  + G + S K ++DPS G  K  GF  F  PE A RAL  +
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 373 NGKMIVSKPLYVAVAQR 389
           NG  +  K L V V  +
Sbjct: 63  NGLELGGKKLLVKVDAK 79

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 20/71 (28%), Positives = 35/71 (49%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +Y+G L     + +L   FSQ G V  +R+ R   T +S GY +V + +P  A    + +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 92  NFTPLNNKSIR 102
           N   L  + ++
Sbjct: 62  NNYLLFERLLK 72

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

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEM 372
           +Y++ L  +   E LK +FS++GT+    + R       KG  F+ F TPEEA +A   +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 373 N 373
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|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 = 48.4 bits (116), Expect = 2e-07
 Identities = 18/63 (28%), Positives = 33/63 (52%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + V+N+    T ++L+++F  +G + S  + +  DG  + F FV F    +A  A+EA
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 269 LNG 271
           L  
Sbjct: 61  LKS 63

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

 Score = 48.8 bits (116), Expect = 2e-07
 Identities = 24/59 (40%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 220 TTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           TT+ DL+++F  YG +    V+ D   G+S+ F FV FE  DD+ +A+E  NG + D R
Sbjct: 11  TTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGR 69

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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 48.5 bits (115), Expect = 2e-07
 Identities = 25/71 (35%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF++NL   +  + L + FS  G+++  +I  + +G+SKG G V+F++ ESA+ A   +N
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 180 GMLINDKQVFV 190
           G+ IN +++ V
Sbjct: 61  GIKINGREIDV 71

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 48.9 bits (116), Expect = 2e-07
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R
Sbjct: 21  TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 79

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 48.9 bits (116), Expect = 2e-07
 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID 176
            N+FI +L +    + L   F  FGN++S K+  D  +  SK FGFV ++N  SAQ AI 
Sbjct: 8   ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 67

Query: 177 KLNGMLINDKQVFV 190
            +NG  I  K++ V
Sbjct: 68  AMNGFQIGMKRLKV 81

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

 Score = 49.2 bits (117), Expect = 2e-07
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRAL 369
              L+++NL     +E L   FS+FG++     + D S G +KG+GFV F      +  L
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 370 A 370
            
Sbjct: 61  K 61

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|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 53.7 bits (129), Expect = 2e-07
 Identities = 51/298 (17%), Positives = 92/298 (30%), Gaps = 43/298 (14%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE--A 268
           V V+NL +   + DL +    +G ++  +++       K    V FE+ + A   V    
Sbjct: 5   VHVRNLPQDVVEADLVEALIPFGPVSYVMML-----PGKRQALVEFEDEESAKACVNFAT 59

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQ--FEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
                   +  +       + +E +  G   F+ A    V     L + ++N    I  +
Sbjct: 60  SVPIYIRGQPAFF---NYSTSQEIKRDGNSDFDSAGPNKV-----LRVIVENPMYPITLD 111

Query: 327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-------- 378
            L ++F+ +G +         +        V F +   A  A A +NG  I         
Sbjct: 112 VLYQIFNPYGKVLRIVTFTKNNVF---QALVEFESVNSAQHAKAALNGADIYNGCCTLKI 168

Query: 379 --SKPLYVAVAQRKEERRARLQAQFSQMRPVAMGP----SVPPRMPMYPPGPSGLGQQFL 432
             +KP  + V    ++ R          R   +        P  +  +P      G    
Sbjct: 169 EYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSH 228

Query: 433 YGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPV 490
            G   P     + G        P   P     P +    ++       P G  G G V
Sbjct: 229 GGPLAPLAGGDRMG--------PPHGPPSRYRPAYEAAPLAPAISSYGPAG-GGPGSV 277

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). Length = 481

>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 = 47.6 bits (114), Expect = 3e-07
 Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN--PADAARAL 88
          +++V +LD++V + +L  LFS+ G++  VR+ ++    +S GY YV + N      A  L
Sbjct: 1  TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEALKL 59

Query: 89 D 89
          D
Sbjct: 60 D 60

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

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 21/76 (27%), Positives = 36/76 (47%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
           T  +F+ NL+ +I  + L   F  +G +    I     GQ   + FV+F N + A  A  
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 177 KLNGMLINDKQVFVGH 192
            ++G  I   Q+ +G+
Sbjct: 62  AMSGQYIGRNQIKIGY 77

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

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          L+VG L  NV    L ++FS  G V  V +  D       GY YV + +P DA +A+  +
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 92 N 92
          +
Sbjct: 61 D 61

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

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

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 21/71 (29%), Positives = 35/71 (49%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL   + +E L ELF + G +   K+ +DP+G  K   FV F        A+  +N
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 374 GKMIVSKPLYV 384
           G  +  + L +
Sbjct: 64  GIRLFGRELRI 74

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 8/70 (11%)

Query: 314 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           +++ NL  D +  E L+E+FS++G I    +        KG GFV F   E+A  A+A  
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 373 NGKMIVSKPL 382
           NG+ I  + L
Sbjct: 56  NGREIAGQKL 65

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

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 26/71 (36%), Positives = 37/71 (52%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NLD  +  K L + FS  G ++   I  D  G+S+G G V FE    A  AI   N
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62

Query: 180 GMLINDKQVFV 190
           G L+ D+ + V
Sbjct: 63  GQLLFDRPMHV 73

This subgroup corresponds to the RRM2 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. 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). . Length = 76

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

 Score = 48.5 bits (115), Expect = 3e-07
 Identities = 30/87 (34%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +G NL+I +L     D+ L ++F  FG + S KV  D  + +SK  GFV++  P  A  A
Sbjct: 6   EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRA 395
           +  MNG  I  K L V + + K + + 
Sbjct: 66  IQAMNGFQIGMKRLKVQLKRSKNDSKP 92

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

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 22/65 (33%), Positives = 40/65 (61%), Gaps = 7/65 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV+NL  + T+E L+K FG++G +     ++D       + F++F+  D A KA+E +N
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 271 GKKFD 275
           GK+ +
Sbjct: 57  GKELE 61

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|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 53.6 bits (129), Expect = 3e-07
 Identities = 25/121 (20%), Positives = 32/121 (26%), Gaps = 10/121 (8%)

Query: 394 RARLQAQFSQMRPVAM--GPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQ 451
           + R QA      P  +      P +      GP        Y Q P           +  
Sbjct: 164 QQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPG--YPQPPQGHPEQVQPQQFLP 221

Query: 452 QLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMP----HQMPPR 507
              P   PA  P+P          QQ Q PG  +   P           P     Q PP+
Sbjct: 222 A--PSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQ 279

Query: 508 G 508
            
Sbjct: 280 N 280

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 176
           +F+  L      K L D F+ FG +  C I  D  +G+S+GFGF+ F++  S +  ++  
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 177 --KLNGMLINDKQ 187
             +L+G LI+ K+
Sbjct: 62  EHRLDGRLIDPKK 74

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 47.8 bits (113), Expect = 3e-07
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID 176
            N+++  L K++  K L   FS +G I++ +I  D  +G S+G GF++F+ +  A+ AI 
Sbjct: 3   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62

Query: 177 KLNG 180
            LNG
Sbjct: 63  GLNG 66

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 47.9 bits (115), Expect = 3e-07
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++  +   + +++L  LF + G I   ++M D SG+++G  FV ++  E A RA+ +++
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 374 GKMI-VSKPLYV 384
              I   K L V
Sbjct: 64  NYEIRPGKRLGV 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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 47.8 bits (113), Expect = 3e-07
 Identities = 20/57 (35%), Positives = 35/57 (61%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
          +++G L +  +   L D FS+ G++    V RD +T+RS G+G+V +A+PA   + L
Sbjct: 2  MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58

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

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 22/59 (37%), Positives = 34/59 (57%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          +L+VG L    T+  L ++FS+ G +  +R+ RD+ T  S GY +V Y +  DA RA  
Sbjct: 5  TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+V ++ F   D  L  +F Q G +L V +    + R S G+G+V +AN ADA RA + L
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEII--FNERGSKGFGFVTFANSADADRAREKL 60

Query: 92  NFTPLNNKSIRIMYS 106
           + T +  + I +  +
Sbjct: 61  HGTVVEGRKIEVNNA 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  L   +  +   + FS FG ++  ++  D  +G+S+GFGFV F+++ + +      
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFS-- 59

Query: 179 NGML-INDKQVFV 190
            GML +  KQV V
Sbjct: 60  AGMLELGGKQVEV 72

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

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV  + E   +ED+   F E+G I +  +  D   G  K +  + +E   +A  A+E L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 270 NGKKF 274
           NGK+ 
Sbjct: 69  NGKEL 73

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

 Score = 47.8 bits (113), Expect = 4e-07
 Identities = 28/73 (38%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 116 GTG-NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
           GTG  IF+ NL    D   L   F  FG + + K+  D  + + KGFGFV   N + A  
Sbjct: 1   GTGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60

Query: 174 AIDKLNGMLINDK 186
           AI  LNG  + D+
Sbjct: 61  AIASLNGYRLGDR 73

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

 Score = 47.9 bits (114), Expect = 4e-07
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +++ +L     +++LKK F ++GT+ +  V R    G SK +GF+ F N + AA A +++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 270 NG 271
           N 
Sbjct: 62  NN 63

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

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL    T+E+ K++F +YG ++   + ++     K FGF+  +   +A KA   L+
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 271 GKKFDDRE 278
           G     R+
Sbjct: 59  GIMRKGRQ 66

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

 Score = 47.6 bits (113), Expect = 4e-07
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK- 177
           +FI  L+      +L + F  FG +  C +  D  +G+S+GFGF+ F+  +S    + K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 178 --LNGMLINDKQ 187
             L+G +I+ K+
Sbjct: 61  HILDGKIIDPKR 72

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|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 = 47.3 bits (113), Expect = 4e-07
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 16/79 (20%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRV-----CRDLSTRRSLGYGYVNYANPADA 84
           T+++VG LD  VT+ +L  LF   G+++ V++     C           G+V + + A A
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGC-----------GFVQFVHRAAA 50

Query: 85  ARALDVLNFTPLNNKSIRI 103
             A+  L  T +    IR+
Sbjct: 51  EAAIQQLQGTIIGGSRIRL 69

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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 21/66 (31%), Positives = 34/66 (51%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++ N   S D   + D F  +G ILS +  +    +++ F +VQF + ESA  A+  LN
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLN 62

Query: 180 GMLIND 185
           G L   
Sbjct: 63  GKLGEG 68

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           ++I +L        L   FS FG +   +++    +G+SKG+ FV+FE+ E A+   + +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 179 NGMLINDK 186
           N  L+ ++
Sbjct: 62  NNYLLFER 69

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

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 25/71 (35%), Positives = 45/71 (63%), Gaps = 5/71 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NLY+  L  ++  +++++LFS++G I + +++ D  +GIS+G GF+ F    EA  A+  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 372 MNGKMIVSKPL 382
           +NG+    KPL
Sbjct: 63  LNGQ----KPL 69

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

 Score = 47.6 bits (113), Expect = 4e-07
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 10/84 (11%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV--- 266
           +FV  L     + DL + F ++G +  A V+ D   GK + FGFV F+N D A KA    
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 267 -EALNGKKFDDREWYVGKAQKKSE 289
              +NG + +     V KA  K E
Sbjct: 62  FHPINGHRVE-----VKKAVPKEE 80

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

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N++I  L +++  K + D FS FG I++ ++  D  +G S+G  F++F+ +  A+ AI  
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 178 LNG 180
            NG
Sbjct: 62  FNG 64

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

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+VG+L ++     L + F + G+V+ VR+ +D    RS G+G+V +A    A +AL+ 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKALE- 58

Query: 91  LNFTPLNNKSIRI 103
            +   L  + IR+
Sbjct: 59  KSGEELLGREIRV 71

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|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 = 47.2 bits (113), Expect = 5e-07
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
           ++ N+     +E+L E+FSE G + S +++ D  +G  KG GF  F   E A+ A+  +N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 374 GKMIVSKPLYV 384
           G     + L 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 7/87 (8%)

Query: 306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 365
           +DK+   ++++  L   +  E+L E FS  G I    +++  +  +  + F+ F   + A
Sbjct: 1   IDKY---SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFA-FIKFEREQAA 56

Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEE 392
           +RA+   N  M+ +K ++V   Q KE 
Sbjct: 57  ARAVESENHSMLKNKTMHV---QYKEI 80

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|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 = 46.9 bits (112), Expect = 5e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++  L  ++ +++L+ LF  FG I   K+   P G  KG GFV F     A  A+ ++ 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PPG--KGCGFVQFVHRAAAEAAIQQLQ 58

Query: 374 GKMIVSKPLYVA 385
           G +I    + ++
Sbjct: 59  GTIIGGSRIRLS 70

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

 Score = 47.2 bits (112), Expect = 5e-07
 Identities = 22/68 (32%), Positives = 41/68 (60%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NLD   T++ LK+IF   G + +  ++ D + K   +GFV +  + DA  A++ LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 271 GKKFDDRE 278
           G++ ++ E
Sbjct: 61  GRQIENNE 68

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

 Score = 47.4 bits (112), Expect = 5e-07
 Identities = 22/64 (34%), Positives = 42/64 (65%), Gaps = 1/64 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NLY+  L  ++  ++L++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 372 MNGK 375
           +NG+
Sbjct: 64  LNGQ 67

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 19/86 (22%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITS----------------AVVMRDG--DGKSKCF 251
            VFV NL  +T  +DLKK+F ++G I S                   ++    D K    
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 252 GFVNFENADDAAKAVEALNGKKFDDR 277
            +V F+  + A KA++ LNG +F+  
Sbjct: 62  AYVVFKEEESAEKALK-LNGTEFEGH 86

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 47.4 bits (112), Expect = 5e-07
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
           L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS   E   A+A
Sbjct: 5   LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 47.1 bits (112), Expect = 6e-07
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG +DF   ++ L   FSQ G V  V++  D +   S GYG+V +    DA + L   
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAG-VSKGYGFVTFETQEDAQKILQEA 63

Query: 92  NFTPLNNKSIRIMYSHRDPSIRK 114
           N     +K + I       +IRK
Sbjct: 64  NRLCFRDKKLNI-----GQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
           + NL        L   F  +G +    I  D  + +S+GF FV+F +K  A++A+D ++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 181 MLINDKQVFV 190
             ++ +++ V
Sbjct: 63  KELDGRELRV 72

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

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

 Score = 47.0 bits (112), Expect = 6e-07
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 129 IDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
              + L D FS+FG +L  ++  D  +GQSKGFGFV+F + E     +
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

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

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           +FV N+D  TT E+L++ F   GTI    ++ D   G+ K F ++ F +      A+  L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 270 NGKKFDDRE 278
           N  +F  R+
Sbjct: 61  NESEFRGRQ 69

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

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

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           S++VG++D+  T  +L + F   G +  + +  D  T +  G+ Y+ + + +    AL +
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-L 59

Query: 91  LNFTPLNNKSIRI 103
           LN +    + I++
Sbjct: 60  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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 37 LDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN 92
          +  +VT  QL+ LF  +  +    + RD  T +S G+ YV Y+NPA A  A + LN
Sbjct: 7  VSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLN 62

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 47.6 bits (114), Expect = 6e-07
 Identities = 21/72 (29%), Positives = 42/72 (58%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +Y+G L + +T+  +  +FSQ G+++ + + RD  T +S G+ ++ Y +      A+D L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 92  NFTPLNNKSIRI 103
           N   L  ++IR+
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|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 47.3 bits (112), Expect = 6e-07
 Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID 176
            N+++  L K++  K +   FS +G I++ +I  D  +G S+G GF++F+ +  A+ AI 
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK 61

Query: 177 KLNG 180
            LNG
Sbjct: 62  GLNG 65

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

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

 Score = 47.0 bits (112), Expect = 6e-07
 Identities = 21/73 (28%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++ ++   +    +   FS FG I S  ++ D  + + KGF FV++E  E+AQ A++++
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 179 NGMLINDKQVFVG 191
           NG+++  + + VG
Sbjct: 63  NGVMLGGRNIKVG 75

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

 Score = 47.0 bits (112), Expect = 6e-07
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +Y+ ++   + ++ +++ FS FG I S  +  DP +   KG  FV +  PE A  AL +M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 373 NGKMI 377
           NG M+
Sbjct: 63  NGVML 67

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

 Score = 47.5 bits (112), Expect = 6e-07
 Identities = 25/84 (29%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NLY+  L  ++  ++L++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 372 MNGKMI--VSKPLYVAVAQRKEER 393
           +NG+     ++P+ V  A    ++
Sbjct: 67  LNGQKPPGATEPITVKFANNPSQK 90

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

>gnl|CDD|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 = 46.9 bits (112), Expect = 6e-07
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L+I +L   + +E LK LF E+G I S  ++       +G  +V   T ++A RAL ++ 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI-----PPRGCAYVCMETRQDAHRALQKLR 59

Query: 374 GKMIVSKPLYVAVAQRKE 391
              +  K + VA A  K 
Sbjct: 60  NVKLAGKKIKVAWAPNKG 77

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

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

 Score = 51.6 bits (123), Expect = 7e-07
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
           G NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F +  ++ RA+
Sbjct: 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166

Query: 370 AEMNGKMIVSKPLYVAVAQ 388
             +NG  + +K L V+ A+
Sbjct: 167 KNLNGITVRNKRLKVSYAR 185

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

 Score = 47.0 bits (111), Expect = 7e-07
 Identities = 28/73 (38%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 116 GTG-NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
           GTG  IF+ NL    D   L   F  FG + + K+  D  + + KGFGFV   N + A  
Sbjct: 1   GTGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60

Query: 174 AIDKLNGMLINDK 186
           AI  LNG  + D+
Sbjct: 61  AIASLNGYRLGDR 73

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|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 25/57 (43%), Positives = 38/57 (66%), Gaps = 1/57 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
           L++ NL  ++  ++LKE FS+FG + SC V  D  +G+SKG GFV+FS+ +    AL
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL 58

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

 Score = 47.0 bits (111), Expect = 7e-07
 Identities = 28/81 (34%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+ NL    D   L   F  FG + + K+  D  + + KGFGFV   N + A  AI  L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 179 NGMLINDKQVFVGHFLRKQER 199
           NG  + D+ + V     KQ +
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHK 84

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

 Score = 47.4 bits (112), Expect = 7e-07
 Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 268
           N+F+ +L +   D+DL ++F  +G + SA V  D     SKCFGFV+++N   A  A++A
Sbjct: 9   NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68

Query: 269 LNG 271
           +NG
Sbjct: 69  MNG 71

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

 Score = 47.0 bits (112), Expect = 7e-07
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           I +  +D S+    L + FS+ G +   ++  D    ++ F FV+F + ESA +A+  L+
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSAL-NLS 60

Query: 180 GMLINDKQVFVGH 192
           G L+    + V  
Sbjct: 61  GTLLGGHPLRVSP 73

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 47.0 bits (111), Expect = 8e-07
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++    L   FSS G + S K+  D  +G S G+GFV + N + A+ AI+ 
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 178 LNGMLINDKQVFVGH 192
           LNG+ +  K + V +
Sbjct: 63  LNGLRLQSKTIKVSY 77

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 47.2 bits (113), Expect = 8e-07
 Identities = 28/74 (37%), Positives = 36/74 (48%), Gaps = 16/74 (21%)

Query: 122 IKNLDKSIDHKALHDTFSSFGN---------ILSCKIATD-------GSGQSKGFGFVQF 165
           I+NL KS+D K L + F    +         I   KI  D       G G+SKG+GFV+F
Sbjct: 5   IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 166 ENKESAQNAIDKLN 179
            N E A  A+  LN
Sbjct: 65  TNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 46.6 bits (111), Expect = 8e-07
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 10/73 (13%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKV---MRDPSGISKGSGFVAFSTPEEASRAL 369
           NL++  L  +     LK+LFS++G +   K+    R P   ++  GFV  ++ EEA++ +
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPG--ARCFGFVTMASVEEAAKCI 58

Query: 370 A-----EMNGKMI 377
                 E++G++I
Sbjct: 59  QHLHRTELHGRVI 71

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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 46.6 bits (111), Expect = 9e-07
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++V +LD+ V   +L ++F   G+V+   +  D    +S G G V + +P +A +A+ + 
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEHPIEAVQAISMF 59

Query: 92  NFTPLNNKSIRI 103
           N   L ++ +R+
Sbjct: 60  NGQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 46.9 bits (112), Expect = 9e-07
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 216 LDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKK 273
           L+    +  +   F E G +TS  ++R+   GKS  +GFV F   + A +A+++LNGK 
Sbjct: 7   LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKP 65

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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 46.6 bits (110), Expect = 9e-07
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 7/68 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV+NL  + T+E L+K F E+G +     ++D       + FV+FE  D A +A++ +N
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 271 GKKFDDRE 278
           GK+ +  E
Sbjct: 57  GKEIEGEE 64

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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 46.5 bits (111), Expect = 9e-07
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTIT--SAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
           ++V NL   TTDEDL+    E G +   S        +GKSK F +V F +   AA   E
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 268 ALNGKKFDDRE 278
            L G++F+ ++
Sbjct: 61  KLEGREFNGKK 71

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 25/61 (40%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          ++V +L F+VT   L DLF + G VL   V  D    RS G+G V + +P DA RA+++ 
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDG-RSKGFGTVLFESPEDAQRAIEMF 59

Query: 92 N 92
          N
Sbjct: 60 N 60

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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 211 VFVKNLDESTTDEDLKKIF-GEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           +FV +L    TD  L++ F   Y ++  A VVM    G+SK +GFV F + D+  +A+  
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 269 LNGKKFDDREWYVGKA 284
           +NG     R   V  A
Sbjct: 64  MNGVYCSSRPMRVSPA 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 3/78 (3%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC--RDLSTR-RSLGYGYVNYANPADAA 85
           TT+LYVG+L+  VT+  L   F + G + SV++   R    R R+   G+V + N ADA 
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 86  RALDVLNFTPLNNKSIRI 103
           RALD L+   +    +++
Sbjct: 61  RALDELDGKDVMGYELKL 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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL  ++ +  L+  F  FG IT   + R   G +   GF+ F   + A RA   M+
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 374 GKMIVSKPLYV 384
           GK++   P+ +
Sbjct: 70  GKVLRRNPIKI 80

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 8/63 (12%)

Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           VFV NL+ +  + EDL++IF +YG I   + +  G      +GFV F+N +DA  AV   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKIL-GISLHKG------YGFVQFDNEEDARAAVAGE 55

Query: 270 NGK 272
           NG+
Sbjct: 56  NGR 58

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

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 132 KALHDTFSSFGNILSCKI--ATDGSGQSKGFGFVQFENKESAQNAIDKLNG 180
           K L   FS FG      I    D +G++KG+ FV+F   E A+ A+  LNG
Sbjct: 22  KVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNG 72

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 46.8 bits (111), Expect = 1e-06
 Identities = 19/61 (31%), Positives = 38/61 (62%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV  L++  T+++++++F  YG +    +MRD   +S+   FV + + + A  A++ALN
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 271 G 271
           G
Sbjct: 62  G 62

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

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIAT-DGSGQSKGFGFVQFENKESAQNAIDKL 178
           ++++ L K+  H+ L   FS +G ++   +     +G  KGF F++FE  E AQ A   L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 179 N 179
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 20/62 (32%), Positives = 32/62 (51%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           VKNL    ++E L++ F ++G +  AVV+ D  G+S   G V F     A  A++  +  
Sbjct: 4   VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCSEG 63

Query: 273 KF 274
            F
Sbjct: 64  CF 65

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 20/69 (28%), Positives = 38/69 (55%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NLD  +  + + + F   G ++  KI  D  G+ K F FV F+++ S   A++ LN
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 180 GMLINDKQV 188
           G+ +  + +
Sbjct: 64  GIKLYGRPL 72

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +F+  L   +    L + FS FG +   ++  D  +G+ +GFGFV F+N +SA  A   +
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA-VV 60

Query: 179 NGMLINDKQVFVGHFLRKQE 198
               IN  +V V   + K+E
Sbjct: 61  KFHPINGHRVEVKKAVPKEE 80

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

 Score = 47.1 bits (111), Expect = 1e-06
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID 176
            N+++  L K++  K L   FS +G I++ +I  D  +G S+G GF++F+ +  A+ AI 
Sbjct: 6   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65

Query: 177 KLNG 180
            LNG
Sbjct: 66  GLNG 69

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

>gnl|CDD|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 = 46.2 bits (110), Expect = 1e-06
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 28  LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
            +T+L++G L   VT+  L +LF + G++ S+ +   +  R   G  YV      DA RA
Sbjct: 1   CSTTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDM---IPPR---GCAYVCMETRQDAHRA 54

Query: 88  LDVLNFTPLNNKSIRI 103
           L  L    L  K I++
Sbjct: 55  LQKLRNVKLAGKKIKV 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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FVKNL  + T ++LK++F +   I   +     DG SK   ++ F+   +A KA+E   
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDIR--LPSGK-DGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 271 GKKFDDR 277
           G + D R
Sbjct: 63  GAEVDGR 69

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L I NL  +   ++ +EL   FG +  C  V  + +G SKG GFV +   + A+RA +++
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 373 NGKMIVSKPLYV 384
            GK + S+ LYV
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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           ++YV D+D  VT+ QL  LFS  GQV+  RVC D      L + ++ + +   A  AL  
Sbjct: 4   TVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAALS- 60

Query: 91  LNFTPLNNKSIRIMYS 106
           L+ T L    +R++ S
Sbjct: 61  LSGTMLGFYPVRVLPS 76

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+VK   +  T +D+++ F ++G + +  + RD D K K   FV F+  +DA K +E   
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK-E 60

Query: 271 GKKFDDRE 278
             K+ ++E
Sbjct: 61  KLKYKEKE 68

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 211 VFVKNLDESTTDEDL----KKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 266
           VFV +L  S +D++L     + F +YGT+    V+RD   +   + FV F N DDA  A+
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRP--YAFVQFTNDDDAKNAL 62

Query: 267 EALNGKKFDDR 277
               G   D R
Sbjct: 63  AKGQGTILDGR 73

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

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 20/58 (34%), Positives = 31/58 (53%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          L+VG L +  T   L   FSQ G+V+   + +D +T RS G+G+V + +P      L 
Sbjct: 2  LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLA 59

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V VKNL + TT+  +++ F + G I    ++    G       + FE  D+A  A+   +
Sbjct: 3   VKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGG---LVAVIEFETEDEALAALTK-D 58

Query: 271 GKKFDDRE 278
            K+    E
Sbjct: 59  HKRLGGNE 66

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +Y+ NL + + +E L ELF + G + +  + +D  +   +G GFV F + E+A  A+  M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 373 NGKMIVSKPLYV 384
           N   +  KP+ V
Sbjct: 61  NMIKLYGKPIRV 72

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

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 4/85 (4%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           ++++ +L F+ T+ +L +LFSQ G+V   R+ +D  T  S G  +V +     A + L+ 
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 91  LNFTPLNNKSIRIMYSHRDPSIRKS 115
            +    N +   +    R   +  +
Sbjct: 62  AD----NAEDSGLSLDGRRLIVTLA 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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           ++V  L E   ++ L   F  +G I    +  D    K + F FV FE  +DAA A++ +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 270 NG 271
           N 
Sbjct: 61  NE 62

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

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 18/63 (28%), Positives = 30/63 (47%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
             + + NLD  +    + + F+ FG +    +  D SG+S G   V FE +  A  A+ +
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 178 LNG 180
            NG
Sbjct: 61  YNG 63

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 18/72 (25%), Positives = 37/72 (51%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +YV  +  ++++  +  +F   G++ S  +  D  T +  GYG++ Y NP  A  A+  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 92  NFTPLNNKSIRI 103
           N   L  + +R+
Sbjct: 63  NLFDLGGQQLRV 74

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

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI    KS+    L + F+ FG I    +  D  + +SKG  +V+F    SA  A++++
Sbjct: 6   LFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEM 64

Query: 179 NGMLIND 185
           NG  +  
Sbjct: 65  NGKCLGG 71

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|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 = 45.9 bits (109), Expect = 2e-06
 Identities = 22/61 (36%), Positives = 29/61 (47%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  L K      +   F  FG I  C I     G SKG  FV+F +   AQ AI+ L+
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 180 G 180
           G
Sbjct: 64  G 64

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

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 38/192 (19%), Positives = 78/192 (40%), Gaps = 25/192 (13%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
           + +++ NL     ++ +K++   +G + +  +++D   G SK + F  +++      A+ 
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIA 355

Query: 268 ALNGKKFDDREWYV-----GKAQKKSEREQELKGQFEQAMKETVDKFQG-------LNLY 315
           ALNGK   D + +V     G  Q   +    +      A   +    Q        + L 
Sbjct: 356 ALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLT 415

Query: 316 IKNLGDSIDD--------EKLKELFSEFGTITSCKVMRDPSGISKGSG----FVAFSTPE 363
               GD + D        E +K  FS++G + +  + R     +   G    F+ ++   
Sbjct: 416 NLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVR 475

Query: 364 EASRALAEMNGK 375
            A +A+  MNG+
Sbjct: 476 SAEKAMEGMNGR 487

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

 Score = 45.7 bits (108), Expect = 2e-06
 Identities = 22/63 (34%), Positives = 35/63 (55%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           +LYV  L   +T  +L  LFSQ G++++ R+ RD  T  S G G++ +    +A  A+ 
Sbjct: 1  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 90 VLN 92
           LN
Sbjct: 61 GLN 63

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

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 23/61 (37%), Positives = 32/61 (52%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          +Y+G L     + +L   FSQ G V +VRV R   T  S  YG++ + NP  AA A   +
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 92 N 92
          N
Sbjct: 62 N 62

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 9/76 (11%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-------DGKSKCFGFVNFENADD 261
             ++VKNL +  T+EDL  IFG +  + S+   ++        +G+ K   FV F + + 
Sbjct: 2   KRLYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEI 59

Query: 262 AAKAVEALNGKKFDDR 277
           A KA+  +NG     +
Sbjct: 60  ATKALNLVNGYVLKGK 75

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

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
          L+VG+L F  T+ +L   F +VG++  VR+     + +  G+ +V++     A  AL
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKA 265
           V  L   TT++DLK  F  +G +    V +D   G+SK FGFV F + +D  K 
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V+     T++  +++IF  YG +    ++         F FV FE+ + A +A ++++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVH 54

Query: 271 GKKFDDREWYV 281
           GK  ++   YV
Sbjct: 55  GKVLNNNPLYV 65

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

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY++NL   I  E+L +LF ++G I   ++       ++G+ FV +    +A  A   ++
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE--TRGTAFVVYEDIYDAKNACDHLS 62

Query: 374 G 374
           G
Sbjct: 63  G 63

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 45.7 bits (108), Expect = 2e-06
 Identities = 23/83 (27%), Positives = 39/83 (46%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
           P   +  T N+FI NLD ++    L   F  +G I    I     GQ   + F++F+N +
Sbjct: 1   PEDDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLD 60

Query: 170 SAQNAIDKLNGMLINDKQVFVGH 192
            A  A   ++G +I    + +G+
Sbjct: 61  MAHRAKVAMSGRVIGRNPIKIGY 83

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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 10/71 (14%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N+YI N+ DS+ +EKL+  FS++G I S   +R+     K   FV F+    A +A+  +
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLRE-----KNCAFVNFTNISNAIKAIDGV 59

Query: 373 NGKMIVSKPLY 383
                 S PL+
Sbjct: 60  K-----SHPLF 65

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD------GSGQSKGFGFVQFENKESAQN 173
           +F+KNL+ S  ++ L D F      +  ++ T       G   S GFGFV F+ KE AQ 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 174 AIDKLNGMLINDKQVFV 190
           A+  ++G +++   + V
Sbjct: 63  ALKAMDGFVLDGHTLVV 79

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V Y++  +   A++
Sbjct: 5  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 322 SIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           S  +E L+E F EFG I    +++D  +G SKG G+V F  P +A+ AL
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 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|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 = 45.7 bits (109), Expect = 2e-06
 Identities = 19/61 (31%), Positives = 33/61 (54%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L ++N+      ++L+ELFS FG + S ++ +   G  +G  FV F T +EA  A+  + 
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62

Query: 374 G 374
            
Sbjct: 63  S 63

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

 Score = 45.9 bits (108), Expect = 2e-06
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFE--NADDAA 263
           +F  +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FGFV F   N  DAA
Sbjct: 1   QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60

Query: 264 KA 265
            A
Sbjct: 61  MA 62

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 7/75 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L+++NL  ++ +E L++ FSEFG +   K ++D         FV F   + A RA+ EMN
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 374 GKMIVSKPLYVAVAQ 388
           GK I  + + + +A+
Sbjct: 57  GKEIEGEEIEIVLAK 71

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 4/60 (6%)

Query: 314 LYIKNLG--DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           +Y+K      ++DD  ++E F +FG + + ++ RD     KGS FV F T E+A + L +
Sbjct: 2   VYVKGFPKDATLDD--IQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK 59

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 23/66 (34%), Positives = 39/66 (59%), Gaps = 6/66 (9%)

Query: 120 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNA 174
           IF+K  D S+      ++L + FSS G I    I TD  +G SKGF +++F++ +  + A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 175 IDKLNG 180
           + +L+G
Sbjct: 62  L-ELDG 66

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 31/63 (49%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
             I +KNL      K +   FSS+G + S ++       ++GF FV+F   + A NA++ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 178 LNG 180
           L  
Sbjct: 61  LKD 63

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 46.1 bits (109), Expect = 2e-06
 Identities = 30/98 (30%), Positives = 50/98 (51%), Gaps = 16/98 (16%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
           +++FV+N+ + T  EDL++ FG YG I    V  D    + + F +V FE+  DA  A+ 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKET 305
            L      DR+W  G+         +++ QF Q  ++T
Sbjct: 61  NL------DRKWICGR---------QIEIQFAQGDRKT 83

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+ NL   + +  + +LFS+ G   SCK++ D +G +    FV F     A+ +LA MN
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAG-NDPYCFVEFFEHRHAAASLAAMN 60

Query: 374 GKMIVSKPLYV 384
           G+ I+ K + V
Sbjct: 61  GRKIMGKEVKV 71

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

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 267
           +FV  L  +TT ED+K+ F ++G +  A++M D    + + FGFV FE+ D   K  E
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           ++Y+G+L +++T+  + + F    ++ SVR+  D  T    G+G+V++A+      AL  
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK- 58

Query: 91  LNFTPLNNKSIRI 103
           L+ T L  + IRI
Sbjct: 59  LDGTVLCGRPIRI 71

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 8/68 (11%)

Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV N D  +T   DL++ F  YG + +  + R+       F FV +E  +DA KA+E+ 
Sbjct: 2   LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRN-------FAFVQYETQEDATKALEST 54

Query: 270 NGKKFDDR 277
           N  K  DR
Sbjct: 55  NMSKVLDR 62

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L V +L F  T++ L  LFS  G V  V + R     +  G+ +V + + ADA +A+  +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKGV 60

Query: 92  NFTPLNNKSI 101
           N   +  + +
Sbjct: 61  NGKKIKGRPV 70

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|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 = 44.8 bits (107), Expect = 3e-06
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          L+VG L    T+  +  LF + G +  V + RD  T +S G  +V +++  +A +A++ L
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 92 N 92
          +
Sbjct: 62 H 62

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

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 212 FVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           FV  L ++  D   L+K+F + G  T   +    +G+ + F FV +  A+DA +A +ALN
Sbjct: 6   FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65

Query: 271 GKKF 274
           G   
Sbjct: 66  GHSL 69

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

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 18/58 (31%), Positives = 35/58 (60%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           L+VG L+   +DS L   F++ G++    V  D +T+RS G+G++ +++  +A  A+
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

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

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLF-SQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           S++VGDL   V +S L  LF S+     S ++  D  T  S GYG+V +++  D  RAL 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 90  VLNFTPLNNKSIRIMYS 106
            +       + +RI  +
Sbjct: 63  EMQGVYCGGRPMRISTA 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 16/56 (28%), Positives = 31/56 (55%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
          L+V  L+++ T+S+L   F + G +  +R+ RD  T +  GY ++ + +  D   A
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59

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

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA-- 370
           +++  L   + +E+ KE FS+FG +   ++M+D  +G S+G GFV F +     R  +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 371 --EMNGKMIVSKP 381
             E+ GK +  K 
Sbjct: 62  MLELGGKQVEVKR 74

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

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 45.2 bits (108), Expect = 3e-06
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 120 IFIKNLDKSID----HKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           ++I NL++ I      ++L+  FS FG +L   I    + + +G  FV F++ ESA NA+
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVL--DIVASKTLKMRGQAFVVFKDVESATNAL 59

Query: 176 DKLNGMLINDK 186
             L G    DK
Sbjct: 60  RALQGFPFYDK 70

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

 Score = 45.5 bits (107), Expect = 3e-06
 Identities = 23/74 (31%), Positives = 42/74 (56%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++V +L     +S L+ LF   G V +V+V RD +T +  G+G+V   N  +AA A+  L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 92  NFTPLNNKSIRIMY 105
           N   L ++ +++ +
Sbjct: 64  NGYRLGDRVLQVSF 77

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

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+VG+L+  V +  LY+LF Q G +  V +C+D    +   +G+V + +      A+ +
Sbjct: 3   TLFVGNLECRVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYAIAL 61

Query: 91  LNFTPLNNKSIRI 103
           LN   L  + I++
Sbjct: 62  LNGIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           NLYI  L  ++  + ++++FS FG I + +V+ D  +G+S+G  F+ F    EA  A+  
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 372 MNG 374
            NG
Sbjct: 62  FNG 64

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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           LYVG+L +  TD  L    ++ G   V S++     +  +S G+ YV +A+ A AA   +
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 90  VLNFTPLNNKSIRIMY 105
            L     N K   + Y
Sbjct: 61  KLEGREFNGKKCVVTY 76

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCR--DLSTRRSLGYGYVNYANPADAARA 87
           T + V +L F  T   +  LFS  GQ+ SVRV +  D S R   G+ +V ++   +A  A
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSAR---GFAFVEFSTAKEALNA 57

Query: 88  LDVLNFTPLNNKSIRIMYS 106
           ++ L  T L  + + + Y+
Sbjct: 58  MNALKDTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 45.5 bits (108), Expect = 3e-06
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           NV++ NL ES ++E+L++   ++G I    ++++     K   FV+F +  +A K V  L
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTL 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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NLD   +D++L+ +F ++G +    +       S+   FV F +   A  A++ALN
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKD--IRETPLRPSQK--FVEFYDIRAAEAALDALN 59

Query: 271 GKKFDDREW 279
           G+ F     
Sbjct: 60  GRPFLGGRL 68

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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           + ++ L  S  +E +++ FS          ++ D  G   G  +V F++PE+A RAL + 
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 373 NGKM 376
           N KM
Sbjct: 62  NNKM 65

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 4/52 (7%)

Query: 221 TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           ++++L+KIF +YG + S VV+     K K    V F +   A  AVE   G 
Sbjct: 17  SEDELRKIFSKYGDV-SDVVVSS---KKKGSAIVEFASKKAAEAAVENECGL 64

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+V NL  +    +L++ FG YG + S  V R+  G    F FV FE+  DAA AV  L+
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 62

Query: 271 GK 272
           G+
Sbjct: 63  GR 64

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

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 45.1 bits (106), Expect = 3e-06
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM---RDPSGISKGSGFVAFSTPEEASR 367
           G NL++  L  +     LK LFS++G +   KV+   R P   ++  GFV  ST EEA++
Sbjct: 1   GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPG--ARCYGFVTMSTSEEATK 58

Query: 368 ALA-----EMNGKMI 377
            +      E++G+MI
Sbjct: 59  CINHLHRTELHGRMI 73

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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 12/70 (17%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID--- 176
           +F+ NL      + +   F  +G +L C I        K +GFV  ++K +A  AI    
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII-------KNYGFVHMDDKTAADEAIRNLH 55

Query: 177 --KLNGMLIN 184
             KL+G+ IN
Sbjct: 56  HYKLHGVAIN 65

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

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
           T  +FI NL+K+  +  L + F  FG I+   I   G   +  + F+Q+ +  S   A+ 
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPA--YAFIQYADIASVVKAMR 59

Query: 177 KLNGMLINDKQVFVG 191
           K++G  + + +V +G
Sbjct: 60  KMDGEYLGNNRVKLG 74

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

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +YVG+L    T  +L D F + G + SV V      R   G+ +V + +P DA  A+  L
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRAL 56

Query: 92  NFTPLNNKSIRIMYSHR 108
           +   +    +R+  S  
Sbjct: 57  DGRRICGNRVRVELSRG 73

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

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

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +Y+ NL  S+ +  L ++FS++G +    +++D  +  SKG  F+ F   E+A + +  +
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 373 NGKMIVSKPLYVAVA 387
           N K +  + L  ++A
Sbjct: 64  NNKELFGRTLKCSIA 78

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

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 5/57 (8%)

Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           L   FS FGNI++  I+ +   + K  GFV FE  ESA  AI +LNG  +   Q+ V
Sbjct: 19  LKKAFSPFGNIIN--ISME---KEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKV 70

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISK------GSGFVAFSTPEEASR 367
           +YI NL  S  +E L+E   +F  ++     +   G         G  +  FS+PE+A +
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 368 ALAEMNGKMIVSKPLYV 384
            + ++NGK+  ++ L+V
Sbjct: 62  VVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 45.1 bits (106), Expect = 4e-06
 Identities = 23/74 (31%), Positives = 43/74 (58%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++V +L  +  +S L+ LF   G V +V+V RD +T +  G+G+V   N  +AA A+  L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 92  NFTPLNNKSIRIMY 105
           N   L ++ +++ +
Sbjct: 66  NGYRLGDRVLQVSF 79

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 44.8 bits (106), Expect = 4e-06
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 7/73 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IF+ N+D+    + L   F ++G +LSC +        + F FV    + +A  AI++LN
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM-------RQFAFVHLRGEAAADRAIEELN 55

Query: 180 GMLINDKQVFVGH 192
           G  ++ +++ V H
Sbjct: 56  GRELHGRKLVVEH 68

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

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

 Score = 44.7 bits (105), Expect = 4e-06
 Identities = 22/65 (33%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N++V  L ++ T ++L+++F +YG  ITS +++    G S+  GF+ F+   +A +A++ 
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 269 LNGKK 273
           LNG+K
Sbjct: 64  LNGQK 68

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 44.7 bits (105), Expect = 4e-06
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALA-- 370
           ++I  L      + L++ FS+FG I  C VMRDP+   S+G GFV F+ P    + LA  
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQP 61

Query: 371 --EMNGKMIVSK 380
             E++ K I  K
Sbjct: 62  HHELDSKTIDPK 73

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|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 = 44.6 bits (106), Expect = 4e-06
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 9/65 (13%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS--AVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           +++ +L +  T+EDLK +F EYG I S   +  R       C  +V  E   DA +A++ 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRG------C-AYVCMETRQDAHRALQK 57

Query: 269 LNGKK 273
           L   K
Sbjct: 58  LRNVK 62

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

 Score = 44.8 bits (106), Expect = 4e-06
 Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFEN 258
           +FV  L   TT E L++ F +YG +   V+M+D    +S+ FGFV F++
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50

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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDA-AKAVEA 268
           +FV  L  S T+ DL++ F  +GT++   ++ +   G  + F +++   ++    K    
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 269 LNGKKF 274
           LNG K+
Sbjct: 62  LNGTKW 67

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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)

Query: 209 NNV-FVKNLDESTTDEDLKKIFGEY-GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 266
           N + F++NL E TT E L+ +F ++ G     +V        +   FV FE  + A  A+
Sbjct: 2   NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVAL 55

Query: 267 EALNGKK 273
           +AL G K
Sbjct: 56  QALQGFK 62

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 45.4 bits (107), Expect = 4e-06
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 7/89 (7%)

Query: 28  LTTSLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPAD 83
              ++Y+ +L+  +   +L    + +FS+ GQ+L + V R L  R   G  +V +   + 
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSS 58

Query: 84  AARALDVLNFTPLNNKSIRIMYSHRDPSI 112
           A  AL  +   P  +K +RI Y+  D  I
Sbjct: 59  ATNALRSMQGFPFYDKPMRIQYAKTDSDI 87

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++ NL  S+ +  LH  FS +G ++   I  D  + +SKG  F+ F ++E A   +  L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 179 NGMLINDKQVF 189
           N      K++F
Sbjct: 64  NN-----KELF 69

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

 Score = 44.4 bits (105), Expect = 5e-06
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 211 VFVKNLDESTTDEDLKKIF-GEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           +FV +L     + DL  +F   + +  SA +M D   G S+ +GFV F + +D  +A+  
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 269 LNGKKFDDREWYVGKA 284
           + G     R   +  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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 44.7 bits (105), Expect = 5e-06
 Identities = 22/74 (29%), Positives = 43/74 (58%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++V +L  +  +S L+ +F   G V +V+V RD +T +  G+G+V   N  +AA A+  L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 92  NFTPLNNKSIRIMY 105
           N   L ++ +++ +
Sbjct: 66  NGYRLGDRVLQVSF 79

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

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 17/77 (22%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
           N +F+  L    +++ +K++   +G + +  +++D   G SK + F  + +     +A+ 
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 268 ALNGKKFDDREWYVGKA 284
            LNG +  D++  V +A
Sbjct: 61  GLNGMQLGDKKLTVQRA 77

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

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 44.2 bits (104), Expect = 5e-06
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 7/75 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L+++NL +++ +E L++ F +FG +   K ++D         F+ F   + A +A+ EMN
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 374 GKMIVSKPLYVAVAQ 388
           GK +  + + +  A+
Sbjct: 57  GKELEGENIEIVFAK 71

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK 375
           I N+   +  E L  L S +GT+ +C+ +  P+     +  V + +PE+A +A+ ++NG 
Sbjct: 5   ISNIPPHVRWEDLDSLLSTYGTVKNCEQV--PTKSETATVNVTYESPEQAQQAVNKLNGH 62

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) 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 = 76

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 45.0 bits (107), Expect = 5e-06
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
            ++V  +   TT  +L++ F  +G I    +    DG +  +GFV +  A DA +A+E
Sbjct: 4   VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFRAIE 59

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L +++L   + ++  ++L   FG  +S +VM    G  K + F  F   + AS+AL+ ++
Sbjct: 2   LLVRHLPPELSEDDKEDLLKHFG-ASSVRVMS-RRGKLKNTAFATFDNEQAASQALSRLH 59

Query: 374 GKMIVSKPLYV 384
              I+ K L V
Sbjct: 60  QLKILGKRLVV 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 40  NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN- 98
           +VT+  L + F+  G++  + V +D  T+ S G  YV +A  + AARA++ +N   L   
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 99  -KSIRIM 104
            K ++++
Sbjct: 73  TKPLKVL 79

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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 44.5 bits (105), Expect = 6e-06
 Identities = 26/79 (32%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 314 LYIKNLGDSIDD-EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L I+NL  SI    KLK++F  +G +    + R   G   G  FV     + A  AL   
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 373 NGKMIVSKPLYVAVAQRKE 391
           NG  I  +P+ V  A +K 
Sbjct: 63  NGLEIDGRPVAVDWAVQKN 81

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV+NL    T + LK  F E G +  A +  + +GKSK  G V FE+ + A +A   +N
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMN 60

Query: 271 GKKFDDRE 278
           G K + RE
Sbjct: 61  GYKLNGRE 68

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

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
            ++++ +L   I  + +K  F+ FG I+  +V++D  +G SKG GFV+F    +A  A+ 
Sbjct: 2   FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 371 EMNGKMIVSKPLYVAVAQR 389
           +M G+ +  + +    A R
Sbjct: 62  QMGGQWLGGRQIRTNWATR 80

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

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 19/71 (26%), Positives = 35/71 (49%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++ NLD  +    L   F   G + + KI  D + +   +GFV++     A+ A+  LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 180 GMLINDKQVFV 190
           G  I + ++ V
Sbjct: 61  GRQIENNEIRV 71

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 44.1 bits (105), Expect = 6e-06
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  + + +    L   F   G I   ++  D SG ++G+ FV + NKE+AQ A+ +L+
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 180 GMLIN 184
              I 
Sbjct: 64  NYEIR 68

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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 268
           N++V  L  +T   DLK +F +YG +  A V+ +     ++C+GFV    +++A K +  
Sbjct: 3   NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62

Query: 269 LNGKKFDDR 277
           L+  +   R
Sbjct: 63  LHRTELHGR 71

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|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 43.9 bits (103), Expect = 6e-06
 Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 268
           N++V  L  +T   DLK +FG+YG + SA V+ +     +KC+G V   ++ + A+ +  
Sbjct: 1   NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISH 60

Query: 269 LN 270
           L+
Sbjct: 61  LH 62

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains 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. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 43.8 bits (104), Expect = 7e-06
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L + NL      + L+ +F ++G +    + RD  +  S+G  FV F    +A  A+  M
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 373 NGKMIVSKPLYVA 385
           +GK +  + L V 
Sbjct: 61  DGKELDGRELRVQ 73

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

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

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 23/77 (29%), Positives = 40/77 (51%)

Query: 28  LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
            T  L+V +L ++  +  L  LFS+ G++  V V  D  + +S G+ YV + +P DA +A
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 88  LDVLNFTPLNNKSIRIM 104
              L+      + I I+
Sbjct: 61  YKELDGKVFQGRLIHIL 77

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

 Score = 44.1 bits (104), Expect = 7e-06
 Identities = 21/65 (32%), Positives = 33/65 (50%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          T+LYV +L   +T+ +L  +F   G ++   + RD ST    G  +V Y    +A  A+ 
Sbjct: 1  TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 90 VLNFT 94
           LN T
Sbjct: 61 SLNGT 65

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

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 44.1 bits (104), Expect = 7e-06
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+ NL   + ++ LK++F   G + + K++ D +      GFV +    +A  AL  +N
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 374 GKMI 377
           G+ I
Sbjct: 61  GRQI 64

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

 Score = 44.2 bits (104), Expect = 7e-06
 Identities = 20/65 (30%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N++V  L ++ + ++++++F +YG  ITS +++    G S+  GF+ F+   +A +A++ 
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 269 LNGKK 273
           LNG+K
Sbjct: 63  LNGQK 67

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

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V++  L     + D+++ F  YG I   + +++G      FGFV FE+  DA  AV  LN
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIRE-INLKNG------FGFVEFEDPRDADDAVYELN 54

Query: 271 GK 272
           GK
Sbjct: 55  GK 56

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

 Score = 44.4 bits (105), Expect = 7e-06
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
           +F+  +D  +D   +   F+ +G++   KI TD +G SKG+GFV F +    Q  ++
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVE 64

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

 Score = 44.2 bits (104), Expect = 7e-06
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 266
           +FV  + E T +  L+  F +YG I    +M D G GK + F FV F++ D   K V
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 43.9 bits (103), Expect = 7e-06
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAK 264
           T+   +FV  L  +T  ED+K+ F ++G +  A++M D    + + FGFV FEN D   K
Sbjct: 1   TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK 60

Query: 265 AVE 267
             E
Sbjct: 61  VCE 63

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
           L++  L + + +E L+E FS++G + S +++ D  +G  +G  FV F   +   + + 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVL 59

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

 Score = 43.9 bits (103), Expect = 8e-06
 Identities = 21/74 (28%), Positives = 42/74 (56%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++ +L  +  +  L+ +F   G V +V+V RD +T +  G+G+V   N  +AA A+  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 92  NFTPLNNKSIRIMY 105
           N   L +K +++ +
Sbjct: 64  NGYRLGDKILQVSF 77

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

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.9 bits (104), Expect = 8e-06
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 42 TDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          T+  L + F + G +  V + +D +T  S G+GYV +  P+ AA AL+
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 43.9 bits (104), Expect = 9e-06
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 174
            +G +FI+NL  +   + L   FS +G +    +  D  + + KGF FV +   E A  A
Sbjct: 1   ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 175 IDKLNGMLINDKQVFVGHFL 194
             +L+G       VF G  L
Sbjct: 61  FAELDG------TVFQGRLL 74

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.1 bits (104), Expect = 9e-06
 Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK------SKCFGFVNFENADDAAK 264
           +FVKNL+ STT++ L   F        A V    D K      S  FGFV F+  + A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 265 AVEALNGKKFDDREWYVGKAQK 286
           A++A++G   D     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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.7 bits (104), Expect = 9e-06
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS---GFVAFSTPEEASRALA 370
           L++ N   S D   +++LF ++G I S   +R PS     +    +V F++PE A+ A+A
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAAVA 59

Query: 371 EMNGKMI 377
            +NGK+ 
Sbjct: 60  LLNGKLG 66

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 21/60 (35%), Positives = 31/60 (51%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L +KNL   + +E L++ FS+FG +    V+ D  G S G G V FS    A  A+   +
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCS 61

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

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+  LG+ + ++ L++ F +FG I S  V+       +   FV F+T E A +A   + 
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVVP-----RQQCAFVTFTTREAAEKAAERLF 58

Query: 374 GKMIV 378
            K+I+
Sbjct: 59  NKLII 63

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

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 43.7 bits (103), Expect = 9e-06
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA--NPADAARAL 88
            ++VG+L F   +  L+ +F + G +  VR+ RD  T    G+ YV +   N  + A  L
Sbjct: 1   CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLL 60

Query: 89  DVLNFTPLNNKSIRIM 104
           +   F P+  + +R+ 
Sbjct: 61  NEKKFPPMLPRELRVS 76

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

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 22/56 (39%), Positives = 36/56 (64%), Gaps = 5/56 (8%)

Query: 221 TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD 276
           + E+L ++F +YGT+   +VM  G  K  CF  V++ + +DAA A +ALNGK+ + 
Sbjct: 16  SREELLRVFEKYGTVED-LVMPPG--KPYCF--VSYSSIEDAAAAYDALNGKELEL 66

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 28/56 (50%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
          L+V  L+   TD  L  +FS+ G++ S  V RD  T  SL Y ++ +    D   A
Sbjct: 6  LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 22/73 (30%), Positives = 38/73 (52%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NLD ++    L   F  FG I    I   G GQ+  +GF++FEN + A  A   ++
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 180 GMLINDKQVFVGH 192
           G ++    + +G+
Sbjct: 70  GKVLRRNPIKIGY 82

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 19/57 (33%), Positives = 35/57 (61%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
          +++G L +  T   L + FS+ G++    V RD +T+RS G+G+V +++PA   + L
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVL 57

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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG---YGYVNYANPADAARA 87
           +L+V  L      + L  LFS+ G+V+  ++   ++  RS G   +G+V  A+  +AA+ 
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKI---VTNARSPGARCFGFVTMASVEEAAKC 57

Query: 88  LDVLNFTPLNNKSIRI 103
           +  L+ T L+ + I +
Sbjct: 58  IQHLHRTELHGRVISV 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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 43.5 bits (102), Expect = 1e-05
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
            ++++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F    +A  A+ 
Sbjct: 2   FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

Query: 371 EMNGKMIVSKPLYVAVAQR 389
            M G+ +  + +    A R
Sbjct: 62  HMGGQWLGGRQIRTNWATR 80

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

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           LY++N+ D+   + L+ LF ++G I    +  D  +   +G  +V F    +A  AL  +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 373 NGKMIVSKPLYVAVAQ--RK 390
           +    + + + +  AQ  RK
Sbjct: 63  DRTRFLGREIEIQFAQGDRK 82

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 43.6 bits (102), Expect = 1e-05
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTD+ L++ F ++GT+T  VVMRD   K S+ FGFV +   ++   A
Sbjct: 1   QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

Query: 266 VEA 268
           + A
Sbjct: 61  MSA 63

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+VG+LD  VT+  +++LF Q G V+ V++ +D   +    + +VN+ +      A+++
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQ-FAFVNFKHEVSVPYAMNL 61

Query: 91  LNFTPLNNKSIRI 103
           LN   L  + + I
Sbjct: 62  LNGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           ++++NL   +  +KLKE FS+ G +   ++  + +G SKG G V F +PE A +A   MN
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 374 GKMI 377
           G  I
Sbjct: 61  GIKI 64

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 132 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           + L + FS +G I    I  D  S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 24  RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

Query: 191 GHFLRK 196
              + K
Sbjct: 84  DFSITK 89

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 44.0 bits (103), Expect = 1e-05
 Identities = 22/65 (33%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N++V  L ++ T ++L+++F +YG  ITS +++    G S+  GF+ F+   +A +A++ 
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 269 LNGKK 273
           LNG+K
Sbjct: 67  LNGQK 71

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 14/37 (37%), Positives = 23/37 (62%)

Query: 154 SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           +G+SKGF +V+F ++ +A    +KL G   N K+  V
Sbjct: 38  NGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVV 74

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKLNG 180
           I NL  +   +   +    FGN+  C  + ++ +G SKG+GFV++  K+SA  A   L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 181 MLINDKQVFV 190
             +  + ++V
Sbjct: 64  KQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 314 LYIKNLGDSIDDEKL----KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +++ +L  S  D++L     E FS++GT+   KV+RD     +   FV F+  ++A  AL
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQ--RPYAFVQFTNDDDAKNAL 62

Query: 370 AEMNGKMIVSKPL 382
           A+  G ++  + +
Sbjct: 63  AKGQGTILDGRHI 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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 211 VFVKNLDESTTDEDLK----KIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 265
           +FVK  D S  ++D++    + F   G IT   +  D + G SK F ++ F++ D   KA
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 266 VEALNGKKFDDREWYVGKA 284
           +E L+G         V +A
Sbjct: 62  LE-LDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           ++I NL   I    + + F     I S ++ATD  +G+ KGFG V F ++ES   A+ KL
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KL 59

Query: 179 NGMLINDKQVFVG 191
           +G ++  + + + 
Sbjct: 60  DGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N VFV  +D    + +++  F +YG++    ++ D  G SK +GFV+F +  D  K VE+
Sbjct: 6   NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVES 65

Query: 269 ---LNGKKF 274
               +GKK 
Sbjct: 66  QINFHGKKL 74

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 43.6 bits (102), Expect = 1e-05
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 267
            N++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV 
Sbjct: 2   TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61

Query: 268 AL 269
           AL
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|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESA 171
           R   +  +F+ NL   ID   L + F SFGN++  +I T G  G+   FGFV F++ E  
Sbjct: 1   RYPDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPV 60

Query: 172 Q 172
           Q
Sbjct: 61  Q 61

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 33  YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN 92
           +VG+L FN     L  +F  +  V SVR+ RD  T +  G+ YV + +      AL+  +
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 93  FTPLNNKSIRI 103
               +++S+R+
Sbjct: 63  GALFDDRSLRV 73

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|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 131 HKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
              L D F  FG ++   +        K +G+ ++ ++ESA+ AI  L+G  +N  ++ V
Sbjct: 13  DYILEDVFCRFGGLIDVYLVPG-----KNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
           ++ NL     + DL+++F E+    S+V+++ G      + FV+  +   A KA+E LNG
Sbjct: 2   YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGG-----YAFVDCPDQSWADKAIEKLNG 56

Query: 272 KKFDDRE 278
           K    + 
Sbjct: 57  KILQGKV 63

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 39/72 (54%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L V +L +  T   L  +F + G+V  V + RD  TR S G+ +V + +  DA  A+D +
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 92  NFTPLNNKSIRI 103
           +   L+ + +R+
Sbjct: 61  DGKELDGRELRV 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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 42.9 bits (102), Expect = 2e-05
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 6/56 (10%)

Query: 326 EKLKE----LFSEFGTITSCKVM--RDPSGISKGSGFVAFSTPEEASRALAEMNGK 375
           EKLK+    +FS+FG      +    D +G +KG  FV F+TPEEA  A+  +NG 
Sbjct: 18  EKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGY 73

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 5/71 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NL   I  +   + FS +G +    +  +     KGFGF++ + + +A+ A  +L+
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 180 GMLINDKQVFV 190
           G++   +Q+ V
Sbjct: 59  GIMRKGRQLRV 69

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

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 265
           +FV NL  +   ++LK+ F ++G + S  V  D + G SK +GFV+F + D    A
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENA 57

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++ N+  +   ++L+ LF EFG +  C  +       K   FV     EEA  A+  +N
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEALN 55

Query: 374 GKMIVSKPLYV 384
           GK +  + + V
Sbjct: 56  GKEVKGRRINV 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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR-----SLGYGYVNYANPADAA 85
           +L+V +L+F+ T+  L D F  +   +  RV      +R     S+G+G+V +     A 
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 86  RALDVLNFTPLNNKSIRIMYSHR 108
            AL  ++   L+  ++ + +SHR
Sbjct: 62  AALKAMDGFVLDGHTLVVKFSHR 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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 5/53 (9%)

Query: 42 TDSQLYDLFSQVGQVLSVRV--CRDLSTRRSLGYGYVNYANPADAARALDVLN 92
            S + DLF Q G++LS+R    R   TRR   + YV + +P  AA A+ +LN
Sbjct: 13 DQSDIRDLFEQYGEILSIRFPSLRFNKTRR---FCYVQFTSPESAAAAVALLN 62

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 7/78 (8%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD--LSTRRSLGYGYVNYANPADAARAL 88
           ++YVG+LD   T  QL + FSQ G+V  VR+  D    TR    Y +V +A       AL
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR----YAFVEFAEQTSVINAL 61

Query: 89  DVLNFTPLNNKSIRIMYS 106
             LN      + +++ +S
Sbjct: 62  K-LNGAMFGGRPLKVNHS 78

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 42.8 bits (100), Expect = 2e-05
 Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA--NPADAA 85
          L++G L F  TD  L + F + G +    V RD  T+RS G+G+V Y+     DAA
Sbjct: 5  LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 2/66 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           L++ +L   +D+  +K  F+  G T+ S K++R+  +G   G  FV F+    A R L +
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 372 MNGKMI 377
           +NGK I
Sbjct: 62  LNGKPI 67

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 24/75 (32%), Positives = 39/75 (52%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L V  L    T+  L ++FS+ G +  V +  D  +RRS G+ +V + N  DA  A +  
Sbjct: 12  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 92  NFTPLNNKSIRIMYS 106
           N   L+ + IR+ +S
Sbjct: 72  NGMELDGRRIRVDFS 86

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 371
           +++  L      + LK+ F++FG +T C +  DP +G S+G GF+ F       + L + 
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 372 ---MNGKMIVSK 380
              ++G++I  K
Sbjct: 62  EHRLDGRLIDPK 73

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|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 = 43.1 bits (102), Expect = 2e-05
 Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++I +L K +  + L + F  +G I S  +        +G  +V  E ++ A  A+ KL 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-----PRGCAYVCMETRQDAHRALQKLR 59

Query: 180 GMLINDKQV 188
            + +  K++
Sbjct: 60  NVKLAGKKI 68

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++ ++D+ +  + L   FS+ G ++ C++  D +   + F F++F ++E A+ A+    
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR-FAFIEFTDEEGARAALSLSG 63

Query: 180 GML 182
            ML
Sbjct: 64  TML 66

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           L++  L      E L+  FS++G +  C +M+D  +  S+G GFV F  P      LA  
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 371 --EMNGKMIVSKP 381
              ++G+ I  KP
Sbjct: 62  PHTLDGRTIDPKP 74

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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 21/61 (34%), Positives = 32/61 (52%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + VKNL    T +D++ +F  YG + S  V +  D  ++ F FV F  A +A  A+ AL 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 271 G 271
            
Sbjct: 63  D 63

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + VKN    TT E+L+ +F  +G +T  ++   G         V F N   A  A +A
Sbjct: 1   TTILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAG-----TIAIVEFANPQQARLAFKA 55

Query: 269 LNGKKFDDREWYVGKA 284
           L  ++F D   Y+ K 
Sbjct: 56  LAYRRFKDSILYLEKG 71

This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 3/66 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTIT-SCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           L++ +L   +D+  +K++++  G    + KV+R   SG++ G  FV F +P  A  AL+ 
Sbjct: 2   LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS- 60

Query: 372 MNGKMI 377
           +NG  I
Sbjct: 61  LNGTPI 66

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|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 47.8 bits (113), Expect = 2e-05
 Identities = 32/101 (31%), Positives = 40/101 (39%), Gaps = 10/101 (9%)

Query: 406 PVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMP 465
           P +  P      P  PP P  L Q  ++ Q  P+  PPQ  FG  Q  VP +       P
Sbjct: 259 PSSRHPQSSHHGPG-PPMPHALQQGPVFLQ-HPSSNPPQ-PFGLAQSQVPPLPLPSQAQP 315

Query: 466 NFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPP 506
           +   P      Q Q+P       P +Q   P P MPH  PP
Sbjct: 316 HSHTPPSQSALQPQQP-------PREQPLPPAPSMPHIKPP 349

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

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 371 --EMNGKMIVSK 380
             E++ K I  K
Sbjct: 63  RHELDSKTIDPK 74

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|241046 cd12602, RRM2_SF2_plant_like, RNA recognition motif 2 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 8/69 (11%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V V  L  S + +DLK      G +  + V RDG G +   G V+F N DD   A+    
Sbjct: 3   VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTT---GIVDFTNYDDMKYAI---- 55

Query: 271 GKKFDDREW 279
            +K DD E+
Sbjct: 56  -RKLDDTEF 63

This subfamily corresponds to the RRM2 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 76

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 29/97 (29%), Positives = 50/97 (51%), Gaps = 16/97 (16%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           ++FV+N+ ++T  EDL++ FG YG I    V  D    + + F ++ FE+  DA  A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKET 305
           LN      R+W  G+         +++ QF Q  ++T
Sbjct: 62  LN------RKWVCGR---------QIEIQFAQGDRKT 83

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 36/70 (51%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           IFI  L + +    L       G I   ++  D +G ++G+ FV F NK+ A+NAI +LN
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63

Query: 180 GMLINDKQVF 189
              I + ++ 
Sbjct: 64  NYEIRNGRLL 73

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++ NLD+ +  + L + F   G +++  I  D  +   +G+GFV+F ++E A  AI  +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 179 NG 180
           N 
Sbjct: 61  NM 62

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

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 23/72 (31%), Positives = 41/72 (56%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+++VG++   V+D  +  L  + G+VLS +  +D ST +   +G+  + +P  A RAL 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 90  VLNFTPLNNKSI 101
           +LN   L  K +
Sbjct: 61  LLNGLELGGKKL 72

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           V++ +L     + +L+K F ++GT+T   + R    GKSK + FV FE+ + A    E +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 270 NG 271
           N 
Sbjct: 62  NN 63

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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV+NL    T + LK+ F + G +  A +  + +GKSK  G V F++ + A KA   +N
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 271 GKKFDDRE 278
           G K + RE
Sbjct: 61  GIKINGRE 68

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y+ ++   + +E+L  LFS  G +  C+V  DP+ + + + F+ F T EE +RA   ++
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFA-FIEF-TDEEGARAALSLS 62

Query: 374 GKMIVSKPLYV 384
           G M+   P+ V
Sbjct: 63  GTMLGFYPVRV 73

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 120 IFIKNLDKSIDHKALH----DTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           +F+ +L  S     L     + FS +G ++  K+  D   +   + FVQF N + A+NA+
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRP--YAFVQFTNDDDAKNAL 62

Query: 176 DKLNGMLIN 184
            K  G +++
Sbjct: 63  AKGQGTILD 71

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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           I I N+   +  + L    S++G + +C ++ T     +     V +E+ E AQ A++KL
Sbjct: 3   IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATV---NVTYESPEQAQQAVNKL 59

Query: 179 NG 180
           NG
Sbjct: 60  NG 61

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) 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 = 76

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L + NL  S   E+ +EL   +G I  C  V  + +G SKG GFV +   + AS+A  E+
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 373 NGKMIVSKPLYV 384
            GK +    L+ 
Sbjct: 62  LGKQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIA-TDGSGQSKGFGFVQFENKESAQNAIDKLNG 180
           + NL  S   +   +   ++GNI  C +  ++ +G SKG+GFV++  K+SA  A  +L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 181 MLINDKQVFV 190
             + +  +F 
Sbjct: 64  KQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 42.9 bits (100), Expect = 3e-05
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
          +Q   T+LY+  L  N TD  L  L    G+++S +   D +T +  GYG+V++ +PA A
Sbjct: 3  DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAA 62

Query: 85 ARALDVL 91
           +A+  L
Sbjct: 63 QKAVSAL 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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 42.9 bits (100), Expect = 3e-05
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 9/85 (10%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N++++ L  +TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV A
Sbjct: 9   NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSA 68

Query: 269 LNGKKFDDREWYVGKAQKKSEREQE 293
           L             +AQ   ++EQ+
Sbjct: 69  LKASGV--------QAQMAKQQEQD 85

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

 Score = 42.4 bits (99), Expect = 3e-05
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+ NL   + +  + +LFS+ G   SCK++ + +  +    FV F    +A+ ALA MN
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMN 60

Query: 374 GKMIVSKPLYV 384
           G+ I+ K + V
Sbjct: 61  GRKILGKEVKV 71

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|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
           +KNL + + ++ L + FS FG +    +  D  G+  G G V+F  K SA+ A+D+
Sbjct: 4   VKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDR 59

This subgroup corresponds to the RRM2 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. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer 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 = 80

>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 42.1 bits (99), Expect = 3e-05
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 136 DTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           + F  FG +L  +I      Q + FGFV FEN E+ +  + K N   I   +V V
Sbjct: 18  EYFGQFGPVLDVRIP---YQQKRMFGFVTFENAETVKRILSKGNPHFICGSRVRV 69

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 12/82 (14%)

Query: 314 LYIKNLGDSIDDEKLKE----LFSEFG---TITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
           +YI NL D I  E+LK     LFS+FG    I + K M+      +G  FV F     A+
Sbjct: 4   IYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMK-----MRGQAFVIFKELSSAT 58

Query: 367 RALAEMNGKMIVSKPLYVAVAQ 388
            AL ++ G     KP+ +  A+
Sbjct: 59  NALRQLQGFPFYGKPMRIQYAK 80

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NLG +  +E+L++LFS        K+     G      FV F     A++AL  + 
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGP---VCFVEFEDVSFATQALNSLQ 61

Query: 374 GKMIVSK 380
           G ++ S 
Sbjct: 62  GAVLSSS 68

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTF-SSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI N+   +  + L D F    G +   ++  D  G+S+G G V+F++KES Q A++ +
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETM 61

Query: 179 NGMLINDKQVFV 190
           N   +  +++ V
Sbjct: 62  NRYELKGRKLVV 73

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

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG L  +VT+ +  + FSQ G+V+  ++ +D  T RS G+G+V + +   A   +   
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 92  NFTPLNNKSIRI 103
               L  K + +
Sbjct: 61  GMLELGGKQVEV 72

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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE-- 267
           +F+  L   TT +DLK  F ++G +    +  D   G+S+ FGFV F+ ++   K ++  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 268 --ALNGKKFDDRE 278
              LNGK  D + 
Sbjct: 61  EHKLNGKVIDPKR 73

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 371
           ++I  L      + LK+ FS+FG +  C +  DP +G S+G GFV F   E   + + + 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 372 ---MNGKMIVSK 380
              +NGK+I  K
Sbjct: 61  EHKLNGKVIDPK 72

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 322 SIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 374
           S+  E+L  LF     +  C + RDP +G SKG  +V +S P  A  A  ++NG
Sbjct: 10  SVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 63

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

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG L  +V +  L + FSQ G V    V  D  T +  G+G+V Y    D+A    V+
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFV-YFQNHDSADKAAVV 60

Query: 92  NFTPLNNKSIRI 103
            F P+N   + +
Sbjct: 61  KFHPINGHRVEV 72

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

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 21/58 (36%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA--NPADAARA 87
          L++G L F  T+  L + + Q G++    V RD +++RS G+G+V ++  N  DAA A
Sbjct: 5  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 7/69 (10%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F++NL  ++  + L  +FS FG +   K       + K + FV FE +++A  A+D++N
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEERDAAVRAMDEMN 56

Query: 180 GMLINDKQV 188
           G  I  +++
Sbjct: 57  GKEIEGEEI 65

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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 269
           V ++ L  S T+ED++  F         + +  D DG+     +V F + +DA +A+   
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRAL-RK 60

Query: 270 NGKKFDDR 277
           +  K   R
Sbjct: 61  HNNKMGGR 68

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 7/64 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VF+  L+ +  ++D+++ F  YG I      RD D K + FGFV F++  DA  AV  L+
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRI------RDIDLK-RGFGFVEFDDPRDADDAVYELD 54

Query: 271 GKKF 274
           GK+ 
Sbjct: 55  GKEL 58

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 314 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           L ++N+  +  +  KL E FS+FGTI + +V       +  S  V FST EEA +A  
Sbjct: 4   LEVRNIPPELNNITKLNEHFSKFGTIVNIQV-----NYNPESALVQFSTSEEAKKAYR 56

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 8/65 (12%)

Query: 120 IFIKNLDKSIDHKA-LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI NL+  +  K+ +   FS +G I+ C +        KGF FVQ+ N+ +A+ A+   
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 56

Query: 179 NGMLI 183
           +G +I
Sbjct: 57  DGRMI 61

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 41.7 bits (98), Expect = 4e-05
 Identities = 25/64 (39%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           ++FV NL+ +   ++LK    E+ +  +  V     G SK FG+V+FE+A+D  KA+E L
Sbjct: 2   SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKALE-L 60

Query: 270 NGKK 273
            GKK
Sbjct: 61  TGKK 64

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin 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. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 41.7 bits (99), Expect = 5e-05
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 10/72 (13%)

Query: 212 FVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFG--FVNFENADDAAKA 265
           ++ NL+E    ++LK+    +F ++G +   V  +      K  G  FV F++ + A  A
Sbjct: 3   YINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK----TLKMRGQAFVVFKDVESATNA 58

Query: 266 VEALNGKKFDDR 277
           + AL G  F D+
Sbjct: 59  LRALQGFPFYDK 70

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|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 = 41.8 bits (99), Expect = 5e-05
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 4/59 (6%)

Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFG----FVQFENKESAQNAIDKLNGMLINDKQV 188
           + +    +G +LS  I    +      G    FV+F + E AQ A   L G   + + V
Sbjct: 28  VKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTV 86

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 20/50 (40%), Positives = 31/50 (62%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP 81
          L+VG+L + V   +L + FSQ G+V S  V  D  T  S GYG+V++++ 
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 42.0 bits (99), Expect = 5e-05
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 32  LYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
           ++V  L  + +D +L     + FS+ G ++ V+V RD    R   Y +V + N  DA  A
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDDAKNA 61

Query: 88  LDVLNFTPLNNKSIRI 103
           L     T L+ + IR 
Sbjct: 62  LAKGQGTILDGRHIRC 77

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

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+LYVG L   VT+  L D F Q G++ S+ V      R+     +V +     A +A +
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV----PRQ--QCAFVTFTTREAAEKAAE 55

Query: 90  VL-NFTPLNNKSIRIMYSH 107
            L N   +N + +++ +  
Sbjct: 56  RLFNKLIINGRRLKLKWGR 74

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

>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 7/65 (10%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           N +++ NL  + T EDL+++FG+    +T  V+++ G      + FV++ + + A +A+E
Sbjct: 2   NKLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSG------YAFVDYPDQNWAIRAIE 55

Query: 268 ALNGK 272
            L+GK
Sbjct: 56  TLSGK 60

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L++ N+  S+ +E LKELF++  GT+ + K       ++     +   + EEA  AL  +
Sbjct: 2   LHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMA----LIQMGSVEEAIEALIAL 57

Query: 373 -NGKMIVSKPLYVA 385
            N ++  S  L V+
Sbjct: 58  HNYQLSESSHLRVS 71

This subfamily corresponds to the RRM4 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 = 76

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 41.6 bits (97), Expect = 5e-05
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 9/67 (13%)

Query: 211 VFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           ++V+NL   T+++ +KK FG++  G +     +RD       + FV+F + +DA  A+  
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-------YAFVHFTSREDAVHAMNN 56

Query: 269 LNGKKFD 275
           LNG + +
Sbjct: 57  LNGTELE 63

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL   I +E  K+LF ++G  +   + RD     +G GF+   +   A  A AE++
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 58

Query: 374 GKMIVSKPLYV 384
           G ++ ++PL +
Sbjct: 59  GTILKNRPLRI 69

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

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN--PADAA 85
          L+VG L  +VT+  L + FSQ G V SV +  D  T +  G+ +V + +  P D  
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI 57

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 8/78 (10%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIAT-------DGSGQSKGFGFVQFENKESAQ 172
           ++I NL  S   + L +    F   +S  I +           +  G  + +F + E A+
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDF-EPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 173 NAIDKLNGMLINDKQVFV 190
             +  LNG +  ++++FV
Sbjct: 61  KVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
           ++  L   + +  L E FS+ G +   +++RD  S  SKG  +V F   E    AL  + 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LT 61

Query: 374 GKMIVSKPLYV 384
           G+ ++ +P+ V
Sbjct: 62  GQRLLGQPIMV 72

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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+++  L  +     L   FS +G ++  KI T+  S  ++ FGFV   + E A   I  
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 178 LNGMLINDKQVFV 190
           L+   ++ + + 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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 11/84 (13%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEASRALAEM 372
           L++ NL   I +++LKE F EFG +   ++  +   G     GFV F  PE   + LA  
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA-- 63

Query: 373 NGKMIVSKPLYVAVAQR--KEERR 394
                 +KP+Y     R   EE++
Sbjct: 64  ------NKPIYFRGDHRLNVEEKK 81

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

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 7/64 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V++  L     ++D+++ FG YG +   + +++G      +GFV FE++ DA  AV  LN
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLE-IDLKNG------YGFVEFEDSRDADDAVYELN 54

Query: 271 GKKF 274
           GK  
Sbjct: 55  GKDL 58

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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTI-------TSAV-VMRDGD-GKSKCFGFVNFENADD 261
           VFV NL  +TT++DL + FG  G I          + + +D D G+ K    V +++   
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 262 AAKAVEALNGKKF 274
           A+ A+E  N K F
Sbjct: 61  ASAAIEWFNNKDF 73

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

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 7/61 (11%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++++NL  S   + L + FS +G +   K   D       + FV FE ++ A  A++++N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 180 G 180
           G
Sbjct: 57  G 57

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

 Score = 40.8 bits (96), Expect = 7e-05
 Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 127 KSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID 176
           KS   + L + F  FG+I    I  D  +G+SKGFG+V+F     A  A++
Sbjct: 10  KSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 41.2 bits (97), Expect = 7e-05
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEA 268
           +FV NL    T+++LK+ F E+G +    +  + G G+   FGFV F++ +   K +  
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

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

 Score = 41.2 bits (97), Expect = 7e-05
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 33  YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD--LSTRRSLGYGYVNYANPADAARALDV 90
           +VG +D ++++  L + FS  G+V  VR+C D   S R    + +V +A+   A  AL+ 
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR----FAFVEFADAESALSALN- 58

Query: 91  LNFTPLNNKSIRIMYS 106
           L+ T L    +R+  S
Sbjct: 59  LSGTLLGGHPLRVSPS 74

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 41.1 bits (96), Expect = 7e-05
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  + +  +   L D F  +G I   +I TD GSG+ +GF FV F++ +S    +DK+
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS----VDKI 58

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 41.4 bits (97), Expect = 7e-05
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 12/81 (14%)

Query: 210 NVFVKNLDEST-----TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           NV++ N+ +        +++L+K   +YG I S  ++R+     K   F+NF N  +A  
Sbjct: 4   NVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE-----KACAFINFMNIPNAIA 58

Query: 265 AVEALNGKK--FDDREWYVGK 283
           A++ LNGKK          GK
Sbjct: 59  ALQTLNGKKPYDTIVRINYGK 79

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

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 9/66 (13%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN-- 270
           V NLD S +++DL +IFG YG I     +R+   K +   F+ F +   A  A++ALN  
Sbjct: 6   VFNLDPSVSNDDLHQIFGAYGEIKE---IRETPNK-RHHKFIEFYDVRSAEAALKALNRS 61

Query: 271 ---GKK 273
              GK+
Sbjct: 62  EIAGKR 67

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|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 12/75 (16%)

Query: 210 NVF-VKNLDESTTDEDLKK-IFGE---YGTITSAVVMRDGDGKSKCFG--FVNFENADDA 262
           N+F      E   D+++K+ +  E   +G +    V      K+   G  +V F+  + A
Sbjct: 8   NMFDPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVD-----KNSPEGVVYVKFKTVEAA 62

Query: 263 AKAVEALNGKKFDDR 277
            K ++ALNG+ FD R
Sbjct: 63  QKCIQALNGRWFDGR 77

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|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 7/69 (10%)

Query: 210 NVFVKNLDESTTDEDLKK-IFGEY---GTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
            + VKNL   ++D  LK  +F E+   G +TS  V   G G  + +  V F   +DA KA
Sbjct: 1   GIIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKVH--GTGSER-YAIVFFRKPEDAEKA 57

Query: 266 VEALNGKKF 274
           +E   GK F
Sbjct: 58  LEVSKGKLF 66

This subfamily corresponds to the RRM2 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 8/72 (11%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYV +L  + T+ QL +LFS+ G+V  V+  +D        Y +V++    DA +A++ +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 92  NFTPLNNKSIRI 103
           N   L    I +
Sbjct: 56  NGKELEGSPIEV 67

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|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 = 40.9 bits (96), Expect = 8e-05
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           +++ N+     +E+LK++FSE G + S +++ D  +G  KG GF  +   E A  A+  +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 373 NGKMIVSKPLYVAVA 387
           NG  +  + L V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L  ++T+ +L + F + G VL VR+       R   +G+V + +P    + L   
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA-- 63

Query: 92  NFTPLNNKSIRIMYSHR 108
                 NK I     HR
Sbjct: 64  ------NKPIYFRGDHR 74

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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NLD +TT + L + F + G +   V M   + +   + FV F        A+  LN
Sbjct: 7   IYVGNLDPTTTADQLLEFFSQAGEV-KYVRMAGDETQPTRYAFVEFAEQTSVINAL-KLN 64

Query: 271 GKKFDDR 277
           G  F  R
Sbjct: 65  GAMFGGR 71

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>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 = 41.1 bits (97), Expect = 8e-05
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          T L V ++ F  T  +L +LFS  GQV SVR+ +        G+ +V +    +A  A++
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEAQNAME 59

Query: 90 VLNFTPL 96
           L  T L
Sbjct: 60 ALKSTHL 66

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

 Score = 41.1 bits (96), Expect = 8e-05
 Identities = 19/66 (28%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 132 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           + L + FS +G +    +  D  +G+S+GF FV FE  + ++ A++  NGM ++ +++ V
Sbjct: 14  RDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRV 73

Query: 191 GHFLRK 196
            + + K
Sbjct: 74  DYSITK 79

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             ++VG +  ++ + +L  LF + G +  +R+  D S   + GY +V Y N   A RA+ 
Sbjct: 2   CEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVK 60

Query: 90  VLNFTPLNNKSIR 102
                 L+N  IR
Sbjct: 61  Q-----LHNYEIR 68

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 314 LYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +++K    S+ ++ ++    E FS  G IT   +  D  +G SKG  ++ F + +   +A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 369 LAEMNGKMIVSKPLYV 384
           L E++G  +    L V
Sbjct: 62  L-ELDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 41.1 bits (96), Expect = 8e-05
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
          +++G L +  T   L + F Q G+V    V RD  T+RS G+G+V + + A   + L
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
           V NL  S T E+ +++   YG I    +V  +  G SK +GFV +   D A+KA   L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 272 KKFDDREWYV 281
           K+  +   + 
Sbjct: 64  KQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 41.1 bits (96), Expect = 8e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +YI NL + +  E+LK+    +FS+FG I     ++      +G  FV F     A+ AL
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVVFKDISSATNAL 59

Query: 370 AEMNGKMIVSKPLYVAVAQ 388
             M G     KP+ +A ++
Sbjct: 60  RSMQGFPFYDKPMRIAYSK 78

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 5/64 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++  LG      +L+  F  FG I             +   ++ + + E A  A   + 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG-----RNYAYIEYESIEAAQAAKEALR 55

Query: 374 GKMI 377
           G  +
Sbjct: 56  GFPL 59

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|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 41.5 bits (98), Expect = 8e-05
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 374
             NL D+ID+  LK++  ++G +   K+   P +    G   V F + + A R + ++N 
Sbjct: 7   FSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQ 66

Query: 375 KMIVSKPLYV 384
             ++ K + V
Sbjct: 67  TSVMGKIIKV 76

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 41.2 bits (96), Expect = 8e-05
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V+NL  STT+E ++K   E+ +I    V R    K + + FV+F N +DA  A+ ALN
Sbjct: 11  LYVRNLMLSTTEETIEK---EFNSIKPGAVERVK--KIRDYAFVHFSNREDAVDAMNALN 65

Query: 271 GKKFD 275
           GK  D
Sbjct: 66  GKVID 70

This subgroup corresponds to the RRM3 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. ACF 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 = 83

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

 Score = 45.3 bits (107), Expect = 9e-05
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           +YI NL   + ++++KEL   FG + +  +++D  +G+SKG  F  +  P     A+A +
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 373 NGKMIVSKPLYVAVA 387
           NGK      L+V  A
Sbjct: 358 NGKDTGDNKLHVQRA 372

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

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 9/59 (15%)

Query: 32 LYVGDLD-FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          ++VG+L+   V+   L ++FS+ G++L + + +        GYG+V + N  DA  A+ 
Sbjct: 3  VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK--------GYGFVQFDNEEDARAAVA 53

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|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 5/60 (8%)

Query: 46  LYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY 105
           L D   Q G V    V      R   G G V + +  D  RAL  L+ T    + +R+  
Sbjct: 17  LKDFGRQAGDVTYADV-----DRDQEGEGVVEFTSQEDMERALRKLDGTEFRGRRVRVEE 71

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 41.1 bits (96), Expect = 9e-05
 Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++K L +   +E LKE F   G+I +  V    +G SKG GFV FS+ E+A  A   M 
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60

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

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE- 371
           +++  L  ++ +  L++ FS+FGT+T   VM D      +G GF+ F + +   + + E 
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 372 ---MNGKMIVSK 380
              +NGK +  K
Sbjct: 65  FHDINGKKVEVK 76

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|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 = 9e-05
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +FI  + K  +   +   FS FG I  C+I     G S+G  FV F  +  AQ AI  ++
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NL  S T++D+ ++F   G +  A ++R G  +      V +   DDA  A++  N
Sbjct: 3   LVVSNLHPSVTEDDIVELFSAIGALKRARLVRPGVAE------VVYVRKDDALTAIDKYN 56

Query: 271 GKKFDDRE 278
            ++ D + 
Sbjct: 57  NRELDGQP 64

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. 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. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 40.8 bits (95), Expect = 9e-05
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 7/69 (10%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           V N+  S T+++L+  F EYG +    +++D       + FV+ E A+DA +A+  L+  
Sbjct: 5   VGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLDNT 57

Query: 273 KFDDREWYV 281
           +F  +  +V
Sbjct: 58  EFQGKRMHV 66

This subgroup corresponds to the RRM2 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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NL     + D++ +F +YG I  A+ +++       F FV FE+  DA  AV   +
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPI-KAIDLKNRRRGPP-FAFVEFEDPRDAEDAVRGRD 59

Query: 271 GKKFD 275
           G  FD
Sbjct: 60  GYDFD 64

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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 8/64 (12%)

Query: 212 FVKNL-DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           F+ NL  +  + EDL +IF  YG +   V+          +GFV F++ +  A A+    
Sbjct: 3   FIGNLPTKRVSKEDLFRIFSTYGELAQIVL-------KNAYGFVQFDSPESCANAINCEQ 55

Query: 271 GKKF 274
           GK  
Sbjct: 56  GKMI 59

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.9 bits (95), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF   E+ +     +   
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 270 NGK 272
           NGK
Sbjct: 62  NGK 64

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 40.9 bits (95), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 35/63 (55%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+++ NL  S  +++L+ +   +G + S  ++RD +G S+  GF   E+ +     ++  
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 270 NGK 272
           NGK
Sbjct: 63  NGK 65

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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           VFV  L     + DL + F + G +    ++RD +  +SK   +V F + +    A+  L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60

Query: 270 NGKKF 274
            G++ 
Sbjct: 61  TGQRL 65

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

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 8/74 (10%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYV     + ++S + ++FS  G V  V++           + +V + +   A RA D +
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDSV 53

Query: 92  NFTPLNNKSIRIMY 105
           +   LNN  + + Y
Sbjct: 54  HGKVLNNNPLYVTY 67

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

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

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           +++  L      + LKE FS+FG +  C +  DP +G S+G GFV F       + L   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 371 --EMNGKMIVSK 380
             +++G++I  K
Sbjct: 61  EHKLDGRVIDPK 72

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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 27/85 (31%), Positives = 48/85 (56%), Gaps = 13/85 (15%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           GAS N      +Y+G++D ++T+ +L + FSQ G++ SV   R+ +        +VN+ N
Sbjct: 1   GASRN------VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNC------AFVNFTN 48

Query: 81  PADAARALDVLNFTPLNNKSIRIMY 105
            ++A +A+D +   PL  K  +I Y
Sbjct: 49  ISNAIKAIDGVKSHPL-FKKFKISY 72

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID-- 176
           +F+  L      + L   FS +G ++ C I  D  + +S+GFGFV+F++       +   
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 177 --KLNGMLINDK 186
              L+G  I+ K
Sbjct: 62  PHTLDGRTIDPK 73

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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 38/74 (51%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +KNL      + ++ LFS +G + S +V +     ++G  FV FST +EA  A+  + 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 374 GKMIVSKPLYVAVA 387
              ++ + L +  A
Sbjct: 63  DTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
           G + + NLD  I  + L   FS FG +    I       S+   FV+F +  +A+ A+D 
Sbjct: 2   GTLLVFNLDSPISDQELRSLFSQFGEVKD--IRETPLRPSQ--KFVEFYDIRAAEAALDA 57

Query: 178 LNGMLINDKQV 188
           LNG      ++
Sbjct: 58  LNGRPFLGGRL 68

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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 6/61 (9%)

Query: 324 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 383
            +++L+++FS++G ++   V+       KGS  V F++ + A  A+    G    S PL 
Sbjct: 17  SEDELRKIFSKYGDVSDV-VVSSKK---KGSAIVEFASKKAAEAAVENECGL--PSNPLL 70

Query: 384 V 384
           V
Sbjct: 71  V 71

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 14/60 (23%), Positives = 34/60 (56%), Gaps = 7/60 (11%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL    T+++++ +F +YG +    ++++       +GFV+ ++   A +A+  L+
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN-------YGFVHMDDKTAADEAIRNLH 55

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

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 13/47 (27%), Positives = 32/47 (68%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 360
           +++  +   +D+ +++  F+++G++   K++ D +G+SKG GFV+F 
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFY 54

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 40.9 bits (95), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 35/63 (55%)

Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           T+LY+  L    TD  L  L    G+++S +   D +T +  GYG+V++ +P+ A +A+
Sbjct: 1  KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 89 DVL 91
            L
Sbjct: 61 TAL 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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 315 YIKNLGDSIDDEKLKELF-SEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +I N+   +  + LK+LF  + G +T  ++ +D  G S+G G V F   E   +AL  MN
Sbjct: 3   FISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMN 62

Query: 374 GKMIVSKPLYV 384
              +  + L V
Sbjct: 63  RYELKGRKLVV 73

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

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 11/82 (13%)

Query: 29  TTSLYVGDLDF-----NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPAD 83
           + ++Y+G++       N+ + +L     + G++ S+R+ R+          ++N+ N  +
Sbjct: 2   SRNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREK------ACAFINFMNIPN 55

Query: 84  AARALDVLNFTPLNNKSIRIMY 105
           A  AL  LN     +  +RI Y
Sbjct: 56  AIAALQTLNGKKPYDTIVRINY 77

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

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD--GSGQSKGFGFVQFENKESAQNAIDK 177
           I ++N+      K L + FS+FG + + ++     G+G  +GFGFV F  K+ A+ A   
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 178 L 178
           L
Sbjct: 63  L 63

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 4/65 (6%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           V NL  S +++ L+++F +  +I     +   +G+ K + FV FE+A+DA +A+ + N  
Sbjct: 6   VNNLSYSASEDSLQEVFEKATSIR----IPQNNGRPKGYAFVEFESAEDAKEALNSCNNT 61

Query: 273 KFDDR 277
           + + R
Sbjct: 62  EIEGR 66

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+V +++ NV D +L  LF Q G + ++      +  +  G+  V+Y +   A RA   L
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTL-----YTACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 92  NFTPLNNKSIRIMYS 106
             T L  + + I +S
Sbjct: 59  QGTELGGRKLDIHFS 73

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|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 45.0 bits (106), Expect = 1e-04
 Identities = 40/181 (22%), Positives = 53/181 (29%), Gaps = 5/181 (2%)

Query: 398 QAQFSQMRPVAMGP-SVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPG 456
           Q Q   M     GP        M  PG  G G Q    Q        Q     QQQL   
Sbjct: 174 QGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQ 233

Query: 457 MRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLG 516
                  M     P  +Q Q GQ+  G+ G  P Q     + +   Q PP+    +  LG
Sbjct: 234 Q---QQQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLG 290

Query: 517 RNMQDF-PFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLG 575
                      G       P+      P      GQ +    +S         + R + G
Sbjct: 291 MLPNQMQQMPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQMKLRNMRG 350

Query: 576 E 576
           +
Sbjct: 351 Q 351

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++   +   +  + +  TFS FG I+  ++  D     KG+ FV+F + ESA +AI  +N
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD-----KGYSFVRFNSHESAAHAIVSVN 57

Query: 180 GMLI 183
           G  I
Sbjct: 58  GTTI 61

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

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +Y+  +     +++++  FS  G I    +M  P +G  +G  F+ F T E A RALA +
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 373 NGKMIVSKPLYV 384
           +G+ +  + L V
Sbjct: 60  DGEDMGGRFLKV 71

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 266
           N + ++ L  S T+ED++     +G       +MR    G S+ F FV F + ++A + +
Sbjct: 3   NTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWM 62

Query: 267 EALNGK 272
           E   GK
Sbjct: 63  ELNQGK 68

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 6/65 (9%)

Query: 215 NLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 273
           N+ ++  +E +K  F + G  +    +  D +G       V FE+  DA KA  +LNG +
Sbjct: 7   NVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG-----ALVEFESPSDAGKASLSLNGSQ 61

Query: 274 FDDRE 278
           F  + 
Sbjct: 62  FGGKT 66

This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           L +KNL   + +E L++ FS+FG +    V+ D  G   G GFV F+    A +AL
Sbjct: 2   LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL 57

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 5/67 (7%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCR--DLSTRRSLGYGYVNYANPADAARA 87
          + + V +L   VT+ +L + F   G+V  V+V R  D  +RR   +G+V + +  DA +A
Sbjct: 1  SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRR---FGFVGFKSEEDAQQA 57

Query: 88 LDVLNFT 94
          +   N T
Sbjct: 58 VKYFNKT 64

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           V+V NLDE  T+E L ++F + G + +  + +D      + +GFV F + +DA  A++ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 270 NGKK 273
           N  K
Sbjct: 61  NMIK 64

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|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 = 40.6 bits (96), Expect = 2e-04
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 11/70 (15%)

Query: 318 NLGDSIDDEKLKELF-------SEFGTITSCKVMRDPSGISKGSG----FVAFSTPEEAS 366
              +  DDE+ +E+         ++G + S  + R  +      G    FV F+  E+A 
Sbjct: 11  TPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQ 70

Query: 367 RALAEMNGKM 376
           +A   + G+ 
Sbjct: 71  KAQLALAGRK 80

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           + +++ N+ +    E+L+ LF  +G + SC VMR          FV       A RA+ E
Sbjct: 1   VKIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-------FAFVHLRGEAAADRAIEE 53

Query: 372 MNGKMIVSKPLYV 384
           +NG+ +  + L V
Sbjct: 54  LNGRELHGRKLVV 66

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           ++I  L      + L E  S FG +  C +  DP +G S+G GFV F       + L   
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 371 --EMNGKMIVSK 380
             +++GK+I  K
Sbjct: 62  EHKLDGKLIDPK 73

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
           FV  + +S T E L ++F     +    + RD   GKSK F +V + N   A  A E LN
Sbjct: 4   FV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLN 62

Query: 271 GKKF 274
           G ++
Sbjct: 63  GFEY 66

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           T  ++VG L  NVT++ L   FSQ G V  V V  D   +R  G+G++ + +  D+   +
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES-EDSVDQV 60

Query: 89  DVLNFTPLNNKSIRI 103
              +F  +N K + +
Sbjct: 61  VNEHFHDINGKKVEV 75

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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 268
           +FV  L   T+ +DLK  F ++G +T   +  D + G+S+ FGF+ F++A    K +E  
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 269 ---LNGKKFDDRE 278
              L+G+  D ++
Sbjct: 62  EHRLDGRLIDPKK 74

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 5/60 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N+YI NL +S  +E+L+E   +FG I   K++++     K   FV F +   A + +  +
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTL 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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 39.8 bits (94), Expect = 2e-04
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN-YANPADAARALDV 90
          L+VG L  +VT+S L + FS+ G V  V + +        G+ Y++   + A   +    
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 91 LN 92
          LN
Sbjct: 62 LN 63

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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +YI NL + I  ++LK+    +FS FG I    V R      +G  FV F     A+ AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 63

Query: 370 AEMNGKMIVSKPLYVAVAQRKEE 392
             M G     KP+ +  A+   +
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSD 86

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 5/64 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++  L + +  K L D F  FG I S  +        +   FV F  +E+A+ A ++L 
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVV-----PRQQCAFVTFTTREAAEKAAERLF 58

Query: 180 GMLI 183
             LI
Sbjct: 59  NKLI 62

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

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 269
           VFV NL     +E L ++FG+ G I    ++RD      K F +V F++ +   KA+  L
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL-LL 60

Query: 270 NGKKF 274
           N KKF
Sbjct: 61  NEKKF 65

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 7/73 (9%)

Query: 117 TGNIFIKN--LDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           T ++ + N  L   +  + L   F  +G +    +        K + FV + + E A  A
Sbjct: 1   TQHLVVANGGLGNGVSREELLRVFEKYGTVEDLVMPPG-----KPYCFVSYSSIEDAAAA 55

Query: 175 IDKLNGMLINDKQ 187
            D LNG  +   Q
Sbjct: 56  YDALNGKELELPQ 68

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
            +L++ NL  + D ++LK   SEF +  +  V     G SK  G+V F + E+  +AL E
Sbjct: 1   FSLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKAL-E 59

Query: 372 MNGKMIVSKPL 382
           + GK ++   +
Sbjct: 60  LTGKKLLGNEI 70

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin 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. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
           FV+N++ +  DE+L+ +F ++G I +         K + F  V++ +   A +A  AL G
Sbjct: 5   FVRNINSNVEDEELRALFEQFGDIRTLY----TACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 272 KKFDDR 277
            +   R
Sbjct: 61  TELGGR 66

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|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
           +KNL   + ++ L   FS FG +    +  D  G+  G GFV+F  K +A+ A+++
Sbjct: 4   VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALER 59

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y   +   + ++ +++ FS FG I   +V  +     KG  F+ FST E A+ A+  +N
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVN 57

Query: 374 GKMI 377
           G  I
Sbjct: 58  GTTI 61

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

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 4/60 (6%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           + NLD + + E L+ IF  YG +     +R+   K +   FV F +  DAAKA+ A+NGK
Sbjct: 6   IFNLDPTVSSETLRSIFQVYGDVKE---LRETPCK-REQRFVEFFDVRDAAKALRAMNGK 61

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 18/61 (29%), Positives = 33/61 (54%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          L+VG +   +T+ ++  +F + G VL V + +D  T    G  +V Y+   +A RA+  L
Sbjct: 2  LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 92 N 92
          +
Sbjct: 62 H 62

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 15/64 (23%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           +FV ++  + T+++++ +F E+G +    +++D   G  +   FV +   D+A +A+ AL
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 270 NGKK 273
           + ++
Sbjct: 62  HNQR 65

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|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           L ++NL   + +E L+E FS+FG +    V+ D  G S G G V F++   A +A 
Sbjct: 2   LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAF 57

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           VFV  L E  T+EDL++ F ++G +T   + +        F FV F + + A  
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRA----FAFVTFADPEVAQS 52

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

>gnl|CDD|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 = 40.5 bits (95), Expect = 2e-04
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
           FV  +  +  ++DL+ +F ++G I    V++D   G  K   F+ +   + A KA  AL+
Sbjct: 9   FVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSALH 68

Query: 271 GKK 273
            +K
Sbjct: 69  EQK 71

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

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 9/67 (13%)

Query: 211 VFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           ++V+NL  STT+E +K  F ++  G +     +RD       + FV+F N +DA  A+  
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-------YAFVHFFNREDAVAAMSV 56

Query: 269 LNGKKFD 275
           +NGK  D
Sbjct: 57  MNGKCID 63

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is 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 = 74

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+V NL       +L++ F  YG + +  + R+  G    F FV FE+  DA  AV  L+
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 57

Query: 271 GK 272
           GK
Sbjct: 58  GK 59

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

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEY-GTITSAVVMRDGDGKSKC-FGFVNFENADDAAKAV 266
             +FV  L     + +L  +F  + G   S +V ++  G  K   GFV+F +A  AA A+
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 267 EALNGKKFDDREWYV 281
           +AL G +FD     V
Sbjct: 61  DALQGYRFDPDTSSV 75

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 40.2 bits (93), Expect = 2e-04
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N++++ L   TTD+DL K+   YG I S   + D +  + K +GFV+F++   A KAV +
Sbjct: 6   NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65

Query: 269 L 269
           L
Sbjct: 66  L 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 8/72 (11%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L    T  +L  LF + G V    V ++        YG+V+     DA  A+  L
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53

Query: 92  NFTPLNNKSIRI 103
           N      K I +
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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF   E+ +     +   
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 270 NGK 272
           NGK
Sbjct: 62  NGK 64

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 19/87 (21%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQV---------GQVLSVRVCRDLS------TRRSLGYG 74
           T L + +L  +V + +L +LF +           ++  V++ RDL         +S GYG
Sbjct: 1   TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60

Query: 75  YVNYANPADAARALDVLNFTPLNNKSI 101
           +V + N   A +AL  LN    NN  I
Sbjct: 61  FVEFTNHEHALKALRALN----NNPEI 83

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+K L +    + L +   SF   ++ +I TD  +G SKGFGFV F ++E A+ A + +
Sbjct: 3   LFVKGLSEDTTEETLKE---SFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 179 NGMLINDKQV 188
               I+  +V
Sbjct: 60  EDGEIDGNKV 69

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

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 20/73 (27%), Positives = 36/73 (49%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           NL+I NL  ++ + +L+  F ++G I    + R   G      F+ F   + A RA   M
Sbjct: 10  NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 373 NGKMIVSKPLYVA 385
           +G++I   P+ + 
Sbjct: 70  SGRVIGRNPIKIG 82

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

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFG-NILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           +++ +L+  +D   +   F+S G  +LS KI  +  +G   G+ FV+F ++ +A+  + K
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 178 LNGMLIN 184
           LNG  I 
Sbjct: 62  LNGKPIP 68

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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 15/58 (25%), Positives = 33/58 (56%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          ++VG L ++ +   L D F++ G+V    +  D +T RS G+G++ + + +   + L+
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLE 59

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L++  L   + +  L E FS+FG +   +V+ D  +G  +G GFV F   + A +A A +
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA-AVV 60

Query: 373 NGKMIVSKPLYVAVAQRKEE 392
               I    + V  A  KEE
Sbjct: 61  KFHPINGHRVEVKKAVPKEE 80

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

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+++  L  + T +D++ +F  +G I ++ V+ D   G S+   F+ F+   +A +A+ +
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 269 LNGKK 273
            NG K
Sbjct: 62  FNGHK 66

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

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N++I NL +S   + L +    FG I   KI  +     K   FV F +  +A   +  L
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTL 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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITS--AVVMRDGDGKSKCFGFVNFENADDAAKAV 266
             + + N+      EDL  +   YGT+ +   V  +  +  +     V +E+ + A +AV
Sbjct: 1   RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKS-ETATV---NVTYESPEQAQQAV 56

Query: 267 EALNGKKFDD 276
             LNG +++ 
Sbjct: 57  NKLNGHEYEG 66

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) 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 = 76

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+V  L  N   + L +LF + G+VLS +V  +  +  +  YG V  ++ A+ AR +  
Sbjct: 1   NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISH 60

Query: 91  LNFTPLNNKSIRI 103
           L+ T L+ + I +
Sbjct: 61  LHRTELHGQQISV 73

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains 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. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV NL    T+ED KK+F +YG  +   + RD     + FGF+  E+   A  A   L+
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 58

Query: 271 GKKFDDR 277
           G    +R
Sbjct: 59  GTILKNR 65

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

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++I  L   +  K +   F  +G +L   +         G+GFV+FE+   A +A+ +LN
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDL-------KNGYGFVEFEDSRDADDAVYELN 54

Query: 180 GMLINDKQVFVGH 192
           G  +  ++V V H
Sbjct: 55  GKDLCGERVIVEH 67

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V  L   T+  +L++ F  +G I   +    G      + ++ +E+ + A  A EAL 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRR-IDYDPGRN----YAYIEYESIEAAQAAKEALR 55

Query: 271 GKKFDDRE 278
           G       
Sbjct: 56  GFPLGGPG 63

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 9/76 (11%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++  L        L   F  FG I             + + ++++E+ E+AQ A + L 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRID-----YDPGRNYAYIEYESIEAAQAAKEALR 55

Query: 180 GMLINDKQVFVGHFLR 195
           G  +       G  LR
Sbjct: 56  GFPLGGP----GRRLR 67

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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y+ NLG      +L+  FS +G + +  + R+P G +    FV F  P +A  A+  ++
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFA----FVEFEDPRDAEDAVRGLD 57

Query: 374 GKMIVSKPLYVAVA 387
           GK+I    + V ++
Sbjct: 58  GKVICGSRVRVELS 71

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.4 bits (91), Expect = 3e-04
 Identities = 22/66 (33%), Positives = 36/66 (54%)

Query: 26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAA 85
          Q   T+LY+  L    TD  L  L    G+++S +   D +T +  GYG+V++ +PA A 
Sbjct: 1  QLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQ 60

Query: 86 RALDVL 91
          +A+  L
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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE-- 267
           +FV NL   TT EDL   F   G   S  ++ D   GKSK   FV F+ A+   KA++  
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 268 --ALNGKK 273
              L G+K
Sbjct: 63  HTLLKGRK 70

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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEA- 268
           +FV  L   TT+E +++ FG++G I    + M     K + F F+ F++ +   K +E  
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61

Query: 269 ---LNGKKFD 275
              + GKK +
Sbjct: 62  FHVIGGKKVE 71

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS--------AVVMRDGDGKSKCFGFVNFENADDA 262
           +++  L +  T++ L ++FG  G I            +  D + + K    V +++   A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 263 AKAVEALNGKKF 274
             A+E  NG +F
Sbjct: 61  QAAIEWFNGYEF 72

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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 33  YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS-TRRSLGYGYVNYANPADAARALDVL 91
           Y+G+L ++VT+  + + F  +  V SVR+ R+     R  G+GY  + +     +AL  L
Sbjct: 5   YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS-L 62

Query: 92  NFTPLNNKSIRI 103
           N   L N+ IR+
Sbjct: 63  NDESLKNRRIRV 74

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 22/74 (29%), Positives = 37/74 (50%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            +L++  L    TD+ L   F   G V+S +V  D  T  S  +G+V+Y NP  A  A+ 
Sbjct: 5   CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64

Query: 90  VLNFTPLNNKSIRI 103
            +N   +  K +++
Sbjct: 65  AMNGFQIGTKRLKV 78

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

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 120 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +F+   D  +   + +   F  FG ++ C I        K F FV+FE+ E A  A++ L
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI-------RKTFAFVEFEDSEDATKALEAL 54

Query: 179 NGMLINDKQVFV 190
           +G  I+   + V
Sbjct: 55  HGSRIDGSVLTV 66

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           ++++NL      + LK+ F+E G +    +  + +G SKG G V F +PE A RA   MN
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMN 60

Query: 374 G 374
           G
Sbjct: 61  G 61

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|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 = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          L+VG L+   T+ ++ ++FS  G+V  + + RD   ++S G  +V Y++   A  A+  L
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 92 N 92
          N
Sbjct: 61 N 61

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

 Score = 39.9 bits (93), Expect = 4e-04
 Identities = 17/59 (28%), Positives = 28/59 (47%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           +L+V +L ++ T+  L   FS+ G V       D ST R+ G G+V + +       L
Sbjct: 2  FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG L  N T   +   F Q G+V    +  D +T R  G+G+V + +  D    +  +
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60

Query: 92  NFTPLNNKSI 101
           +F  +NNK +
Sbjct: 61  HFHEINNKMV 70

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 11/62 (17%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSV----RVCRDLSTRRSLGYGYVNYANPADAARA 87
          +YVG +  + T S+L   F   G++  +    R   D        YG+V Y    DA RA
Sbjct: 5  IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGD-------NYGFVTYRYACDAFRA 57

Query: 88 LD 89
          ++
Sbjct: 58 IE 59

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            +Y+  +       +L++ F  FG I    +     G +   GFV +    +A RA+   
Sbjct: 4   VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFRAIEHG 61

Query: 373 N 373
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 19/63 (30%), Positives = 35/63 (55%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G  ++I  L   + +++L  L  + G I   ++M D +G ++G  FV FS  +EA  A+ 
Sbjct: 1   GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIK 60

Query: 371 EMN 373
           ++N
Sbjct: 61  QLN 63

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

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 25/84 (29%), Positives = 46/84 (54%), Gaps = 3/84 (3%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +LYVG+L  +VT+  +  LFSQ+G   S ++  + ++     Y +V +    DAA AL  
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 58

Query: 91  LNFTPLNNKSIRIMYSHRDPSIRK 114
           +N   +  K +++ ++   PS +K
Sbjct: 59  MNGRKILGKEVKVNWA-TTPSSQK 81

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 21/56 (37%), Positives = 29/56 (51%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           L +KNL   + +E L+E FS FG +    V+ D  G   G G V F+    A +AL
Sbjct: 2   LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57

This subgroup corresponds to the RRM2 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. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer 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 = 80

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 8/69 (11%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNI--------LSCKIATDGSGQSKGFGFVQFENKESA 171
           I+I  L   +   +L + F   G I           KI TD   + KG   V +++  +A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 172 QNAIDKLNG 180
           Q AI+  NG
Sbjct: 61  QAAIEWFNG 69

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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  + + +    L   F   G I   ++  + SG+++G+ FV +  KE AQ AI  LN
Sbjct: 4   VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILN 63

Query: 180 GMLINDKQVFVG 191
              I   + F+G
Sbjct: 64  NYEIRPGK-FIG 74

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

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAV--- 266
           +FV  + E T +  L+  F EYG I +  ++ D   GK + FGFV F++ D   K V   
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQK 62

Query: 267 -EALNGKKFDDRE 278
              +NG   + R+
Sbjct: 63  YHTINGHNAEVRK 75

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family proteins

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 15/64 (23%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L ++NL   ID   L+ L  + G + +  +      +  G+  + +S+ EEA++A + +N
Sbjct: 4   LVLRNLTPQIDGSTLRTLCMQHGPLLTFHL-----NLRHGNALIRYSSKEEAAKAQSALN 58

Query: 374 GKMI 377
             ++
Sbjct: 59  NCVL 62

This subfamily corresponds to the RRM of the GW182 family which includes three paralogs of TNRC6 (GW182-related) proteins comprising GW182/TNGW1, TNRC6B (containing three isoforms) and TNRC6C in mammal, a single Drosophila ortholog (dGW182, also called Gawky) and two Caenorhabditis elegans orthologs AIN-1 and AIN-2, which contain multiple miRNA-binding sites and have important functions in miRNA-mediated translational repression, as well as mRNA degradation in Metazoa. The GW182 family proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. Members in this family are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The only exception is the worm protein that does not contain a recognizable RRM domain. The GW182 family proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. . Length = 71

>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6 (LARP6) and similar proteins

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 17/80 (21%)

Query: 218 ESTTDEDLKKIFGEYGTITSAVVMRDGD----------------GKSKCFGFVNFENADD 261
           E +T E + ++F   G I    ++R G                 G  +C   V FE  + 
Sbjct: 11  EESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKEC-AVVEFEKLEA 69

Query: 262 AAKAVEALNGKKFDDREWYV 281
           A KAVE L+ +        V
Sbjct: 70  ARKAVEELSARDDWRDGIKV 89

This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 42.6 bits (100), Expect = 5e-04
 Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 2/94 (2%)

Query: 304 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP 362
            T  +     +++  L     +  L E FS+ G +   + ++D  S  SKG  +V F   
Sbjct: 82  LTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDV 141

Query: 363 EEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           E   +ALA + G+M++ +P+ V  +Q ++ R A+
Sbjct: 142 ESVIKALA-LTGQMLLGRPIIVQSSQAEKNRAAK 174

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

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+ +L   +  + L   FS + +    K+  D  +G+SKG+GFV F +      A+ ++
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 179 NG 180
           NG
Sbjct: 69  NG 70

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

 Score = 39.1 bits (91), Expect = 5e-04
 Identities = 20/62 (32%), Positives = 36/62 (58%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
          +L++  L     D++L  +F   G V+S +V  D +T +S  +G+V++ NPA A  A+  
Sbjct: 6  NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 91 LN 92
          +N
Sbjct: 66 MN 67

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

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L++  L     + KL+  F E+G I   +++RD  +G  +G  F+ F    +   A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 373 NGKMI 377
           +GK I
Sbjct: 64  DGKKI 68

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

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-------SGQSKGFGFVQFENKESAQ 172
           +++KNL K +  + L   F  F  + S     +         G+ KG  FV F ++E A 
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 173 NAIDKLNGMLINDK 186
            A++ +NG ++  K
Sbjct: 62  KALNLVNGYVLKGK 75

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|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK 375
           +  L +    + LK+   + G +T   V RD  G     G V F++ E+  RAL +++G 
Sbjct: 5   VSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGE----GVVEFTSQEDMERALRKLDGT 60

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 19/58 (32%), Positives = 33/58 (56%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
          ++VG L ++ T   L + FS+ G+V+   +  D  T RS G+G+V + + A   + LD
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58

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

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

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE-- 267
           +FV  L   TT +DLK+ F ++G +    +  D   G+S+ FGFV F++A    K ++  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 268 --ALNGKKFDDR 277
              L+G+  D +
Sbjct: 61  EHKLDGRVIDPK 72

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

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 16/72 (22%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           ++++N+  +     L   F  +G I+   I  D  + + +GF +VQFE+   A++A+  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 179 NGMLINDKQVFV 190
           +      +++ +
Sbjct: 63  DRTRFLGREIEI 74

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 20/71 (28%), Positives = 34/71 (47%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL   + +E + ELF + G +   K+ +D  G  K   FV F        A+  +N
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 374 GKMIVSKPLYV 384
           G  +  +PL +
Sbjct: 64  GIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIF-GEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
            V V NL +  T+  +++ F  + G I   ++  +  GKS     + F+ A DA KA + 
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 269 LNGKKFDDR 277
            NG+  D  
Sbjct: 61  FNGRIDDGN 69

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

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

 Score = 39.9 bits (93), Expect = 5e-04
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAV 266
           +FV+NL    T+E L   F ++G++  A  V+    G++K  GFV F++       +
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 374
           ++  +  S+ ++ LKE FS  G +T  ++  D    ++   FV F+  E A  AL  ++G
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSAL-NLSG 61

Query: 375 KMIVSKPLYV 384
            ++   PL V
Sbjct: 62  TLLGGHPLRV 71

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V  +D S +++DLK+ F   G +T   +  D    ++ F FV F +A+ A  A+  L+
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSALN-LS 60

Query: 271 GK 272
           G 
Sbjct: 61  GT 62

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           L++  L  S+ +  L+E FS FGT++  ++++   +G  +G  ++   T E   +  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKC 58

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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 39.2 bits (91), Expect = 5e-04
 Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 46  LYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY 105
           LY LFSQ G V+ +     L T +  G  +V +   + A  AL  L   P   K +RI Y
Sbjct: 22  LYALFSQFGHVVDIVA---LKTMKMRGQAFVIFKELSSATNALRQLQGFPFYGKPMRIQY 78

Query: 106 SHRDPSI 112
           +  D  I
Sbjct: 79  AKTDSDI 85

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

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

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 12/73 (16%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTI----TSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           L+++N+  +++DE+L+ LF +FG I    T+CK         +G   V++     A RA 
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLYTACK--------HRGFIMVSYYDIRAARRAK 55

Query: 370 AEMNGKMIVSKPL 382
             + G  +  + L
Sbjct: 56  RALQGTELGGRKL 68

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

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F++N++ +++ + L   F  FG+I +       + + +GF  V + +  +A+ A   L 
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRT----LYTACKHRGFIMVSYYDIRAARRAKRALQ 59

Query: 180 GMLINDKQVFVGHF 193
           G  +  +++ + HF
Sbjct: 60  GTELGGRKLDI-HF 72

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|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 38.5 bits (89), Expect = 5e-04
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++   +   +  + +  TFS FG I+  ++  +     KG+ F++F   ESA +AI  +N
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVN 57

Query: 180 GMLI 183
           G  I
Sbjct: 58  GTTI 61

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDPSGISKGSGFVAFSTPEEA 365
           +YI  L D + ++ L ELF   G I           K+  D     KG   V +  P  A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 366 SRALAEMNGKMIVSKPLYVA 385
             A+   NG       + V+
Sbjct: 61  QAAIEWFNGYEFRGNKIKVS 80

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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 17/64 (26%), Positives = 32/64 (50%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  + + +    L   F S G I   ++  D  G+++G+ FV +  K  A+ A+ +LN
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

Query: 180 GMLI 183
              I
Sbjct: 64  NYEI 67

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

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 266
           +FV  + E T +  L+  F +YG I +  VM D   GK + F FV F++ D   K V
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQV------LSVRVCRDLSTRRSLGYGYVNYANPADA 84
            +Y+ +L ++ ++  L +       V       +VR  R     R LG  Y  +++P  A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRS-RRVRPLGIAYAEFSSPEQA 59

Query: 85  ARALDVLNFTPLNNKSIRIMY 105
            + +  LN     N+ + +  
Sbjct: 60  EKVVKDLNGKVFKNRKLFVKL 80

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNA 174
           +FI  L       +L + FS +G I  C +  D  + +S+GFGFV F +      A
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA 57

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VFV  +     +++L  +F + G I    +M D  G ++ + FV + N + A +AV+ L+
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 271 GKK 273
             +
Sbjct: 64  NYE 66

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

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 32  LYVGDLDFNVTDSQLYDLFS-QVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           LY+G+L  +V +S L  LF      V SV V +        GY +V+  + + A +A++ 
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG-------GYAFVDCPDQSWADKAIEK 53

Query: 91  LNFTPLNNKSIRIMYSH 107
           LN   L  K I + +S 
Sbjct: 54  LNGKILQGKVIEVEHSV 70

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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 8/65 (12%)

Query: 120 IFIKNL-DKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI NL  K +  + L   FS++G +    +          +GFVQF++ ES  NAI+  
Sbjct: 2   LFIGNLPTKRVSKEDLFRIFSTYGELAQIVL-------KNAYGFVQFDSPESCANAINCE 54

Query: 179 NGMLI 183
            G +I
Sbjct: 55  QGKMI 59

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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK---CFGFVNFENADDAAKAVE 267
           ++V NL      +D++ +F +YG I      RD D K++    F FV FE+  DA  AV 
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAI------RDIDLKNRRGPPFAFVEFEDPRDAEDAVY 55

Query: 268 ALNGKKFD 275
             +G  +D
Sbjct: 56  GRDGYDYD 63

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 322 SIDDEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPEEASRA 368
           S  ++ L+ELF ++G +    V+RD S     SKG  FV F T + A  A
Sbjct: 12  SWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 6/62 (9%)

Query: 222 DEDLK-KIFGE---YGTITSAVVMRDGDGKSKCF--GFVNFENADDAAKAVEALNGKKFD 275
           DEDLK +I  E   YG + + +V      ++      FV F +AD+A KAV ALNG+ F 
Sbjct: 16  DEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFG 75

Query: 276 DR 277
            R
Sbjct: 76  GR 77

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain. . Length = 85

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 39.1 bits (92), Expect = 6e-04
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 209 NNVFVKNLDESTTDED-LKK--IFGEYGTITSAVVMRDGDGKSK---CFG-FVNFENADD 261
           N V+V  L     DE+ LKK   FG+YG I   V+ R+             +V +   +D
Sbjct: 6   NLVYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKED 65

Query: 262 AAKAVEALNGKKFDDR 277
           A + ++A++G   D R
Sbjct: 66  ALRCIQAVDGFYLDGR 81

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

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

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 21/61 (34%), Positives = 33/61 (54%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          LYV  L   +T  +L  LFS  G++++ R+  D  T  S G G++ +    +A RA+  L
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 92 N 92
          N
Sbjct: 63 N 63

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

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSS-FGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           IF+ +L   ++   L   F S F +  S KI TD  +G S+G+GFV+F ++   Q A+ +
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 178 LNGMLINDKQVFVG 191
           + G+    + + + 
Sbjct: 64  MQGVYCGGRPMRIS 77

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

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 42.4 bits (100), Expect = 7e-04
 Identities = 29/149 (19%), Positives = 41/149 (27%), Gaps = 4/149 (2%)

Query: 414 PPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVS 473
           PP+ P   P P    Q+ L  +   A +  +       Q    + P G P      P   
Sbjct: 136 PPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQG 195

Query: 474 QGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGR---NMQDFPFDMGAGS 530
             +Q           P Q   Q     P Q P         L +    +Q   F   +  
Sbjct: 196 PPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPA-QPPLPPQLPQQPPPLQQPQFPGLSQQ 254

Query: 531 MLPVPVDMGAGIPRRDASVGQPMPITALS 559
           M P P        +      QP P    +
Sbjct: 255 MPPPPPQPPQQQQQPPQPQAQPPPQNQPT 283

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++KNL  +I  ++LKE+F +   I   ++     G SKG  ++ F T  EA +AL E  
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDI---RLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 374 G 374
           G
Sbjct: 63  G 63

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 38.3 bits (90), Expect = 7e-04
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)

Query: 37 LDFNVTDSQLYDLFSQVG-QVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
          L F+ T+  + D FS +      + +  D   R + G  YV +A+P DA RAL
Sbjct: 7  LPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPT-GEAYVEFASPEDARRAL 58

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 38.5 bits (89), Expect = 7e-04
 Identities = 21/55 (38%), Positives = 31/55 (56%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           VKNL    ++E L++ F ++G +  AVV+ D  G+    GFV F     A KA+E
Sbjct: 4   VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALE 58

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK- 177
           +F+ NL      + L   F + G   S ++ TD  +G+SKG  FV+F+  E+   A+   
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 178 ---LNGMLIN 184
              L G  IN
Sbjct: 63  HTLLKGRKIN 72

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

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
           F+  +++   +  ++  F ++G   S +V      ++KC GFV FE  + A K   A++ 
Sbjct: 6   FLFGVEDDLPEYKIRDYFEQFGKSKSVIVNH----RAKC-GFVRFETREAAEKFAAAISE 60

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

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 7/61 (11%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F++NL  ++  + L   F  FG +   K       + K + F+ F+ ++ A  A++++N
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMN 56

Query: 180 G 180
           G
Sbjct: 57  G 57

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALN 270
           FV NL  +T   DL  IF +  ++ S  ++RD +  K K F +V FE+ +   +A+E  +
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 271 GKKFDDR 277
           G  FDDR
Sbjct: 63  GALFDDR 69

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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 38.5 bits (89), Expect = 8e-04
 Identities = 24/80 (30%), Positives = 38/80 (47%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           TSL+V ++        L   F + G ++ V V  D  TRR  G+ Y+ + +  DA  AL 
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 90  VLNFTPLNNKSIRIMYSHRD 109
            LN   +  + I I ++  D
Sbjct: 61  NLNRKWVCGRQIEIQFAQGD 80

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 328 LKELFSEFGTITSCKVMRDPSGISK--GSGFVAFSTPEEASRA 368
           L+ELFS FG + + ++ +  +G     G GFV F T ++A RA
Sbjct: 17  LRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 38.2 bits (89), Expect = 8e-04
 Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 313 NLYIKNLGDSIDDE----KLKELFSEFGTITSCKVMRDPSGISKGS-GFVAFSTPEEASR 367
            LY+  +   + +E     L   FS+FG + S KV  + +  + G   FV F +   ASR
Sbjct: 2   TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61

Query: 368 ALAEMNGK-MIVSKPLYVAV 386
           A    NGK +    PL V  
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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.3 bits (90), Expect = 8e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 11/77 (14%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI--------SKGSGFVAFSTPEEA 365
           LY+ NL   I +E+L + F++   + +  + + P            K   FV F T EEA
Sbjct: 4   LYVGNLPPGITEEELVDFFNQ--AMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEA 61

Query: 366 SRALAEMNGKMIVSKPL 382
           + ALA ++G +   +PL
Sbjct: 62  TAALA-LDGIIFKGQPL 77

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L + NL   I D++L+ LFS+FG +   K +R  + +     FV F     A  AL  +N
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEV---KDIR-ETPLRPSQKFVEFYDIRAAEAALDALN 59

Query: 374 GKMIVSKPLYVA 385
           G+  +   L V 
Sbjct: 60  GRPFLGGRLKVK 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|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 38.5 bits (89), Expect = 9e-04
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           LY++NL  S  +E +++ F+    G +   K +RD         FV FS  E+A  A+  
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD-------YAFVHFSNREDAVDAMNA 63

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NGK+I   P+ V +A+
Sbjct: 64  LNGKVIDGSPIEVTLAK 80

This subgroup corresponds to the RRM3 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. ACF 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 = 83

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.1 bits (89), Expect = 9e-04
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRS-LGYGYVNYANPADAARAL 88
          + + V ++ F  T  +L +LFS  G++ +VR+ + ++   S  G+G+V++    DA RA 
Sbjct: 1  SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 89 DVL 91
            L
Sbjct: 61 KAL 63

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 38.2 bits (88), Expect = 9e-04
 Identities = 17/56 (30%), Positives = 32/56 (57%)

Query: 122 IKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
           ++NL   + ++ L + FS FG +    +  D  G+S G G V+F +K +A+ A ++
Sbjct: 4   VRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFER 59

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 38.4 bits (89), Expect = 9e-04
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
           +F+ NL   +D   L + F  +GN++  +I  +  G+   FGFV F++ E  Q
Sbjct: 6   LFVGNLPHDVDKSELKEFFQQYGNVVELRI--NSGGKLPNFGFVVFDDSEPVQ 56

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSK----GFGFVQFENKESAQNAI 175
           +++ NL      + +++ FS  G+I   K    G  +      GF FV++  +E A+NA+
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDI---KRIIMGLDRFTKTPCGFCFVEYYTREDAENAV 57

Query: 176 DKLNGMLINDK 186
             LNG  ++D+
Sbjct: 58  KYLNGTKLDDR 68

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

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG--YGYVNYANPADAAR 86
           T +L+VG+L+  +T+ +L   F + G V  V + R     R  G  Y +V + N   A R
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKR---PPRGQGNAYAFVKFLNLDMAHR 58

Query: 87  ALDVLNFTPLNNKSIRIMY 105
           A   ++   +    I+I Y
Sbjct: 59  AKVAMSGQYIGRNQIKIGY 77

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 8/75 (10%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG++D + +  +L  LF   G VLS  V R         + +V+    A A RA++ L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54

Query: 92  NFTPLNNKSIRIMYS 106
           N   L+ + + + +S
Sbjct: 55  NGRELHGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L  ++T+ +  +LFS+ G+V  V + ++       G+G++      +A +A   L
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57

Query: 92  NFTPLNNKSIRI 103
           +      + +R+
Sbjct: 58  DGIMRKGRQLRV 69

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

>gnl|CDD|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 = 38.0 bits (89), Expect = 0.001
 Identities = 17/70 (24%), Positives = 38/70 (54%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++G L   +++ Q+ +L    G++ +  + +D +T  S GY +  Y +P+   +A+  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 92  NFTPLNNKSI 101
           N   L +K +
Sbjct: 63  NGMQLGDKKL 72

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

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG L  N T+  +   FSQ G+V    +  D  T R  G+G+V + +     +  ++ 
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI- 60

Query: 92  NFTPLNNKSI 101
           +F  +NNK +
Sbjct: 61  HFHEINNKMV 70

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQS-KGFGFVQFENKESAQNAIDKL 178
           IF+  L  +     +   FS FG +    +  D      +GFGFV FE+++      + +
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE-I 60

Query: 179 NGMLINDKQV 188
           +   IN+K V
Sbjct: 61  HFHEINNKMV 70

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           +++  L  +  ++ +K+ FS+FG +    +M D  +   +G GFV F + +   +     
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 371 --EMNGKMIVSK 380
             E+N KM+  K
Sbjct: 62  FHEINNKMVECK 73

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQFENKESAQNA 174
            T  IF+  L  ++    L   FS FG +    +  D   +  +GFGF+ FE+++S    
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 175 IDKLNGMLINDKQVFVGH 192
           +++ +   IN K+V V  
Sbjct: 61  VNE-HFHDINGKKVEVKR 77

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 38.4 bits (89), Expect = 0.001
 Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQNAI 175
           +F++NL      ++L   FS FG++       D S G++KG GFV F+++ +    +
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
          +LYV  L   +T  +L  LFSQ G++++ R+  D  T  S G G++ +    +A  A+  
Sbjct: 4  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 91 LN 92
          LN
Sbjct: 64 LN 65

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMN 373
           YI NL   I ++ ++E F     ITS ++  D  +G  KG G V F+  E    AL +++
Sbjct: 3   YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLD 60

Query: 374 GKMIVSKPLYVA 385
           G ++  +P+ +A
Sbjct: 61  GTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y+ NLG++ +  +L+  F  +G + S  V R+P G +    FV F  P +A+ A+ E++
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 62

Query: 374 GKMI 377
           G+ +
Sbjct: 63  GRTL 66

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

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++I  L      + +   F  +G I    +         GFGFV+FE+   A +A+ +LN
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL-------KNGFGFVEFEDPRDADDAVYELN 54

Query: 180 GMLINDKQVFVGH 192
           G  +  ++V V H
Sbjct: 55  GKELCGERVIVEH 67

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
           +V  L E  T++DL+  F ++G I S  V+     + +C  FV F   + A KA E L  
Sbjct: 5   YVGGLGERVTEKDLRDHFYQFGEIRSITVVP----RQQC-AFVTFTTREAAEKAAERLFN 59

Query: 272 K 272
           K
Sbjct: 60  K 60

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 371
           NLYI+ L     D+ L +L   +G I S K + D +    KG GFV F +P  A +A+  
Sbjct: 3   NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62

Query: 372 M 372
           +
Sbjct: 63  L 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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNF 256
           +F+  L   TT E L++ FG++G +   +VMRD   K S+ FGFV F
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49

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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 7/73 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +FI  L+ +   K +   F  +G I    +        +GFGFV+F++   A +A+ +L+
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDL-------KRGFGFVEFDDPRDADDAVYELD 54

Query: 180 GMLINDKQVFVGH 192
           G  + +++V + H
Sbjct: 55  GKELCNERVTIEH 67

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L++  +  +++++ L+ LF +FG I    V++D  +G+ KG  F+ +   E A +A + +
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

Query: 373 NGK 375
           + +
Sbjct: 68  HEQ 70

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

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           LY++NL  S  +E +K  F++F  G +   K +RD         FV F   E+A  A++ 
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-------YAFVHFFNREDAVAAMSV 56

Query: 372 MNGKMIVSKPLYVAVAQ 388
           MNGK I    + V +A+
Sbjct: 57  MNGKCIDGASIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is 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 = 74

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L ++ T   L   F   G   SVR+  D  T +S G  +V +       +AL  L
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-L 61

Query: 92  NFTPLNNKSIRI 103
           + T L  + I +
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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VFV  +     +++L  +F   G I    +M D DGK++ + FV +    +A +AV  LN
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

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|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAA 263
           KT +       L E    E L   F ++G + S  V  +        + FV F +A  A+
Sbjct: 1   KTLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60

Query: 264 KAVEALNGKKF 274
           +A +A NGK  
Sbjct: 61  RAQKACNGKWL 71

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|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFG-------TITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
           LYI NL       +L+  F+++G       T+ +       S     SGF  F + EEA 
Sbjct: 3   LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62

Query: 367 RALAEMNGKMIVSKPLYVA 385
            ALA +NG+ +  + + V 
Sbjct: 63  EALA-LNGRCLGERAIEVQ 80

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           I I+NL   +  + +HD  S +  +  C +  D S   K    V   N + A  AI KL+
Sbjct: 2   IVIRNLPADVTKQEVHDLLSDYQ-VKYCDV--DKS---KRTAQVTLLNGDQASRAIAKLH 55

Query: 180 GMLINDKQVFV 190
                ++++ V
Sbjct: 56  QSSYKERKISV 66

This subfamily corresponds to the RRM1 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 = 70

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

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+V NL     + +++ +F +YG I   + ++    +   + F+ FE+A DA  A+   +
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVD-IDLKLPP-RPPGYAFIEFEDARDAEDAIRGRD 59

Query: 271 GKKFD 275
           G  FD
Sbjct: 60  GYDFD 64

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

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

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           ++++ N+D     + L   F   G++    I  D  SG  KGF +++F +KES + A+  
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALA- 59

Query: 178 LNGMLINDKQVFV 190
           L+  L   +Q+ V
Sbjct: 60  LDESLFRGRQIKV 72

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

>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53 and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 7/54 (12%)

Query: 138 FSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG 191
           FSS G IL  +     +        +++ ++  A+ A+ K NG +IN   V VG
Sbjct: 21  FSSCGTILEVRYPPGANWIH-----LKYSSRLEAERALSK-NGTIINGG-VMVG 67

This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains. Length = 73

>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +    L++ T+ ED+K+ F ++G +   V   +GD +    G+V F+  + A KA+E   
Sbjct: 4   LKFSGLNKPTSREDIKEAFSQHGEV-KYVDFLEGDKE----GYVRFKTPEAAKKALEKAT 58

Query: 271 --GKKFDDREW 279
               K  + E 
Sbjct: 59  EAKLKIKEAEV 69

This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Length = 102

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N V++  LDES T++ L + F  YG +   V+ R      +    V F+  + A  AV  
Sbjct: 8   NCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDR-----QRGQALVFFDKVEAAQAAVNE 62

Query: 269 LNGKKF 274
           + G+K 
Sbjct: 63  MKGRKL 68

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is 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 = 77

>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 7/65 (10%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           N +++ NL+ES T  DL+K+F ++  + +   +++ G      + FV+  +   A KA+E
Sbjct: 2   NKLYIGNLNESVTPADLEKVFEDHKISYSGQFLVKSG------YAFVDCPDEQWAMKAIE 55

Query: 268 ALNGK 272
             +GK
Sbjct: 56  TFSGK 60

This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). . Length = 77

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 16/59 (27%), Positives = 33/59 (55%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
          +++G L ++ +   L +  S+ G+VL   +  D  T RS G+G+V + + A   + L++
Sbjct: 2  MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELF-SEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
            + + NL   + + +++E F S+ G I    +  +  G S G   + F    +A++A  +
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 372 MNGKMIVSK 380
            NG++    
Sbjct: 61  FNGRIDDGN 69

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++V +L F++T  +L + FSQ G V+   +   +   +S G G V + +P  A +A  ++
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEI--KMENGKSKGCGTVRFDSPESAEKACRLM 59

Query: 92  NFTPLNNKSIRI 103
           N   +N + I +
Sbjct: 60  NGIKINGREIDV 71

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI  L       +L D FS FG I  C +  D  + +S+GFGFV F +  S    +DK+
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPAS----VDKV 57

Query: 179 NG 180
             
Sbjct: 58  LA 59

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 27/95 (28%), Positives = 38/95 (40%), Gaps = 25/95 (26%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILS----------CKIATDGSGQSKGF-------- 160
            +F+ NL  +   K L   F  FG I S           K+    +   K F        
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 161 GFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLR 195
            +V F+ +ESA+ A+ KLNG        F GH +R
Sbjct: 62  AYVVFKEEESAEKAL-KLNG------TEFEGHHIR 89

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           V++ NL    T++D+++ F     ITS  +  D + G+ K FG V+F + +    A++ L
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK-L 59

Query: 270 NGKKFDDR 277
           +G     R
Sbjct: 60  DGTVLCGR 67

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           + ++ L  S   + + D FS          I  D  G+  G  +V+F + E A+ A+ K 
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 179 NGMLIN 184
           N  +  
Sbjct: 62  NNKMGG 67

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 8/88 (9%)

Query: 120 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           I+I NL++ I      K+LH  FS FG IL   I    S + +G  FV F+   SA NA+
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 176 DKLNGMLINDKQVFVGHFLRKQERETVA 203
             + G    DK + + +   K + + +A
Sbjct: 64  RSMQGFPFYDKPMRIQY--AKTDSDIIA 89

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 33/139 (23%), Positives = 45/139 (32%), Gaps = 1/139 (0%)

Query: 397 LQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPG 456
           LQ Q      V  G ++ P  P   P    +  Q     A PA  P Q          P 
Sbjct: 173 LQPQGPPSIQVPPGAALAPSAPPPTPSAQAVPPQGSPIAAQPAPQPQQPSPLSLIS-APS 231

Query: 457 MRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLG 516
           + P   P P+  +   +  QQ  +P       P      P P MPH +       ++P  
Sbjct: 232 LHPQRLPSPHPPLQPQTASQQSPQPPAPSSRHPQSSHHGPGPPMPHALQQGPVFLQHPSS 291

Query: 517 RNMQDFPFDMGAGSMLPVP 535
              Q F         LP+P
Sbjct: 292 NPPQPFGLAQSQVPPLPLP 310

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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           I++ NL   I  + + D F  +G I +  +     G    F FV+FE+   A++A+   +
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRG--PPFAFVEFEDPRDAEDAVRGRD 59

Query: 180 G 180
           G
Sbjct: 60  G 60

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAKAV 266
           + + V+N+    T ++L+++F  +G + +  + +   G G  + FGFV+F    DA +A 
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 267 EAL 269
           +AL
Sbjct: 61  KAL 63

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 16/72 (22%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 121 FIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS--GQSKGFGFVQFENKESAQNAIDKL 178
           ++ NL   +  + + + F    N+ S ++  +    G+ +GFG+ +FE+++S   A+  L
Sbjct: 5   YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL-SL 62

Query: 179 NGMLINDKQVFV 190
           N   + ++++ V
Sbjct: 63  NDESLKNRRIRV 74

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 17/63 (26%), Positives = 34/63 (53%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G  +++  +   + +++L  +F   G I   ++M D  G ++G  FV ++   EA RA+ 
Sbjct: 1   GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVR 60

Query: 371 EMN 373
           E+N
Sbjct: 61  ELN 63

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|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 9/71 (12%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD---GSGQSKGFGFVQFENKES---AQN 173
           +F+  + +S   K L + F  +G +    +  D      QSKG  FV F  +++   AQN
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63

Query: 174 A---IDKLNGM 181
           A   +  L GM
Sbjct: 64  ALHNMKTLPGM 74

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 323 IDDE---KLKELFSEFGTITSCKVMRDPSGISKGS--GFVAFSTPEEASRALAEMNGKM 376
           ID++   +++E   ++G + +  V    S  +  +   FV FS  +EA +A+  +NG+ 
Sbjct: 15  IDEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRF 73

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain. . Length = 85

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

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 5/64 (7%)

Query: 121 FIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNG 180
           F+  ++  +    + D F  FG   S  +           GFV+FE +E+A+     ++ 
Sbjct: 6   FLFGVEDDLPEYKIRDYFEQFGKSKSVIVN-----HRAKCGFVRFETREAAEKFAAAISE 60

Query: 181 MLIN 184
             +N
Sbjct: 61  NGLN 64

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

>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 9/67 (13%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS--GFVAFSTPEEASRA 368
           G+ L I ++G  +  E +K +F++FG +            ++G+  G++ F TPE A +A
Sbjct: 1   GVILKITSIGPGVTREDIKAVFAQFGEVKYVD-------FTEGADTGYIRFKTPEAAQKA 53

Query: 369 LAEMNGK 375
                 K
Sbjct: 54  REAFVEK 60

This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +    + E T+ EDLK+ F E+G + + V    G  +    G+V F+  + A +A+E L 
Sbjct: 4   LHFSGVGEQTSREDLKEAFEEFGEV-AWVDFARGQTE----GYVRFKEENAAKEALEKLK 58

Query: 271 GKK 273
             K
Sbjct: 59  EAK 61

This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 76

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 8/65 (12%)

Query: 120 IFIKNLDKSIDHKALHDT-FSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI NL+ ++  K+  +T FS +G ++ C +        KG+ FVQ+ N+  A+ A+   
Sbjct: 4   VFIGNLNTAVVKKSDVETIFSKYGRVVGCSV-------HKGYAFVQYSNERHARGAVIGE 56

Query: 179 NGMLI 183
           NG ++
Sbjct: 57  NGRVL 61

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|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 11/38 (28%), Positives = 19/38 (50%)

Query: 151 TDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV 188
            D   Q    G V+F      + AI+KL+G  +N +++
Sbjct: 30  ADAHKQRPNEGVVEFATYSDMKRAIEKLDGTELNGRKI 67

This subfamily corresponds to the RRM2 of 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 is 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 = 72

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

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 15/79 (18%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCK--VMRDPSGISK------GSGFVAFSTPEEA 365
           LY+ NL     +E++ ELFS  G I   K  +M    G+ +      G  FV + T E+A
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDI---KRIIM----GLDRFTKTPCGFCFVEYYTREDA 53

Query: 366 SRALAEMNGKMIVSKPLYV 384
             A+  +NG  +  + + V
Sbjct: 54  ENAVKYLNGTKLDDRIIRV 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR-DPSGISKGSGFVAFSTPEEASRAL 369
           L++ NL     +++L+  F   G I   ++M  + SG  KG  FV F   E A+ AL
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 37.1 bits (85), Expect = 0.003
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
          +LYV  L   +T  +L  LFSQ G++++ R+  D  T  S G G++ +    +A  A+  
Sbjct: 7  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 91 LN 92
          LN
Sbjct: 67 LN 68

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

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 16/71 (22%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+KNL  +I    L + F    + +  ++ +   G SKG  +++F+ +  A+ A+++  
Sbjct: 6   LFVKNLPYNITVDELKEVFE---DAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 180 GMLINDKQVFV 190
           G  ++ + + V
Sbjct: 63  GAEVDGRSIVV 73

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
           + NL  + T +  +++   +G +    +V  +  G SK +GFV +   D AA+A   L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 272 KKFDDREWYV 281
           K+   R  YV
Sbjct: 64  KQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 23/80 (28%), Positives = 39/80 (48%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           +SL+V ++  +     L   F + G ++ V V  D  TRR  G+ YV + +  DA  AL 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 90  VLNFTPLNNKSIRIMYSHRD 109
            L+   +  + I I ++  D
Sbjct: 61  NLDRKWICGRQIEIQFAQGD 80

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +LYVG+L  +VT++ +  LFSQ+G   S ++  D  T  +  Y +V +     AA +L  
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAA 58

Query: 91  LNFTPLNNKSIRIMYS 106
           +N   +  K +++ ++
Sbjct: 59  MNGRKIMGKEVKVNWA 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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG+L    T+ ++  LF Q G+VL   + ++        YG+V+  +   A  A+  L
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRNL 54

Query: 92  NFTPLNNKSIRI 103
           +   L+  +I +
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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESA-QNAIDK 177
           +F+  L  S+    L + FS FG +   +I     +G  +GF ++     E+  +     
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 178 LNGMLINDKQVFVGHFLRKQE 198
           LNG        + G  L+ +E
Sbjct: 62  LNGT------KWKGSVLKIEE 76

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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           + +++ NL+E    ++LKK    IF  +G I   +V R    + +   FV F+    A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 61

Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
           A+ ++ G  F D+   +  A+  S+
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSD 86

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 20/96 (20%), Positives = 36/96 (37%), Gaps = 32/96 (33%)

Query: 120 IFIKNL-DKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           + ++N+  +  +   L++ FS FG I++ ++       +     VQF   E A+ A    
Sbjct: 4   LEVRNIPPELNNITKLNEHFSKFGTIVNIQVN-----YNPESALVQFSTSEEAKKAY--- 55

Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVK 214
                               R   A+   FNN F+K
Sbjct: 56  --------------------RSPEAV---FNNRFIK 68

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 9/77 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           LY++NL     ++ +K+ F +F  G +   K +RD         FV F++ E+A  A+  
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-------YAFVHFTSREDAVHAMNN 56

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  +    + V +A+
Sbjct: 57  LNGTELEGSCIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 120 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           I+I NL++ +      K+L+  FS FG IL   I    + + +G  FV F++  SA NA+
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILD--IVALKTLKMRGQAFVVFKDISSATNAL 59

Query: 176 DKLNGMLINDKQVFVGH 192
             + G    DK + + +
Sbjct: 60  RSMQGFPFYDKPMRIAY 76

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

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L V +L ++ ++  L ++F +     S+R+ ++    R  GY +V + +  DA  AL+  
Sbjct: 4   LVVNNLSYSASEDSLQEVFEKA---TSIRIPQN--NGRPKGYAFVEFESAEDAKEALNSC 58

Query: 92  NFTPLNNKSIRIMY 105
           N T +  +SIR+ +
Sbjct: 59  NNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y   +   + ++ +++ FS FG I   +V  D     KG  FV F++ E A+ A+  +N
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD-----KGYSFVRFNSHESAAHAIVSVN 57

Query: 374 GKMI 377
           G  I
Sbjct: 58  GTTI 61

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|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 20/55 (36%), Positives = 31/55 (56%)

Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           V+NL    ++E L++ F ++G +  AVV+ D  G+S   G V F +   A KA E
Sbjct: 4   VRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFE 58

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 18/63 (28%), Positives = 35/63 (55%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G  +++  +   + +++L  LF   G I   ++M + SG ++G  FV ++T EEA  A+ 
Sbjct: 1   GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIR 60

Query: 371 EMN 373
            +N
Sbjct: 61  ILN 63

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|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++  L +S+ ++ L   FS +G +    + R      +G   V F   E A  A+ EM 
Sbjct: 10  VWLDGLDESVTEQYLTRHFSRYGPVVHVVIDR-----QRGQALVFFDKVEAAQAAVNEMK 64

Query: 374 GKMIVSKPLYV 384
           G+ +  + L V
Sbjct: 65  GRKLGGRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is 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 = 77

>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +YI+NL  S+   +LK+ F  FG I  CKV+    G  +  GF+ +   E A+ +L +  
Sbjct: 5   IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRG--EKYGFITYRHSEHAALSLGKGA 62

Query: 374 GKMIVSKP 381
                ++P
Sbjct: 63  SLRKRNEP 70

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK----CFGFVNFENADDAAKAV 266
           ++V NL     ++DL+ +F +YG I      RD + K++     F FV FE+  DA  AV
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRI------RDIELKNRRGLVPFAFVRFEDPRDAEDAV 55

Query: 267 EALNGKKFDD 276
              NG  F  
Sbjct: 56  FGRNGYDFGQ 65

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSS-FGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            FI N+   +  ++L D      G +   ++  D  G+S+G   V+F+ +ES + A++ L
Sbjct: 2   AFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEVL 61

Query: 179 NGMLINDKQVFVGHFLRKQE 198
           N      K V  G  L+ +E
Sbjct: 62  N------KHVLNGRPLKVKE 75

This subgroup corresponds to the RRM1 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 = 76

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           G  +++  +   + +++L  LF + G I   ++M DP +G+++G  FV F T E A  A+
Sbjct: 1   GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

Query: 370 AEMNGKMI 377
              N   I
Sbjct: 61  KLYNNHEI 68

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 7/64 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VF  N +      +++++FG+YG +   V M+ G      F FV  E+  DA  A+  L+
Sbjct: 3   VFCGNFEYDARQSEIERLFGKYGRV-DRVDMKSG------FAFVYMEDERDAEDAIRGLD 55

Query: 271 GKKF 274
             +F
Sbjct: 56  NFEF 59

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa MCM3-associated protein (Map80) and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 314 LYIKNLGDSIDD-EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           +  KN+ D ++D + L+  F +FG     KV R      K S  V F     A  ALA+ 
Sbjct: 3   IQCKNIPDELNDKDWLERHFGKFG-----KVARVYCNPRKKSAVVHFFDHASA--ALAKK 55

Query: 373 NGKMIVSKPL 382
            GK++  KP+
Sbjct: 56  KGKLLQHKPI 65

This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 73

>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 11/72 (15%)

Query: 324 DDEKLKELFSEF-----------GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           D+E L   F EF           G +   KV  +     +G+ +V + + EEA  A    
Sbjct: 30  DEEDLYSDFEEFYDDVLPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMF 89

Query: 373 NGKMIVSKPLYV 384
           NG+    K L  
Sbjct: 90  NGRWYAGKQLTC 101

This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. . Length = 105

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

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
          L++ +L +  T+  L  LFS+ G +  V +  D  T++  G+ +V Y  P  A +A   L
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 92 N 92
          +
Sbjct: 65 D 65

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|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 37  LDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY-GYVNYANPADAARALDVLNFTP 95
           L + VT   L+ +FS  G V  + +       ++ G    V + +   A  A   LN   
Sbjct: 9   LLYPVTVDVLHQVFSPYGAVEKILI-----FEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 96  LNNK--SIRIMYSHR 108
           + +   ++ I +S  
Sbjct: 64  IYDGCCTLDIQFSRL 78

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 5/71 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +KNL     +E+L+ELF +FG++   +++  PS        V F  P +A +A   + 
Sbjct: 3   ILVKNLPFGTTEEELRELFEKFGSLG--RLLLPPSRT---IALVEFLEPSDARKAFKSLA 57

Query: 374 GKMIVSKPLYV 384
            K     PLY+
Sbjct: 58  YKRFKHVPLYL 68

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTIT--SCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
           LY+ NL     DE L+   +E G +   S K      +G SKG  +V F++   A+    
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 371 EMNGKMIVSKPLYVA 385
           ++ G+    K   V 
Sbjct: 61  KLEGREFNGKKCVVT 75

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L V +LD  ++D +L  LFSQ G+V  +R      +++     +V + +   A  ALD 
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALDA 57

Query: 91  LNFTPLNNKSIRIM 104
           LN  P     +++ 
Sbjct: 58  LNGRPFLGGRLKVK 71

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

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 7/64 (10%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL     +++++ LF ++G +  C ++       K  GFV       A  A+  ++
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII-------KNYGFVHMDDKTAADEAIRNLH 55

Query: 374 GKMI 377
              +
Sbjct: 56  HYKL 59

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|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           ++F+ NL+ + D   L    S F +  +  +     G SK FG+V FE+ E  + A+ +L
Sbjct: 2   SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKAL-EL 60

Query: 179 NG 180
            G
Sbjct: 61  TG 62

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin 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. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 31  SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
           ++Y+ +L+  V   +L    Y +FSQ GQ+L +   + L  R   G  +V + + + A  
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMR---GQAFVVFKDISSATN 57

Query: 87  ALDVLNFTPLNNKSIRIMYS 106
           AL  +   P  +K +RI YS
Sbjct: 58  ALRSMQGFPFYDKPMRIAYS 77

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|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 211 VFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 266
           +++ NL+E    E+LKK    IF ++G I   V ++    K +   FV F++   A  A+
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALK--TLKMRGQAFVVFKDISSATNAL 59

Query: 267 EALNGKKFDDR 277
            ++ G  F D+
Sbjct: 60  RSMQGFPFYDK 70

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

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMR-DGDGKSKCFGFVNFENADDAAKAVEAL 269
           V+V  +   +T+++++  F   G I    +M     G+ +   F+ F+  ++AAK   AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT-EEAAKRALAL 59

Query: 270 NGKKFDDR 277
           +G+    R
Sbjct: 60  DGEDMGGR 67

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6 (LARP6) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 15/78 (19%)

Query: 326 EKLKELFSEFGTITSCKVMRD----PSGISKGSG-----------FVAFSTPEEASRALA 370
           E + ELFS  G I   +++R     P  + + S             V F   E A +A+ 
Sbjct: 16  ESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAVVEFEKLEAARKAVE 75

Query: 371 EMNGKMIVSKPLYVAVAQ 388
           E++ +      + V +  
Sbjct: 76  ELSARDDWRDGIKVVLLG 93

This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology motif kinase 1 (UHMK1) and similar proteins

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 223 EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           ED+K+   +YG + S ++ ++  GK + F  V + NA D+  A + L G+ FD +
Sbjct: 28  EDIKEECQKYGPVVSLLIPKENPGKGQVF--VEYANAGDSKAAQKLLTGRIFDGK 80

This subgroup corresponds to the RRM of UHMK1. UHMK1, also termed kinase interacting with stathmin (KIS) or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1 targets two key regulators of cell proliferation and migration, the cyclin-dependent kinase (CDK) inhibitor p27Kip1 and the microtubule-destabilizing protein stathmin. It plays a critical role during vascular wound repair by preventing excessive vascular smooth muscle cell (VSMC) migration into the vascular lesion. Moreover, UHMK1 may control cell migration and neurite outgrowth by interacting with and phosphorylating the splicing factor SF1, thereby probably contributing to the control of protein expression. Furthermore, UHMK1 may be functionally related to microtubule dynamics and axon development. It localizes to RNA granules, interacts with three proteins found in RNA granules (KIF3A, NonO, and eEF1A), and further enhances the local translation. UHMK1 is highly expressed in regions of the brain implicated in schizophrenia and may play a role in susceptibility to schizophrenia. Length = 88

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

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA--NPADAARAL 88
          S+YVG++D+  T  +L   FS  G +  V +  D  +    GY Y+ +A  +  +AA AL
Sbjct: 1  SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60

Query: 89 D 89
          D
Sbjct: 61 D 61

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

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

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 37/139 (26%), Positives = 41/139 (29%), Gaps = 5/139 (3%)

Query: 379  SKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPP 438
            S     A   R   RR    A        A+ P  P R P     P    Q        P
Sbjct: 2870 SPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQP 2929

Query: 439  AIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLP 498
               PP      Q  L P   PAGA  P+  VP    G     PG  R A P  +  QP P
Sbjct: 2930 QPPPPPPPRP-QPPLAPTTDPAGAGEPSGAVPQPWLGALV--PG--RVAVPRFRVPQPAP 2984

Query: 499  IMPHQMPPRGHAYRYPLGR 517
                          + L R
Sbjct: 2985 SREAPASSTPPLTGHSLSR 3003

Length = 3151

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	652
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.98
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.96
smart00517	64	PolyA C-terminal domain of Poly(A)-binding protein	99.96
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.95
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.95
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.95
PF00658	72	PABP: Poly-adenylate binding protein, unique domai	99.94
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.94
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.94
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.93
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.93
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.92
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.91
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.89
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.89
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.88
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.87
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.85
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.82
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.77
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.77
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.75
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.75
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.74
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.73
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.73
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.73
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.72
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.71
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.7
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.68
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.64
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.62
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.58
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.56
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.56
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.54
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.53
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.51
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.5
KOG0122	270	consensus Translation initiation factor 3, subunit	99.5
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.49
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.49
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.49
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.49
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.48
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.48
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.47
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.47
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.46
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.45
KOG0122	270	consensus Translation initiation factor 3, subunit	99.45
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.43
PLN03120	260	nucleic acid binding protein; Provisional	99.43
PLN03120	260	nucleic acid binding protein; Provisional	99.4
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.39
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.38
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.38
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.36
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.36
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.35
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.34
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.34
PLN03121	243	nucleic acid binding protein; Provisional	99.34
PLN03213	759	repressor of silencing 3; Provisional	99.33
smart00362	72	RRM_2 RNA recognition motif.	99.32
smart00362	72	RRM_2 RNA recognition motif.	99.32
PLN03213	759	repressor of silencing 3; Provisional	99.32
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.31
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.31
PLN03121	243	nucleic acid binding protein; Provisional	99.3
smart00360	71	RRM RNA recognition motif.	99.3
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.3
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.29
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.28
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.27
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.26
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.25
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.24
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.23
smart00360	71	RRM RNA recognition motif.	99.23
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.22
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.22
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.22
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.2
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.16
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.16
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.14
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.14
smart00361	70	RRM_1 RNA recognition motif.	99.13
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.13
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.13
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.11
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.1
smart00361	70	RRM_1 RNA recognition motif.	99.1
KOG0226	290	consensus RNA-binding proteins [General function p	98.99
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.95
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.94
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.93
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.91
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.89
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.87
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.84
KOG0226	290	consensus RNA-binding proteins [General function p	98.81
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.78
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.77
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.69
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.69
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.64
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.61
KOG0151	877	consensus Predicted splicing regulator, contains R	98.61
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.59
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.58
KOG4210	285	consensus Nuclear localization sequence binding pr	98.57
KOG4210	285	consensus Nuclear localization sequence binding pr	98.56
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.53
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.47
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.43
KOG0151	877	consensus Predicted splicing regulator, contains R	98.38
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.36
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.31
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.24
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.22
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.09
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.07
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.06
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.86
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.83
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.7
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.69
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.69
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.67
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.64
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.62
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	97.56
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.53
KOG2314	698	consensus Translation initiation factor 3, subunit	97.41
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.36
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.36
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.36
KOG0943	3015	consensus Predicted ubiquitin-protein ligase/hyper	97.29
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.24
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.1
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.0
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	96.99
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.96
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.9
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.88
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.79
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.76
KOG3152	278	consensus TBP-binding protein, activator of basal	96.75
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.68
KOG2314	698	consensus Translation initiation factor 3, subunit	96.65
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.58
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.51
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.34
KOG3152	278	consensus TBP-binding protein, activator of basal	96.25
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.93
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.86
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.77
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.61
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.97
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.95
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.79
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.44
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.15
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.04
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.89
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.8
KOG2135	526	consensus Proteins containing the RNA recognition	93.68
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.51
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.29
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	92.98
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.76
KOG2068	327	consensus MOT2 transcription factor [Transcription	92.5
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	92.35
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.95
KOG2135	526	consensus Proteins containing the RNA recognition	91.71
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	91.38
KOG2068	327	consensus MOT2 transcription factor [Transcription	91.17
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	91.12
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.59
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.56
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	90.22
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	89.81
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	89.51
KOG2893	341	consensus Zn finger protein [General function pred	88.57
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	87.35
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	87.22
KOG2318	650	consensus Uncharacterized conserved protein [Funct	86.12
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	85.91
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	85.88
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	84.34
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	81.79

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

Probab=100.00  E-value=3.4e-99  Score=846.18  Aligned_cols=556  Identities=54%  Similarity=0.864  Sum_probs=440.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      +||||+|||.++||++|+++|+.||+|.+|+||+|..|++|+|||||+|.+.+||++|++.+|+..|.|++|+|+|++++
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeee
Q 006282          110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVF  189 (652)
Q Consensus       110 ~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~  189 (652)
                      ++.+.++.++|||+||+.++++++|+++|+.||.|.+|++..+.+|.++|||||+|.+.++|.+|++++|+..+.++.+.
T Consensus        81 ~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~  160 (562)
T TIGR01628        81 PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY  160 (562)
T ss_pred             ccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHH
Q 006282          190 VGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL  269 (652)
Q Consensus       190 v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l  269 (652)
                      +..+..+..+. ......+++|||+||+.++++++|+++|+.||.|.++.++++.+|+++|||||+|.+.++|.+|++.+
T Consensus       161 v~~~~~~~~~~-~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l  239 (562)
T TIGR01628       161 VGRFIKKHERE-AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM  239 (562)
T ss_pred             Eeccccccccc-cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHh
Confidence            98877666553 12345678999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCccC----CceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q 006282          270 NGKKFD----DREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR  345 (652)
Q Consensus       270 ~~~~~~----g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~  345 (652)
                      ++..+.    ++.+++.++.++.++...+....+....+......+++|||+||++++|+++|+++|+.||.|++|+|+.
T Consensus       240 ~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~  319 (562)
T TIGR01628       240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVML  319 (562)
T ss_pred             CCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEE
Confidence            999999    9999999999999988888777777666666677889999999999999999999999999999999999


Q ss_pred             CCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCC
Q 006282          346 DPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPS  425 (652)
Q Consensus       346 ~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  425 (652)
                      |.+|.++|||||+|.+.++|.+|+.+|||+.++|++|+|.++.+++.+...++.++.+..+....  .+...    +.++
T Consensus       320 d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~~~~~~q~~~~~~~--~~~~~----p~~~  393 (562)
T TIGR01628       320 DEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQ--LPMGS----PMGG  393 (562)
T ss_pred             CCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHHHHHHHHhhhhccC--CCCCC----CCCC
Confidence            99999999999999999999999999999999999999999999999999888887763321111  11000    1110


Q ss_pred             CCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006282          426 GLGQQFLYGQAPPAIIPPQA-GFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQM  504 (652)
Q Consensus       426 ~~~~~~~~~~~~~~~~pp~~-~~~~~~~~~p~~~p~~~~~p~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  504 (652)
                      .++++.++++.+.+++++++ +|+..++           ++++++|+.+.++.++.+       +.++.+++.. ..+..
T Consensus       394 ~~~~p~~~~~~~~~~~~~~p~~~~~~~~-----------~~~~~~~~~~~~p~~~~~-------~~~~~~~~~~-~~~~~  454 (562)
T TIGR01628       394 AMGQPPYYGQGPQQQFNGQPLGWPRMSM-----------MPTPMGPGGPLRPNGLAP-------MNAVRAPSRN-AQNAA  454 (562)
T ss_pred             cccCCCccCCCCcccCCCCCCCCCCCCC-----------CCCCCCCCCCCCCCCCCC-------CCcCCCCCcc-ccccc
Confidence            11122222222211111111 1110000           000000000000000000       0000000000 00000


Q ss_pred             CCC-CCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCccccchhhhhcCChHHHHHHhhhhchhhhh
Q 006282          505 PPR-GHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVE  583 (652)
Q Consensus       505 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~g~~~~~~~~  583 (652)
                      .+. .+.++|+++..  +.          +.++   . +++++++.+.+.+.++++++||+++|++||++|||+|||+|+
T Consensus       455 ~~~~~~~~~~~p~~~--~~----------~~~~---~-~~~~~~~~~~~~~~~~~~~~la~~~p~~q~~~lg~~~~~~~~  518 (562)
T TIGR01628       455 QKPPMQPVMYPPNYQ--SL----------PLSQ---D-LPQPQSTASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVE  518 (562)
T ss_pred             ccccCCCcCCCcccc--CC----------CCCc---c-cccccCCccccccchhHHHHHhhCCHHHHHHHHHHHhHHHHH
Confidence            000 00112222100  00          0000   0 111111223344567899999999999999999999999999


Q ss_pred             hccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHH
Q 006282          584 QLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLR  627 (652)
Q Consensus       584 ~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~  627 (652)
                      +++|++||||||||||||++||||||||+|+|++||+||++||+
T Consensus       519 ~~~~~~~~~~tgm~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (562)
T TIGR01628       519 AIEPALAAKITGMLLEMDNSELLHLLESPELLKSKVDEALEVLK  562 (562)
T ss_pred             hhChhhcCcceEEEecCCHHHHHHHhcCHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999994

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

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

Probab=100.00  E-value=2.3e-61  Score=499.18  Aligned_cols=360  Identities=65%  Similarity=1.015  Sum_probs=343.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      .+||||   +++||++|+++|+.+|+|++||||||. |  |+|||||+|.+++||++||+++|+..++|++|||||+++|
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            689999   899999999999999999999999998 7  9999999999999999999999999999999999999999


Q ss_pred             cccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeee
Q 006282          110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVF  189 (652)
Q Consensus       110 ~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~  189 (652)
                      ++.       |||+||++++|.++|+++|+.||+|++|++.++.+| ++|| ||+|+++++|++|++.+||..+.++.++
T Consensus        76 ~~~-------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~  146 (369)
T KOG0123|consen   76 PSL-------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIY  146 (369)
T ss_pred             Cce-------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeE
Confidence            887       999999999999999999999999999999999999 9999 9999999999999999999999999999


Q ss_pred             ecccccchhhHHHh--hccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHH
Q 006282          190 VGHFLRKQERETVA--IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE  267 (652)
Q Consensus       190 v~~~~~~~~~~~~~--~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~  267 (652)
                      |+.+.++.++....  .....++++++|++.+.+++.|.++|+.+|.|.++.++.+..|++++|+||+|.+.++|..|++
T Consensus       147 vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~  226 (369)
T KOG0123|consen  147 VGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVE  226 (369)
T ss_pred             EeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHH
Confidence            99999887765322  3467789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q 006282          268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP  347 (652)
Q Consensus       268 ~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~  347 (652)
                      .+++..+.+..++|.+++++.++...+...++.............+|||+|++..++++.|++.|+.||+|++++|+.+.
T Consensus       227 ~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~  306 (369)
T KOG0123|consen  227 TLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDE  306 (369)
T ss_pred             hccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEecc
Confidence            99999999999999999999999999998888888888888899999999999999999999999999999999999999


Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHHHHHHHHhhhcC
Q 006282          348 SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQM  404 (652)
Q Consensus       348 ~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r~~~~~~~~~~~  404 (652)
                      .|+++||+||+|.+.++|.+|+..+|+..+.+++++|.++++++.+..+++..+++.
T Consensus       307 ~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~~~~~~~~~~~  363 (369)
T KOG0123|consen  307 NGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRRARLQAVFGAR  363 (369)
T ss_pred             CCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccchhhhhhhccee
Confidence            999999999999999999999999999999999999999999999988887776654

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

Probab=100.00  E-value=4.2e-49  Score=430.36  Aligned_cols=348  Identities=20%  Similarity=0.248  Sum_probs=279.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc--CCcccCCceeEeec
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL--NFTPLNNKSIRIMY  105 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l--n~~~i~G~~i~i~~  105 (652)
                      ++++|||+|||+++||++|+++|+.||+|.+|+++++      +|||||+|.+.++|++|++.+  ++..|.|++|+|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            5789999999999999999999999999999999864      369999999999999999964  67889999999999


Q ss_pred             ccCCccccc----------CCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHH
Q 006282          106 SHRDPSIRK----------SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI  175 (652)
Q Consensus       106 s~~~~~~~~----------~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai  175 (652)
                      +......+.          +...+|+|.||+.++++++|+++|+.||.|.+|++.++.   .+++|||+|.+.++|.+|+
T Consensus        75 s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVef~~~~~A~~A~  151 (481)
T TIGR01649        75 STSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVEFESVNSAQHAK  151 (481)
T ss_pred             cCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEEECCHHHHHHHH
Confidence            975432211          123368999999999999999999999999999998753   2479999999999999999


Q ss_pred             HHhcCceecC--eeeeecccccch--------------------hh-----------HHH--------------------
Q 006282          176 DKLNGMLIND--KQVFVGHFLRKQ--------------------ER-----------ETV--------------------  202 (652)
Q Consensus       176 ~~lng~~l~g--~~~~v~~~~~~~--------------------~~-----------~~~--------------------  202 (652)
                      +.|||..+.+  +.+.|.+.....                    ++           ...                    
T Consensus       152 ~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  231 (481)
T TIGR01649       152 AALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGP  231 (481)
T ss_pred             HHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCC
Confidence            9999999865  355555433100                    00           000                    


Q ss_pred             --------------------------------------hhccCcceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeeC
Q 006282          203 --------------------------------------AIKTKFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRD  243 (652)
Q Consensus       203 --------------------------------------~~~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~v~~~~i~~~  243 (652)
                                                            ......++|||+||+. .+++++|+++|+.||.|.+++++++
T Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~  311 (481)
T TIGR01649       232 LAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN  311 (481)
T ss_pred             CCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC
Confidence                                                  0011346899999997 6999999999999999999999986


Q ss_pred             CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHH-------Hh--HHHHHhhhhc---------
Q 006282          244 GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQE-------LK--GQFEQAMKET---------  305 (652)
Q Consensus       244 ~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~-------~~--~~~~~~~~~~---------  305 (652)
                      .    +|||||+|.+.++|..|+..|++..+.|+.|.|.++.........       ..  ..+.......         
T Consensus       312 ~----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~  387 (481)
T TIGR01649       312 K----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANK  387 (481)
T ss_pred             C----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccc
Confidence            3    579999999999999999999999999999999987553211000       00  0000000000         


Q ss_pred             -ccccccceeeecCCCCCCCHHHHHHHhhhcCC--eeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee-
Q 006282          306 -VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP-  381 (652)
Q Consensus       306 -~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~--I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~-  381 (652)
                       ....++.+|||+|||.++++++|+++|+.||.  |+.++++.+.++ ++|+|||+|.+.++|.+|+..|||..|.++. 
T Consensus       388 ~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~  466 (481)
T TIGR01649       388 NNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNG  466 (481)
T ss_pred             cccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCC
Confidence             01134678999999999999999999999998  899998866544 5899999999999999999999999999885 


Q ss_pred             -----EEEEeccc
Q 006282          382 -----LYVAVAQR  389 (652)
Q Consensus       382 -----l~v~~~~~  389 (652)
                           |+|+++++
T Consensus       467 ~~~~~lkv~fs~~  479 (481)
T TIGR01649       467 SAPYHLKVSFSTS  479 (481)
T ss_pred             CccceEEEEeccC
Confidence                 99998875

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=6.1e-44  Score=378.10  Aligned_cols=340  Identities=25%  Similarity=0.431  Sum_probs=234.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      +.++|||+|||.++||++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.+||++|++.||+..|.|++|+|.|+.
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            46899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCe
Q 006282          108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDK  186 (652)
Q Consensus       108 ~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~  186 (652)
                      ....  .....+|||+|||.++++++|+++|+.||.|..+++..+ ..+.++|||||+|.+.++|.+|++.|||..+.++
T Consensus        82 ~~~~--~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~  159 (352)
T TIGR01661        82 PSSD--SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGC  159 (352)
T ss_pred             cccc--ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCC
Confidence            5432  223458999999999999999999999999999999988 4778999999999999999999999999988774


Q ss_pred             --eeeecccccchhhHHHhhccCcce-----EEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCH
Q 006282          187 --QVFVGHFLRKQERETVAIKTKFNN-----VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENA  259 (652)
Q Consensus       187 --~~~v~~~~~~~~~~~~~~~~~~~~-----l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~  259 (652)
                        .+.+.+..................     .....++.....       ...+.+.....    ........+......
T Consensus       160 ~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~----~~~~~~~~~~~~~~~  228 (352)
T TIGR01661       160 TEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTA-------AGIGPMHHAAA----RFRPSAGDFTAVLAH  228 (352)
T ss_pred             ceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccc-------cCCCCccCccc----ccccCcchhhhhhhh
Confidence              455655443221110000000000     000000000000       00000000000    000000000000000


Q ss_pred             HHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCee
Q 006282          260 DDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTIT  339 (652)
Q Consensus       260 ~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~  339 (652)
                      .        .......  ................ ................+.+|||+|||+++++++|+++|++||.|+
T Consensus       229 ~--------~~~~~~~--~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~  297 (352)
T TIGR01661       229 Q--------QQQHAVA--QQHAAQRASPPATDGQ-TAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQ  297 (352)
T ss_pred             h--------hhhcccc--cccccccCCCcccccc-ccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeE
Confidence            0        0000000  0000000000000000 000000001111123456899999999999999999999999999


Q ss_pred             EEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHH
Q 006282          340 SCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  391 (652)
Q Consensus       340 ~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~  391 (652)
                      +|+|++|. +|.+||||||+|.+.++|.+|+..|||..|+|+.|.|.|+..+.
T Consensus       298 ~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       298 NVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             EEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            99999997 89999999999999999999999999999999999999998764

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

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

Probab=100.00  E-value=4.9e-40  Score=368.42  Aligned_cols=266  Identities=37%  Similarity=0.645  Sum_probs=238.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      ..+|||+|||.++++++|+++|+.||.|.+|+|.+|. +++++|||||.|.+.++|++|++++|+..+.|+.|+|.+...
T Consensus        88 ~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~  166 (562)
T TIGR01628        88 VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK  166 (562)
T ss_pred             CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccc
Confidence            4679999999999999999999999999999999984 678999999999999999999999999999999999976554


Q ss_pred             Cccc---ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceec-
Q 006282          109 DPSI---RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIN-  184 (652)
Q Consensus       109 ~~~~---~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~-  184 (652)
                      ....   ......+|||+||+.++++++|+++|+.||.|.++++..+.+|.++|||||.|.+.++|.+|++.+++..+. 
T Consensus       167 ~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~  246 (562)
T TIGR01628       167 KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL  246 (562)
T ss_pred             ccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecc
Confidence            3222   334456799999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             ---CeeeeecccccchhhHHHh------------hccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcc
Q 006282          185 ---DKQVFVGHFLRKQERETVA------------IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK  249 (652)
Q Consensus       185 ---g~~~~v~~~~~~~~~~~~~------------~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~  249 (652)
                         ++.+.+.+...+.++....            .....++|||+||+.++++++|+++|+.||.|.++.++.+.+|.++
T Consensus       247 ~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~  326 (562)
T TIGR01628       247 AKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSR  326 (562)
T ss_pred             cccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcC
Confidence               9999998877665542211            1235578999999999999999999999999999999999999999


Q ss_pred             eeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHh
Q 006282          250 CFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELK  295 (652)
Q Consensus       250 g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~  295 (652)
                      |||||+|.+.++|.+|+..+|+..+.|+.|+|.++..+..+...+.
T Consensus       327 g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~~  372 (562)
T TIGR01628       327 GFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQ  372 (562)
T ss_pred             CeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHHH
Confidence            9999999999999999999999999999999999988876655443

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

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

Probab=100.00  E-value=1.1e-40  Score=308.33  Aligned_cols=313  Identities=31%  Similarity=0.490  Sum_probs=237.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      .....+.|.|.-||..+|++||+.+|..+|+|.+++++||+.++.|+||+||+|.+++||++|+.+||+..+..|.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            35566889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCcee
Q 006282          105 YSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLI  183 (652)
Q Consensus       105 ~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l  183 (652)
                      ++....+.  -...+|+|.+||+.++.++|.++|+.||.|..-+|..| .+|.++|.|||.|...++|++||+.+||..-
T Consensus       117 yARPSs~~--Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P  194 (360)
T KOG0145|consen  117 YARPSSDS--IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKP  194 (360)
T ss_pred             eccCChhh--hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCC
Confidence            88765443  34568999999999999999999999999988888888 6899999999999999999999999999876


Q ss_pred             cCe--eeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhcc----C-CCeeEEEEeeCCCCCcceeEEEee
Q 006282          184 NDK--QVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGE----Y-GTITSAVVMRDGDGKSKCFGFVNF  256 (652)
Q Consensus       184 ~g~--~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~----~-G~v~~~~i~~~~~g~~~g~~fV~f  256 (652)
                      .|.  .|.|.+....+                    ...+..-|..+|..    | |.+.....         .|-+-+.
T Consensus       195 ~g~tepItVKFannPs--------------------q~t~~a~ls~ly~sp~rr~~Gp~hh~~~---------r~r~~~~  245 (360)
T KOG0145|consen  195 SGCTEPITVKFANNPS--------------------QKTNQALLSQLYQSPARRYGGPMHHQAQ---------RFRLDNL  245 (360)
T ss_pred             CCCCCCeEEEecCCcc--------------------cccchhhhHHhhcCccccCCCcccchhh---------hhccccc
Confidence            553  34444332221                    11122223333321    1 11111000         0000000


Q ss_pred             CCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcC
Q 006282          257 ENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG  336 (652)
Q Consensus       257 ~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG  336 (652)
                      ...   ..++..+....+++-.-.+...-                   ......+.||||-||..+.+|.-|..+|.+||
T Consensus       246 ~~~---~~~~~rfsP~~~d~m~~l~~~~l-------------------p~~~~~g~ciFvYNLspd~de~~LWQlFgpFG  303 (360)
T KOG0145|consen  246 LNP---HAAQARFSPMTIDGMSGLAGVNL-------------------PGGPGGGWCIFVYNLSPDADESILWQLFGPFG  303 (360)
T ss_pred             cch---hhhhccCCCccccccceeeeecc-------------------CCCCCCeeEEEEEecCCCchHhHHHHHhCccc
Confidence            111   11111112222221111111100                   01122478999999999999999999999999


Q ss_pred             CeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          337 TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       337 ~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .|+.|+|++|- ++++||||||.+.+.++|..|+..|||..+++|.|.|.|...+
T Consensus       304 Av~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  304 AVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             ceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            99999999996 5899999999999999999999999999999999999998755

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

Probab=100.00  E-value=1.9e-38  Score=315.05  Aligned_cols=283  Identities=26%  Similarity=0.380  Sum_probs=237.4

Q ss_pred             eCCHHHHHHHHhhcCCcccCCceeEeecccCCc--------ccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEE
Q 006282           78 YANPADAARALDVLNFTPLNNKSIRIMYSHRDP--------SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI  149 (652)
Q Consensus        78 F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~~--------~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v  149 (652)
                      ..+.++|.+||.+-     .|..|.|.-.+++-        .......+.|||+.||.++.|++|..+|.+.|.|.++++
T Consensus        41 ~~~~eaal~al~E~-----tgy~l~ve~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRL  115 (506)
T KOG0117|consen   41 VQSEEAALKALLER-----TGYTLVVENGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRL  115 (506)
T ss_pred             cccHHHHHHHHHHh-----cCceEEEeccccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEE
Confidence            34477788887754     35566665444331        112234557999999999999999999999999999999


Q ss_pred             eeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCcee-cCeeeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHH
Q 006282          150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLI-NDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK  227 (652)
Q Consensus       150 ~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l-~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~  227 (652)
                      ++| .+|.++|||||+|.+.++|.+||+.+|++.| .|+.|.|..            +..+++|||+|+|+++++++|.+
T Consensus       116 MmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~------------Svan~RLFiG~IPK~k~keeIle  183 (506)
T KOG0117|consen  116 MMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV------------SVANCRLFIGNIPKTKKKEEILE  183 (506)
T ss_pred             eecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE------------eeecceeEeccCCccccHHHHHH
Confidence            999 7999999999999999999999999999877 567776644            34568899999999999999999


Q ss_pred             HhccCCC-eeEEEEeeC--CCCCcceeEEEeeCCHHHHHHHHHHHC--CCccCCceEEEEccccchHHHHHHhHHHHHhh
Q 006282          228 IFGEYGT-ITSAVVMRD--GDGKSKCFGFVNFENADDAAKAVEALN--GKKFDDREWYVGKAQKKSEREQELKGQFEQAM  302 (652)
Q Consensus       228 ~F~~~G~-v~~~~i~~~--~~g~~~g~~fV~f~~~~~A~~Ai~~l~--~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~  302 (652)
                      .+++.++ |.+|.+..+  +..++||||||+|.++.+|..|...|-  ...+.|..+.|.||....+...+.-.      
T Consensus       184 e~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms------  257 (506)
T KOG0117|consen  184 EMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMS------  257 (506)
T ss_pred             HHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhh------
Confidence            9999985 777777665  457899999999999999999988774  34578999999999887665443211      


Q ss_pred             hhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeE
Q 006282          303 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL  382 (652)
Q Consensus       303 ~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l  382 (652)
                             .-..|||+||+.++|+|.|+++|+.||.|+.|+.++|       ||||.|.++++|.+|++.+||+.|+|..|
T Consensus       258 -------~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~i  323 (506)
T KOG0117|consen  258 -------KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPI  323 (506)
T ss_pred             -------heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceE
Confidence                   1236999999999999999999999999999999988       99999999999999999999999999999


Q ss_pred             EEEecccHHHHHHHH
Q 006282          383 YVAVAQRKEERRARL  397 (652)
Q Consensus       383 ~v~~~~~~~~r~~~~  397 (652)
                      .|.+|++.+.++...
T Consensus       324 EvtLAKP~~k~k~~r  338 (506)
T KOG0117|consen  324 EVTLAKPVDKKKKER  338 (506)
T ss_pred             EEEecCChhhhccch
Confidence            999999988776543

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

Probab=100.00  E-value=9.2e-40  Score=352.74  Aligned_cols=297  Identities=21%  Similarity=0.343  Sum_probs=243.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC-CceeEee
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN-NKSIRIM  104 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~-G~~i~i~  104 (652)
                      +...++|||+|||++++|++|+++|++||+|.+|+|++| .+++|+|||||+|.+.++|++|++.||+..|. |+.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            455799999999999999999999999999999999999 88999999999999999999999999998885 7888887


Q ss_pred             cccCCcccccCCCcceeecCCCccccHHHHHhhhccCCC-eeEEEEeeC--CCCCcccEEEEEEcCHHHHHHHHHHhcC-
Q 006282          105 YSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGN-ILSCKIATD--GSGQSKGFGFVQFENKESAQNAIDKLNG-  180 (652)
Q Consensus       105 ~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~-I~~~~v~~~--~~g~skG~afV~F~t~e~A~~Ai~~lng-  180 (652)
                      ++..        ..+|||+|||.++++++|.+.|+.++. +.++.+...  ..++++|||||+|.+.++|..|+++++. 
T Consensus       134 ~S~~--------~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~g  205 (578)
T TIGR01648       134 ISVD--------NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPG  205 (578)
T ss_pred             cccc--------CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhcc
Confidence            7643        468999999999999999999999873 555544433  3567899999999999999999998853 


Q ss_pred             -ceecCeeeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccC--CCeeEEEEeeCCCCCcceeEEEeeC
Q 006282          181 -MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFE  257 (652)
Q Consensus       181 -~~l~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~~~i~~~~~g~~~g~~fV~f~  257 (652)
                       ..++++.|.|.+..+...... ......++|||+||+.++++++|+++|+.|  |.|.++.+++       +||||+|+
T Consensus       206 ki~l~Gr~I~VdwA~p~~~~d~-~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-------gfAFVeF~  277 (578)
T TIGR01648       206 RIQLWGHVIAVDWAEPEEEVDE-DVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-------DYAFVHFE  277 (578)
T ss_pred             ceEecCceEEEEeecccccccc-cccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-------CeEEEEeC
Confidence             467899999998876543322 122345789999999999999999999999  9999998764       49999999


Q ss_pred             CHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHH-h----HH-----HHHhhhhcccccccceeeecCCCCCCCHHH
Q 006282          258 NADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQEL-K----GQ-----FEQAMKETVDKFQGLNLYIKNLGDSIDDEK  327 (652)
Q Consensus       258 ~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~-~----~~-----~~~~~~~~~~~~~~~~l~V~nlp~~~te~~  327 (652)
                      +.++|.+|++.||+..|.|+.|.|.++.......... .    ..     .+.......-.....++++.|+++..+++-
T Consensus       278 s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~  357 (578)
T TIGR01648       278 DREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAP  357 (578)
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEccCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccc
Confidence            9999999999999999999999999997653321100 0    00     000000011123467899999999999999


Q ss_pred             HHHHhhhcCCee
Q 006282          328 LKELFSEFGTIT  339 (652)
Q Consensus       328 L~~~F~~fG~I~  339 (652)
                      +.++|..+|.|.
T Consensus       358 ~~~~f~~~g~~~  369 (578)
T TIGR01648       358 SLHFPRMPGPIR  369 (578)
T ss_pred             hhhccccCcccc
Confidence            999999998744

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.

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

Probab=100.00  E-value=9.2e-38  Score=337.24  Aligned_cols=281  Identities=24%  Similarity=0.349  Sum_probs=227.9

Q ss_pred             CHHHHHHHHhhcCCcccCCceeEeecccCCcc---cccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCC
Q 006282           80 NPADAARALDVLNFTPLNNKSIRIMYSHRDPS---IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ  156 (652)
Q Consensus        80 ~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~~~---~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~  156 (652)
                      ..++|.+||.++++..+........+....+.   .......+|||+|||.++++++|+++|+.||.|.+|+|+.|.+|.
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~   97 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQ   97 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCC
Confidence            46789999988886655444333333322111   112234689999999999999999999999999999999999999


Q ss_pred             cccEEEEEEcCHHHHHHHHHHhcCceec-CeeeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCC-
Q 006282          157 SKGFGFVQFENKESAQNAIDKLNGMLIN-DKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT-  234 (652)
Q Consensus       157 skG~afV~F~t~e~A~~Ai~~lng~~l~-g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~-  234 (652)
                      ++|||||+|.+.++|.+|++.+|+..+. ++.+.+...            ...++|||+|||.++++++|.+.|++++. 
T Consensus        98 sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S------------~~~~rLFVgNLP~~~TeeeL~eeFskv~eg  165 (578)
T TIGR01648        98 NRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS------------VDNCRLFVGGIPKNKKREEILEEFSKVTEG  165 (578)
T ss_pred             ccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc------------ccCceeEeecCCcchhhHHHHHHhhcccCC
Confidence            9999999999999999999999998885 666555332            34578999999999999999999999964 


Q ss_pred             eeEEEEeeC--CCCCcceeEEEeeCCHHHHHHHHHHHCC--CccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccc
Q 006282          235 ITSAVVMRD--GDGKSKCFGFVNFENADDAAKAVEALNG--KKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ  310 (652)
Q Consensus       235 v~~~~i~~~--~~g~~~g~~fV~f~~~~~A~~Ai~~l~~--~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  310 (652)
                      +.++.+...  ..++++|||||+|+++++|..|++.|+.  ..+.++.|.|.|+..+.+...+             ....
T Consensus       166 vv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~-------------~~~~  232 (578)
T TIGR01648       166 VVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDED-------------VMAK  232 (578)
T ss_pred             ceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccccc-------------cccc
Confidence            444444332  3568899999999999999999988864  3578999999998765432111             1122


Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhc--CCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~f--G~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..+|||+||++++++++|+++|+.|  |+|++|++++       +||||+|.+.++|.+|++.|||..|+|+.|.|.|++
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Ak  305 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAK  305 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            4579999999999999999999999  9999998764       499999999999999999999999999999999998


Q ss_pred             cHHH
Q 006282          389 RKEE  392 (652)
Q Consensus       389 ~~~~  392 (652)
                      +++.
T Consensus       306 p~~~  309 (578)
T TIGR01648       306 PVDK  309 (578)
T ss_pred             CCCc
Confidence            7643

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

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

Probab=100.00  E-value=1.1e-37  Score=309.75  Aligned_cols=253  Identities=25%  Similarity=0.421  Sum_probs=230.2

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc-CCce
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL-NNKS  100 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i-~G~~  100 (652)
                      .+..+..++.||||.||.++.|++|..||..+|+|.++|++.|+.++.++|||||.|.+.++|++|+++||+.+| .||.
T Consensus        76 eg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~  155 (506)
T KOG0117|consen   76 EGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKL  155 (506)
T ss_pred             cCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCE
Confidence            445567899999999999999999999999999999999999999999999999999999999999999999988 5999


Q ss_pred             eEeecccCCcccccCCCcceeecCCCccccHHHHHhhhccCC-CeeEEEEeeC--CCCCcccEEEEEEcCHHHHHHHHHH
Q 006282          101 IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG-NILSCKIATD--GSGQSKGFGFVQFENKESAQNAIDK  177 (652)
Q Consensus       101 i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG-~I~~~~v~~~--~~g~skG~afV~F~t~e~A~~Ai~~  177 (652)
                      |.|..|..        +++|||+|||++.++++|.+.|++.+ .|+.+.+..+  ...+++|||||+|.+...|.-|..+
T Consensus       156 igvc~Sva--------n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrK  227 (506)
T KOG0117|consen  156 LGVCVSVA--------NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRK  227 (506)
T ss_pred             eEEEEeee--------cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhh
Confidence            99988775        36899999999999999999999988 5788888877  3567999999999999999999998


Q ss_pred             hc--CceecCeeeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEe
Q 006282          178 LN--GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVN  255 (652)
Q Consensus       178 ln--g~~l~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~  255 (652)
                      |-  ...++|..+.|.|+.+..+.... .......|||+||+.++|+|.|+++|+.||.|+.|+.++|       ||||.
T Consensus       228 l~~g~~klwgn~~tVdWAep~~e~ded-~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVH  299 (506)
T KOG0117|consen  228 LMPGKIKLWGNAITVDWAEPEEEPDED-TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVH  299 (506)
T ss_pred             ccCCceeecCCcceeeccCcccCCChh-hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEe
Confidence            73  36789999999999988776654 4566678999999999999999999999999999998877       99999


Q ss_pred             eCCHHHHHHHHHHHCCCccCCceEEEEccccchHH
Q 006282          256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSER  290 (652)
Q Consensus       256 f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~  290 (652)
                      |.+.++|.+|++.+|++.++|..|.|..|+...++
T Consensus       300 f~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  300 FAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             ecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence            99999999999999999999999999999876544

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

Probab=100.00  E-value=2.1e-37  Score=313.98  Aligned_cols=343  Identities=27%  Similarity=0.438  Sum_probs=276.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      .||||++||++++.++|.++|+.+|+|..+-|+.++.+..++||+||.|.-.+|+++|+...++..|.|+.|+|..+...
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999877643


Q ss_pred             cccc------------------------cCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEE
Q 006282          110 PSIR------------------------KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF  165 (652)
Q Consensus       110 ~~~~------------------------~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F  165 (652)
                      ....                        ......|.|+|||+.+...+|..+|+.||.|.++.|.....|.-.|||||+|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence            2211                        1124569999999999999999999999999999999888888889999999


Q ss_pred             cCHHHHHHHHHHhcCceecCeeeeecccccchhhHHHh------------------------------------------
Q 006282          166 ENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVA------------------------------------------  203 (652)
Q Consensus       166 ~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~~~~~~------------------------------------------  203 (652)
                      ....+|..|++.+|+..|.|+.|.|.|+.++..-....                                          
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~  245 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEET  245 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccc
Confidence            99999999999999999999999999886432111000                                          


Q ss_pred             h--------------------c----------------------cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEe
Q 006282          204 I--------------------K----------------------TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM  241 (652)
Q Consensus       204 ~--------------------~----------------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~  241 (652)
                      .                    .                      ....+|||+|||+++++++|.+.|++||.|..+.++
T Consensus       246 D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV  325 (678)
T KOG0127|consen  246 DGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIV  325 (678)
T ss_pred             cccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEE
Confidence            0                    0                      000349999999999999999999999999999988


Q ss_pred             eC-CCCCcceeEEEeeCCHHHHHHHHHHHC-----C-CccCCceEEEEccccchHHHHHH--------------------
Q 006282          242 RD-GDGKSKCFGFVNFENADDAAKAVEALN-----G-KKFDDREWYVGKAQKKSEREQEL--------------------  294 (652)
Q Consensus       242 ~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~-----~-~~~~g~~l~v~~a~~~~~~~~~~--------------------  294 (652)
                      .+ .+|.++|+|||.|.+..+|..||....     + ..+.||.|.|..+-.+.+-....                    
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLyLa~EG  405 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLYLAREG  405 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCccceeeeccC
Confidence            77 579999999999999999999998762     2 55789999998886543322210                    


Q ss_pred             -------------------hHHHHHh----hhhcccccccceeeecCCCCCCCHHHHHHHhhh----c-CCee-EEEEec
Q 006282          295 -------------------KGQFEQA----MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSE----F-GTIT-SCKVMR  345 (652)
Q Consensus       295 -------------------~~~~~~~----~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~----f-G~I~-~v~i~~  345 (652)
                                         +..+...    .++..-....+.|.|.|||..+++..|+.+...    | +.+. .|+.+.
T Consensus       406 ~I~~gt~aAeglS~~Dm~kRer~~~~k~k~lknpnlhlSrtRL~i~Nlpramn~KqL~~Ll~~Av~~~at~~kk~~R~~~  485 (678)
T KOG0127|consen  406 LIRDGTPAAEGLSATDMAKRERIAERKRKKLKNPNLHLSRTRLVIRNLPRAMNPKQLNRLLRDAVTGFATKVKKCIRQIK  485 (678)
T ss_pred             ccccCChhhcccchhhHHHHHHHHHHHHHhhcCCceeeehhhhhhhcCccccCHHHHHHHHHHHHhhhhhhcchhhhhhh
Confidence                               0011100    011111234566999999999999999988753    3 3332 234443


Q ss_pred             CC----CCCCccEEEEEeCCHHHHHHHHHHh
Q 006282          346 DP----SGISKGSGFVAFSTPEEASRALAEM  372 (652)
Q Consensus       346 ~~----~g~s~g~afV~F~s~~~A~~A~~~l  372 (652)
                      ..    .+.|.||+|+.|..++.|.+|+..+
T Consensus       486 ~le~~~k~~s~g~aF~~f~EhEhalkalk~~  516 (678)
T KOG0127|consen  486 FLEEEKKNYSEGYAFVGFTEHEHALKALKVL  516 (678)
T ss_pred             hHHhhhhcccccccccCccHHHHHHHhhhcc
Confidence            32    5789999999999999999999855

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.9e-37  Score=285.05  Aligned_cols=236  Identities=25%  Similarity=0.459  Sum_probs=196.0

Q ss_pred             CCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeeccccc
Q 006282          116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLR  195 (652)
Q Consensus       116 ~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~  195 (652)
                      .-++|||+||+.++||+-|..+|+..|.|.+||++.|+-                                  .|.+...
T Consensus         5 ~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~----------------------------------~v~wa~~   50 (321)
T KOG0148|consen    5 EPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDEL----------------------------------KVNWATA   50 (321)
T ss_pred             CCceEEeeccChhhHHHHHHHHHHhccccccceeehhhh----------------------------------ccccccC
Confidence            346899999999999999999999999999999998621                                  1222211


Q ss_pred             chhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCcc
Q 006282          196 KQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKF  274 (652)
Q Consensus       196 ~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~  274 (652)
                      ...++. ......-.+||+.|...++.++|++.|.+||+|.+++|++| .++++|||+||.|.+.++|++||..|+|..+
T Consensus        51 p~nQsk-~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl  129 (321)
T KOG0148|consen   51 PGNQSK-PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL  129 (321)
T ss_pred             cccCCC-CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee
Confidence            111110 11122345999999999999999999999999999999999 6799999999999999999999999999999


Q ss_pred             CCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccE
Q 006282          275 DDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS  354 (652)
Q Consensus       275 ~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~  354 (652)
                      .+|.|+-+|+.+|......-...+++...  ..+...|+|||+||+.-++|++||+.|++||.|.+|+|+++     +||
T Consensus       130 G~R~IRTNWATRKp~e~n~~~ltfdeV~N--Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGY  202 (321)
T KOG0148|consen  130 GRRTIRTNWATRKPSEMNGKPLTFDEVYN--QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGY  202 (321)
T ss_pred             ccceeeccccccCccccCCCCccHHHHhc--cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cce
Confidence            99999999999887332222222332222  23456899999999999999999999999999999999998     889


Q ss_pred             EEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHH
Q 006282          355 GFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER  393 (652)
Q Consensus       355 afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r  393 (652)
                      +||.|.+.|.|.+||..+||..|+|..+++.|.+.....
T Consensus       203 aFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  203 AFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             EEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            999999999999999999999999999999999876543

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

Probab=100.00  E-value=1e-35  Score=321.39  Aligned_cols=168  Identities=23%  Similarity=0.496  Sum_probs=153.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+||+++++|++|+++|+.||+|.+|++++|+.|++++|||||+|.+.++|++|++.||+..|.|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             CCccc---------ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHH
Q 006282          108 RDPSI---------RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK  177 (652)
Q Consensus       108 ~~~~~---------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~  177 (652)
                      ..+..         ......+|||+||+.++++++|+++|+.||.|.+|++..| ..+.++|||||+|.+.++|.+|++.
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            33211         1123468999999999999999999999999999999998 4678999999999999999999999


Q ss_pred             hcCceecCeeeeeccccc
Q 006282          178 LNGMLINDKQVFVGHFLR  195 (652)
Q Consensus       178 lng~~l~g~~~~v~~~~~  195 (652)
                      +|+..++|+.|.|.+...
T Consensus       266 mNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             hCCCeeCCeEEEEEecCC
Confidence            999999999999988764

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.

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

Probab=100.00  E-value=1.6e-36  Score=299.89  Aligned_cols=362  Identities=25%  Similarity=0.371  Sum_probs=245.4

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcc-cCC--
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTP-LNN--   98 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~-i~G--   98 (652)
                      ++.+......|||+-+|..++|+||+++|++||.|.+|.|.+|+.|+.|+|||||.|.+.++|.+|+..|++.. |-|  
T Consensus        27 ~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~  106 (510)
T KOG0144|consen   27 TDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMH  106 (510)
T ss_pred             CCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCC
Confidence            34444567899999999999999999999999999999999999999999999999999999999999998654 455  


Q ss_pred             ceeEeecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHh
Q 006282           99 KSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL  178 (652)
Q Consensus        99 ~~i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~l  178 (652)
                      .+|.|.++..+.. +-....+|||+-|++.++|++++++|++||.|.+|.|.+|..+.+||||||.|.+.|.|..||+.+
T Consensus       107 ~pvqvk~Ad~E~e-r~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~  185 (510)
T KOG0144|consen  107 HPVQVKYADGERE-RIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKAL  185 (510)
T ss_pred             cceeecccchhhh-ccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhh
Confidence            6788877765432 224467899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCce-ecC--eeeeecccccchhhHHHhhc-------------cCcce------------------------EEecCCCC
Q 006282          179 NGML-IND--KQVFVGHFLRKQERETVAIK-------------TKFNN------------------------VFVKNLDE  218 (652)
Q Consensus       179 ng~~-l~g--~~~~v~~~~~~~~~~~~~~~-------------~~~~~------------------------l~V~nlp~  218 (652)
                      |+.. +.|  ..+.|.+....+.+......             ..+.+                        .-+++++.
T Consensus       186 ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~  265 (510)
T KOG0144|consen  186 NGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPP  265 (510)
T ss_pred             ccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccC
Confidence            9854 454  46778877765544333210             01111                        00111110


Q ss_pred             --CCCHHHHHHH-------------------------hccCCCeeE----------------------------------
Q 006282          219 --STTDEDLKKI-------------------------FGEYGTITS----------------------------------  237 (652)
Q Consensus       219 --~~t~~~l~~~-------------------------F~~~G~v~~----------------------------------  237 (652)
                        ......+...                         .+.-|...+                                  
T Consensus       266 L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~  345 (510)
T KOG0144|consen  266 LGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANY  345 (510)
T ss_pred             CCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhc
Confidence              0000000000                         000000000                                  


Q ss_pred             --------EEEe---eCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcc
Q 006282          238 --------AVVM---RDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETV  306 (652)
Q Consensus       238 --------~~i~---~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~  306 (652)
                              ..+.   ....+...-.+...|. -..+..-..++...     .++...+...-..................
T Consensus       346 n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~-~~~~~~~tQa~q~~-----~q~a~~a~~~l~~q~~~~qq~~~~~~~q~  419 (510)
T KOG0144|consen  346 NLAGGMAGAGTTSPVAASLANLQQIGLTPFA-GAAALDHTQAMQQY-----AQSANLAAPGLVGQQATTQQAQMVGNGQV  419 (510)
T ss_pred             ccccccccccccCcccccccccccccCCChh-hhhhHhHHHhhhHh-----hhhhhhcccchhhhhHhhhhhhcccCccc
Confidence                    0000   0000000001122221 00011111111110     01111111100011111111111122334


Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      +...|.+|||.+||-+.-+.+|-..|.+||.|.+.+++.|+ +|.|++|+||.|++..+|.+||..|||+.+++|+|+|.
T Consensus       420 eGpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQ  499 (510)
T KOG0144|consen  420 EGPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQ  499 (510)
T ss_pred             cCCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEE
Confidence            56678999999999999999999999999999999998876 89999999999999999999999999999999999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      +.+.+
T Consensus       500 lk~~~  504 (510)
T KOG0144|consen  500 LKRDR  504 (510)
T ss_pred             eeecc
Confidence            88755

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

Probab=100.00  E-value=4.2e-35  Score=321.27  Aligned_cols=342  Identities=22%  Similarity=0.291  Sum_probs=233.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....++|||+|||.++++++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|.+||. |++..|.|++|.|.+
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            4557899999999999999999999999999999999999999999999999999999999998 999999999999988


Q ss_pred             ccCCccc----------ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCC-CCCcccEEEEEEcCHHHHHHH
Q 006282          106 SHRDPSI----------RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA  174 (652)
Q Consensus       106 s~~~~~~----------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~-~g~skG~afV~F~t~e~A~~A  174 (652)
                      +......          ......+|||+||+.++++++|+++|+.||.|..|.+..+. +|.++|||||+|.+.++|..|
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH
Confidence            7543211          01225789999999999999999999999999999999984 568999999999999999999


Q ss_pred             HHHhcCceecCeeeeecccccchhhHHHhhc-cCcce-EEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeE
Q 006282          175 IDKLNGMLINDKQVFVGHFLRKQERETVAIK-TKFNN-VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG  252 (652)
Q Consensus       175 i~~lng~~l~g~~~~v~~~~~~~~~~~~~~~-~~~~~-l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~  252 (652)
                      ++.|||..+.|+.|.|.+............. ..... -..+..........+...+...+......+. ...+  ....
T Consensus       245 ~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~--~~~~  321 (457)
T TIGR01622       245 LEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIP-GTGS--KIAL  321 (457)
T ss_pred             HHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCC-Cccc--hhhh
Confidence            9999999999999999997643222111000 00000 0000000111222222222222211000000 0000  0000


Q ss_pred             EEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHH-hhhhcccccccceeeecCCCCCCC-------
Q 006282          253 FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ-AMKETVDKFQGLNLYIKNLGDSID-------  324 (652)
Q Consensus       253 fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~V~nlp~~~t-------  324 (652)
                      +..+             .........+....+...      ....... ............+|+|.||-...+       
T Consensus       322 ~~~~-------------~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~  382 (457)
T TIGR01622       322 MQKL-------------QRDGIIDPNIPSRYATGA------LAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFD  382 (457)
T ss_pred             hccc-------------cccccccccccccccccc------cccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHH
Confidence            0000             000000000000000000      0000000 000000123567899999955444       


Q ss_pred             ---HHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHH
Q 006282          325 ---DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER  393 (652)
Q Consensus       325 ---e~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r  393 (652)
                         .++|++.|++||.|++|.|...   .+.|++||.|.+.++|.+|++.|||+.|+|+.|.+.+.....-.
T Consensus       383 ~~~~~dv~~e~~k~G~v~~v~v~~~---~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~  451 (457)
T TIGR01622       383 NEILDDVKEECSKYGGVVHIYVDTK---NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYD  451 (457)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEEeCC---CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHH
Confidence               3689999999999999998743   35799999999999999999999999999999999998876543

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=100.00  E-value=3.7e-35  Score=320.68  Aligned_cols=262  Identities=23%  Similarity=0.344  Sum_probs=209.9

Q ss_pred             CcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHh--cCceecCeeeeecccc
Q 006282          117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL--NGMLINDKQVFVGHFL  194 (652)
Q Consensus       117 ~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~l--ng~~l~g~~~~v~~~~  194 (652)
                      +..|||+|||.++++++|+++|+.||.|.+|++++     ++|||||+|.+.++|.+|++.+  ++..+.|+.|.|.++.
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~-----~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~   76 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP-----GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYST   76 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC-----CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecC
Confidence            46799999999999999999999999999999986     5689999999999999999864  7889999999999886


Q ss_pred             cchhhHHH------hhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHH
Q 006282          195 RKQERETV------AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA  268 (652)
Q Consensus       195 ~~~~~~~~------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~  268 (652)
                      ........      .......+|+|+||++.+++++|+++|+.||.|.++.++++..   +++|||+|.+.++|.+|++.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~---~~~afVef~~~~~A~~A~~~  153 (481)
T TIGR01649        77 SQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN---VFQALVEFESVNSAQHAKAA  153 (481)
T ss_pred             CcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC---ceEEEEEECCHHHHHHHHHH
Confidence            54311111      0112345799999999999999999999999999999987632   46899999999999999999


Q ss_pred             HCCCccCC--ceEEEEccccch--------------------HHHHHHhHHHHHhhh-----------------------
Q 006282          269 LNGKKFDD--REWYVGKAQKKS--------------------EREQELKGQFEQAMK-----------------------  303 (652)
Q Consensus       269 l~~~~~~g--~~l~v~~a~~~~--------------------~~~~~~~~~~~~~~~-----------------------  303 (652)
                      |||..+.+  +.|.|.++....                    +++..+.........                       
T Consensus       154 Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  233 (481)
T TIGR01649       154 LNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLA  233 (481)
T ss_pred             hcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCC
Confidence            99999965  467776654311                    000000000000000                       


Q ss_pred             ----------------------------------hcccccccceeeecCCCC-CCCHHHHHHHhhhcCCeeEEEEecCCC
Q 006282          304 ----------------------------------ETVDKFQGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPS  348 (652)
Q Consensus       304 ----------------------------------~~~~~~~~~~l~V~nlp~-~~te~~L~~~F~~fG~I~~v~i~~~~~  348 (652)
                                                        .......+++|||+||++ .+|+++|+++|+.||.|.+|+|+++  
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~--  311 (481)
T TIGR01649       234 PLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN--  311 (481)
T ss_pred             cccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC--
Confidence                                              000123567999999997 6999999999999999999999987  


Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          349 GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       349 g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                        .+|||||+|.+.++|.+|+..|||..|.|+.|+|.+++..
T Consensus       312 --~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       312 --KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             --CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence              3689999999999999999999999999999999987643

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.1e-34  Score=265.32  Aligned_cols=220  Identities=28%  Similarity=0.511  Sum_probs=192.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ..-++|||+||+++|||+-|..||+++|+|.+++|+.|                                   .++|+|.
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-----------------------------------e~~v~wa   48 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-----------------------------------ELKVNWA   48 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehh-----------------------------------hhccccc
Confidence            34579999999999999999999999999999999887                                   4556665


Q ss_pred             cCCccccc---CCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCce
Q 006282          107 HRDPSIRK---SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGML  182 (652)
Q Consensus       107 ~~~~~~~~---~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~  182 (652)
                      .......+   +..-.+||+.|...++.++|++.|..||+|.+++|++| .++++||||||.|.+.++|++||..|||.-
T Consensus        49 ~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqW  128 (321)
T KOG0148|consen   49 TAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQW  128 (321)
T ss_pred             cCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCee
Confidence            54311111   11335999999999999999999999999999999999 799999999999999999999999999999


Q ss_pred             ecCeeeeecccccchhhHHH----------hhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeE
Q 006282          183 INDKQVFVGHFLRKQERETV----------AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG  252 (652)
Q Consensus       183 l~g~~~~v~~~~~~~~~~~~----------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~  252 (652)
                      |.+|.|+..|+.++......          ..+..+++|||+|++.-+++++|++.|+.||.|.+|++.++     +||+
T Consensus       129 lG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYa  203 (321)
T KOG0148|consen  129 LGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYA  203 (321)
T ss_pred             eccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceE
Confidence            99999999999877632111          12457789999999999999999999999999999999988     7899


Q ss_pred             EEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          253 FVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       253 fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      ||.|++.|+|.+||..+|+..+.|..+++.|.+.
T Consensus       204 FVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  204 FVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             EEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            9999999999999999999999999999988754

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

Probab=100.00  E-value=1.9e-32  Score=304.54  Aligned_cols=254  Identities=23%  Similarity=0.372  Sum_probs=206.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhcc------------CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQV------------GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF   93 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~------------G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~   93 (652)
                      ....++|||||||+++|+++|+++|+.+            +.|.++.+      .+++|||||+|.+.++|..||+ ||+
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CCC
Confidence            4467899999999999999999999975            34555544      3456899999999999999996 999


Q ss_pred             cccCCceeEeecccCCc---------------------------ccccCCCcceeecCCCccccHHHHHhhhccCCCeeE
Q 006282           94 TPLNNKSIRIMYSHRDP---------------------------SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS  146 (652)
Q Consensus        94 ~~i~G~~i~i~~s~~~~---------------------------~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~  146 (652)
                      ..|.|+.|+|.+.+...                           ........+|||+|||..+++++|+++|+.||.|..
T Consensus       245 ~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~  324 (509)
T TIGR01642       245 IIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKA  324 (509)
T ss_pred             eEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeE
Confidence            99999999997544221                           001123467999999999999999999999999999


Q ss_pred             EEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchhhHH----------------H------h
Q 006282          147 CKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERET----------------V------A  203 (652)
Q Consensus       147 ~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~~~~----------------~------~  203 (652)
                      |.++.+ .+|.++|||||+|.+.++|..|++.|||..+.|+.|.|.+.........                .      .
T Consensus       325 ~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (509)
T TIGR01642       325 FNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQI  404 (509)
T ss_pred             EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccc
Confidence            999998 5889999999999999999999999999999999999977642211000                0      0


Q ss_pred             hccCcceEEecCCCCCC----------CHHHHHHHhccCCCeeEEEEeeCC----CCCcceeEEEeeCCHHHHHHHHHHH
Q 006282          204 IKTKFNNVFVKNLDEST----------TDEDLKKIFGEYGTITSAVVMRDG----DGKSKCFGFVNFENADDAAKAVEAL  269 (652)
Q Consensus       204 ~~~~~~~l~V~nlp~~~----------t~~~l~~~F~~~G~v~~~~i~~~~----~g~~~g~~fV~f~~~~~A~~Ai~~l  269 (652)
                      .......|+|.|+....          ..++|+++|++||.|.+|.|.++.    .+.+.|++||+|.+.++|.+|+..|
T Consensus       405 ~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~l  484 (509)
T TIGR01642       405 GGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGM  484 (509)
T ss_pred             cCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHc
Confidence            01234568899986321          236799999999999999998752    3556799999999999999999999


Q ss_pred             CCCccCCceEEEEcccc
Q 006282          270 NGKKFDDREWYVGKAQK  286 (652)
Q Consensus       270 ~~~~~~g~~l~v~~a~~  286 (652)
                      ||..|.|+.|.+.+...
T Consensus       485 nGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       485 NGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             CCCEECCeEEEEEEeCH
Confidence            99999999999988644

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

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

Probab=100.00  E-value=8.4e-33  Score=280.61  Aligned_cols=276  Identities=30%  Similarity=0.471  Sum_probs=229.3

Q ss_pred             cceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccc
Q 006282          118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRK  196 (652)
Q Consensus       118 ~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~  196 (652)
                      .+|||++||++++.++|.++|+.+|.|..|.++++ ..+.++|||||.|+-.|++.+|+...++..+.|+.+.|.....+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            68999999999999999999999999999999999 46689999999999999999999999999999999999888765


Q ss_pred             hhhHHHhh-----------c---------cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEee
Q 006282          197 QERETVAI-----------K---------TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNF  256 (652)
Q Consensus       197 ~~~~~~~~-----------~---------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f  256 (652)
                      ........           +         ...-.|.|+|||+.+.+++|+.+|+.||.|..|.|.+..+|+..|||||.|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence            43331110           0         013359999999999999999999999999999999999999899999999


Q ss_pred             CCHHHHHHHHHHHCCCccCCceEEEEccccchHHHH-------HHhH---------------------------------
Q 006282          257 ENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ-------ELKG---------------------------------  296 (652)
Q Consensus       257 ~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~-------~~~~---------------------------------  296 (652)
                      ....+|..|++.+|+..|.||.+-|.||-.+...+.       .++.                                 
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~  245 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEET  245 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccc
Confidence            999999999999999999999999999865532111       0000                                 


Q ss_pred             --HHH------Hhh------hh------------------cccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEe
Q 006282          297 --QFE------QAM------KE------------------TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM  344 (652)
Q Consensus       297 --~~~------~~~------~~------------------~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~  344 (652)
                        .++      ...      .+                  ..+...+.+|||+|||+++|+++|.++|+.||.|..+.|+
T Consensus       246 D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV  325 (678)
T KOG0127|consen  246 DGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIV  325 (678)
T ss_pred             cccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEE
Confidence              000      000      00                  0001124679999999999999999999999999999998


Q ss_pred             cCC-CCCCccEEEEEeCCHHHHHHHHHHh-----cC-cEecCeeEEEEecccHHHH
Q 006282          345 RDP-SGISKGSGFVAFSTPEEASRALAEM-----NG-KMIVSKPLYVAVAQRKEER  393 (652)
Q Consensus       345 ~~~-~g~s~g~afV~F~s~~~A~~A~~~l-----ng-~~~~g~~l~v~~~~~~~~r  393 (652)
                      .++ +|+|+|+|||.|.+..+|.+||...     .| ..++|+-|.|.++-.+.+-
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA  381 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEA  381 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHH
Confidence            776 8999999999999999999999865     24 7889999999999876543

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

Probab=100.00  E-value=3.7e-32  Score=281.69  Aligned_cols=256  Identities=41%  Similarity=0.659  Sum_probs=233.9

Q ss_pred             ceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchh
Q 006282          119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQE  198 (652)
Q Consensus       119 ~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~  198 (652)
                      .|+|+   +++++..|+++|+.+|.|+++++..|. + +-|||||.|.+.++|.+|+..+|...+.|+.+++.|..+...
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~   77 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS   77 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc
Confidence            57788   889999999999999999999999998 6 999999999999999999999999999999999999765443


Q ss_pred             hHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCce
Q 006282          199 RETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE  278 (652)
Q Consensus       199 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~  278 (652)
                      .           +||+||+++++..+|.++|+.||.|.+|++..+.+| ++|| ||+|++.++|.+|++.+||..+.++.
T Consensus        78 ~-----------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kk  144 (369)
T KOG0123|consen   78 L-----------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKK  144 (369)
T ss_pred             e-----------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCe
Confidence            3           999999999999999999999999999999999999 9999 99999999999999999999999999


Q ss_pred             EEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEE
Q 006282          279 WYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA  358 (652)
Q Consensus       279 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~  358 (652)
                      ++|.....+.++......          ....-+++||+|++..+++++|.++|+.||.|+++.++.+..|+++||+||.
T Consensus       145 i~vg~~~~~~er~~~~~~----------~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~  214 (369)
T KOG0123|consen  145 IYVGLFERKEEREAPLGE----------YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVN  214 (369)
T ss_pred             eEEeeccchhhhcccccc----------hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCcccee
Confidence            999999988877654432          1112357999999999999999999999999999999999999999999999


Q ss_pred             eCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHHHHHHHHhhh
Q 006282          359 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFS  402 (652)
Q Consensus       359 F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r~~~~~~~~~  402 (652)
                      |.+.++|.+|+..||+..+.++.++|.-+..+.++...+...+.
T Consensus       215 f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~  258 (369)
T KOG0123|consen  215 FENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFE  258 (369)
T ss_pred             ecChhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhH
Confidence            99999999999999999999999999999997777766555433

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

Probab=100.00  E-value=4.5e-32  Score=301.55  Aligned_cols=270  Identities=18%  Similarity=0.285  Sum_probs=208.8

Q ss_pred             CCcceeecCCCccccHHHHHhhhccC------------CCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCcee
Q 006282          116 GTGNIFIKNLDKSIDHKALHDTFSSF------------GNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLI  183 (652)
Q Consensus       116 ~~~~lfV~nLp~~~t~~~L~~~Fs~f------------G~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l  183 (652)
                      ...+|||+|||.++++++|+++|+.+            +.|..+.+     +..+|||||+|.+.++|..|+ .|+|..+
T Consensus       174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-----~~~kg~afVeF~~~e~A~~Al-~l~g~~~  247 (509)
T TIGR01642       174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-----NKEKNFAFLEFRTVEEATFAM-ALDSIIY  247 (509)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-----CCCCCEEEEEeCCHHHHhhhh-cCCCeEe
Confidence            45679999999999999999999975            23333433     236899999999999999999 6999999


Q ss_pred             cCeeeeecccccchhhH-----------------------HHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEE
Q 006282          184 NDKQVFVGHFLRKQERE-----------------------TVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV  240 (652)
Q Consensus       184 ~g~~~~v~~~~~~~~~~-----------------------~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i  240 (652)
                      .|+.|.|..........                       ........++|||+|||..+++++|+++|+.||.|..+.+
T Consensus       248 ~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~  327 (509)
T TIGR01642       248 SNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNL  327 (509)
T ss_pred             eCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE
Confidence            99999886443221000                       0001123468999999999999999999999999999999


Q ss_pred             eeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHH--------hHHHHHh--hhhccccc
Q 006282          241 MRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQEL--------KGQFEQA--MKETVDKF  309 (652)
Q Consensus       241 ~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~--------~~~~~~~--~~~~~~~~  309 (652)
                      +++ .+|.++|||||+|.+.++|..|++.|++..+.|+.|.|.++..........        .......  ........
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  407 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGK  407 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCC
Confidence            887 578999999999999999999999999999999999999985432110000        0000000  00011123


Q ss_pred             ccceeeecCCCCC--C--------CHHHHHHHhhhcCCeeEEEEecCC----CCCCccEEEEEeCCHHHHHHHHHHhcCc
Q 006282          310 QGLNLYIKNLGDS--I--------DDEKLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTPEEASRALAEMNGK  375 (652)
Q Consensus       310 ~~~~l~V~nlp~~--~--------te~~L~~~F~~fG~I~~v~i~~~~----~g~s~g~afV~F~s~~~A~~A~~~lng~  375 (652)
                      ...+|+|.|+...  +        ..++|+++|++||.|++|+|+++.    .+.+.|++||+|.+.++|.+|+..|||.
T Consensus       408 ~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr  487 (509)
T TIGR01642       408 PTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR  487 (509)
T ss_pred             CceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCC
Confidence            4568999999532  1        136899999999999999998752    3566899999999999999999999999


Q ss_pred             EecCeeEEEEecccHH
Q 006282          376 MIVSKPLYVAVAQRKE  391 (652)
Q Consensus       376 ~~~g~~l~v~~~~~~~  391 (652)
                      .|+|+.|.|.|.....
T Consensus       488 ~~~gr~v~~~~~~~~~  503 (509)
T TIGR01642       488 KFNDRVVVAAFYGEDC  503 (509)
T ss_pred             EECCeEEEEEEeCHHH
Confidence            9999999999987643

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

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

Probab=99.98  E-value=7.2e-32  Score=283.21  Aligned_cols=328  Identities=25%  Similarity=0.400  Sum_probs=264.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .+..|||+|||+.++|++|..+|                       |||.|..++.|.+|..++++..+.|+.+.|..+.
T Consensus       226 etgrlf~RNLpyt~~eed~~~lf-----------------------a~v~~~~~~~avka~~~~D~k~fqgrmlhvlp~~  282 (725)
T KOG0110|consen  226 ETGRLFVRNLPYTSTEEDLLKLF-----------------------AFVTFMFPEHAVKAYSELDGKVFQGRMLHVLPSK  282 (725)
T ss_pred             hhhhhhhccCCccccHHHHHHhh-----------------------HHHhhhhhHHHHhhhhhccccccccceeeecCcc
Confidence            46799999999999999999999                       8999999999999999999999999999875443


Q ss_pred             CCccc---------------------------------------------------------------------------
Q 006282          108 RDPSI---------------------------------------------------------------------------  112 (652)
Q Consensus       108 ~~~~~---------------------------------------------------------------------------  112 (652)
                      ...+.                                                                           
T Consensus       283 ~k~~~~~~~~~~~~~~k~~ke~~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~~i~d~~~~gsavr~al~etr~~~  362 (725)
T KOG0110|consen  283 EKSTAKEDASELGSDYKKEKELKRKAASASFHSWNTLFMGANAVAGILAQKLGVEKSRILDGSLSGSAVRLALGETRVVQ  362 (725)
T ss_pred             hhhhhhhhHhhcCCcHHHHHHhccccchhcceecccccccccHHHHHHHHHhCCeeeeeechhhcchHHHHHHHHhhhch
Confidence            11000                                                                           


Q ss_pred             ------------------ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHH
Q 006282          113 ------------------RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA  174 (652)
Q Consensus       113 ------------------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~A  174 (652)
                                        .......|+++|||..+..++|..+|..||.|..+.+.  +.|.   -++|+|.+..+|+.|
T Consensus       363 e~~~~~ee~gV~l~~F~~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G~---~aiv~fl~p~eAr~A  437 (725)
T KOG0110|consen  363 EVRRFFEENGVKLDAFSQAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGGT---GAIVEFLNPLEARKA  437 (725)
T ss_pred             hhhhhHHhhCcccccchhhhhhcceeeeccCccccccHHHHHHhhcccccceeecC--cccc---eeeeeecCccchHHH
Confidence                              00011338999999999999999999999999888443  3333   589999999999999


Q ss_pred             HHHhcCceecCeeeeecccccchhh-------------HH----------Hh---------------------hccCcce
Q 006282          175 IDKLNGMLINDKQVFVGHFLRKQER-------------ET----------VA---------------------IKTKFNN  210 (652)
Q Consensus       175 i~~lng~~l~g~~~~v~~~~~~~~~-------------~~----------~~---------------------~~~~~~~  210 (652)
                      +..+....+....+++.|.......             ..          ..                     .....+.
T Consensus       438 frklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~  517 (725)
T KOG0110|consen  438 FRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETK  517 (725)
T ss_pred             HHHhchhhhccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchh
Confidence            9999887776666666544311100             00          00                     0011133


Q ss_pred             EEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCC----cceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK----SKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       211 l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~----~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      |||+||.++.+.+++...|...|.|.++.|....++.    |.|||||+|.+.++|..|++.|+|..+.|..|++..+..
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~  597 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISEN  597 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccC
Confidence            9999999999999999999999999999888765543    569999999999999999999999999999999999873


Q ss_pred             chHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHH
Q 006282          287 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEA  365 (652)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A  365 (652)
                      +......         +.......+++|+|+|||+..+..+++++|..||.|.+|+|... ..+.++|||||.|-+..+|
T Consensus       598 k~~~~~g---------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea  668 (725)
T KOG0110|consen  598 KPASTVG---------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREA  668 (725)
T ss_pred             ccccccc---------cccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHH
Confidence            3222111         11112223789999999999999999999999999999999977 3566799999999999999


Q ss_pred             HHHHHHhcCcEecCeeEEEEecccHHH
Q 006282          366 SRALAEMNGKMIVSKPLYVAVAQRKEE  392 (652)
Q Consensus       366 ~~A~~~lng~~~~g~~l~v~~~~~~~~  392 (652)
                      .+|+..|.+..+.|++|.+.|+.....
T Consensus       669 ~nA~~al~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  669 KNAFDALGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             HHHHHhhcccceechhhheehhccchH
Confidence            999999999999999999999998765

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=4.6e-30  Score=265.02  Aligned_cols=170  Identities=30%  Similarity=0.524  Sum_probs=154.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      .....++|||+|||+++||++|+++|+.||+|.+|+|++|+.|++++|||||+|.+.++|++|++.||+..|.+++|+|.
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            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCcee
Q 006282          105 YSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLI  183 (652)
Q Consensus       105 ~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l  183 (652)
                      |+.....  .....+|||.|||.++++++|+++|+.||.|..|++..| .++.++|||||+|.+.++|.+||+.||+..+
T Consensus       183 ~a~p~~~--~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~  260 (346)
T TIGR01659       183 YARPGGE--SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIP  260 (346)
T ss_pred             ccccccc--ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCcc
Confidence            9875432  223568999999999999999999999999999999998 4899999999999999999999999999988


Q ss_pred             cC--eeeeecccccc
Q 006282          184 ND--KQVFVGHFLRK  196 (652)
Q Consensus       184 ~g--~~~~v~~~~~~  196 (652)
                      .+  +.+.|.+....
T Consensus       261 ~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       261 EGGSQPLTVRLAEEH  275 (346)
T ss_pred             CCCceeEEEEECCcc
Confidence            76  56777765543

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.96  E-value=2.5e-28  Score=252.12  Aligned_cols=169  Identities=31%  Similarity=0.553  Sum_probs=153.1

Q ss_pred             ccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEc
Q 006282          205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  283 (652)
Q Consensus       205 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~  283 (652)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++| .+++++|||||+|.+.++|.+|++.|++..+.++.|.|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            356789999999999999999999999999999999988 5799999999999999999999999999999999999998


Q ss_pred             cccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCH
Q 006282          284 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  362 (652)
Q Consensus       284 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~  362 (652)
                      +....+                  ....++|||+|||..+|+++|+++|++||+|++|+|++|. +|+++|||||+|.+.
T Consensus       184 a~p~~~------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~  245 (346)
T TIGR01659       184 ARPGGE------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKR  245 (346)
T ss_pred             cccccc------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCH
Confidence            754221                  1124689999999999999999999999999999999886 899999999999999


Q ss_pred             HHHHHHHHHhcCcEecC--eeEEEEecccHH
Q 006282          363 EEASRALAEMNGKMIVS--KPLYVAVAQRKE  391 (652)
Q Consensus       363 ~~A~~A~~~lng~~~~g--~~l~v~~~~~~~  391 (652)
                      ++|.+|++.||+..+.+  ++|.|.|+....
T Consensus       246 e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       246 EEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             HHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            99999999999999875  789999998653

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).

>smart00517 PolyA C-terminal domain of Poly(A)-binding protein

Probab=99.96  E-value=3.1e-30  Score=191.20  Aligned_cols=64  Identities=61%  Similarity=0.944  Sum_probs=62.1

Q ss_pred             ChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHH
Q 006282          566 SPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV  629 (652)
Q Consensus       566 ~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~  629 (652)
                      +|++||++|||+|||+|++++|++||||||||||||++|||+||+|+++|++||+||++||++|
T Consensus         1 ~p~~qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~ell~lle~~~~L~~kv~EA~~vl~~~   64 (64)
T smart00517        1 PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRSKVDEALEVLKSH   64 (64)
T ss_pred             CHHHHHHHHhHHHhHHHHhhCcccCCcCeeeeeCCCHHHHHHHhcCHHHHHHHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999999999999999999999999999999864

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly)

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

Probab=99.95  E-value=2.9e-27  Score=234.05  Aligned_cols=239  Identities=19%  Similarity=0.242  Sum_probs=201.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHh-ccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFS-QVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs-~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      .....+++||.|+|+++...+|++||. ..|.|..|.++.|. .++++|||.|+|+++|.+++|++.||...++||+|.|
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~v  118 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVV  118 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEE
Confidence            344567899999999999999999995 67899999999995 5899999999999999999999999999999999999


Q ss_pred             ecccCCccc----ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhc
Q 006282          104 MYSHRDPSI----RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN  179 (652)
Q Consensus       104 ~~s~~~~~~----~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~ln  179 (652)
                      ...+...-.    ......+.|+.++....-+.-|...|+.-|.+..-.+..|.++.+++..+++|++.-.+..++.-++
T Consensus       119 KEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfg  198 (608)
T KOG4212|consen  119 KEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFG  198 (608)
T ss_pred             eccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhccc
Confidence            765542211    1123457999999999999999999999998888888899999999999999999988888886655


Q ss_pred             CceecCeeeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCH
Q 006282          180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENA  259 (652)
Q Consensus       180 g~~l~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~  259 (652)
                      ......+.+.+ +           .......+||.||.+.+..+.|++.|.-.|.|.++.+..|+.|.++||+.++|+++
T Consensus       199 l~~~Flr~~h~-f-----------~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hp  266 (608)
T KOG4212|consen  199 LSASFLRSLHI-F-----------SPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHP  266 (608)
T ss_pred             chhhhhhhccC-C-----------CCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecch
Confidence            54443333332 1           11234568999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHCCCccCC
Q 006282          260 DDAAKAVEALNGKKFDD  276 (652)
Q Consensus       260 ~~A~~Ai~~l~~~~~~g  276 (652)
                      -.|..||..+++.-+.+
T Consensus       267 veavqaIsml~~~g~~~  283 (608)
T KOG4212|consen  267 VEAVQAISMLDRQGLFD  283 (608)
T ss_pred             HHHHHHHHhhccCCCcc
Confidence            99999998888654433

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

Probab=99.95  E-value=8.8e-28  Score=238.09  Aligned_cols=172  Identities=30%  Similarity=0.576  Sum_probs=149.7

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCc-cCC--ceEEEE
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKK-FDD--REWYVG  282 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~-~~g--~~l~v~  282 (652)
                      +.-.+||+.+|+.|+|.||+++|++||.|.+|.+++| .++.++|||||.|.+.++|.+|+.+||... +.|  ..+.|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            3456999999999999999999999999999999999 468999999999999999999999998765 444  466777


Q ss_pred             ccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCH
Q 006282          283 KAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP  362 (652)
Q Consensus       283 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~  362 (652)
                      ++....++.                 ....+|||+-|++.++|.+++++|++||.|++|.|++|..|.|||||||+|.+.
T Consensus       113 ~Ad~E~er~-----------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstk  175 (510)
T KOG0144|consen  113 YADGERERI-----------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTK  175 (510)
T ss_pred             ccchhhhcc-----------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehH
Confidence            775544432                 123469999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCcEe-c--CeeEEEEecccHHHHHH
Q 006282          363 EEASRALAEMNGKMI-V--SKPLYVAVAQRKEERRA  395 (652)
Q Consensus       363 ~~A~~A~~~lng~~~-~--g~~l~v~~~~~~~~r~~  395 (652)
                      +-|..||+.|||..- .  ..+|.|+||..+.+|..
T Consensus       176 e~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  176 EMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             HHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            999999999999744 3  57999999997765553

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

Probab=99.95  E-value=6.3e-27  Score=253.39  Aligned_cols=178  Identities=24%  Similarity=0.423  Sum_probs=153.0

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...++|||+||++++++++|+++|+.||.|.++.++.| .+|+++|||||+|.+.++|..|++.|++..+.|+.|.|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            45678999999999999999999999999999999988 57999999999999999999999999999999999999865


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  363 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~  363 (652)
                      ............       ........++|||+||+.++++++|+++|+.||.|++|+|.+|. +|++||||||+|.+.+
T Consensus       185 ~~~p~a~~~~~~-------~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e  257 (612)
T TIGR01645       185 SNMPQAQPIIDM-------VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ  257 (612)
T ss_pred             cccccccccccc-------ccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHH
Confidence            433211100000       00111234689999999999999999999999999999999986 6789999999999999


Q ss_pred             HHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          364 EASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       364 ~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +|.+|+..||+..++|+.|+|.++..+
T Consensus       258 ~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       258 SQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             HHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            999999999999999999999988743

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.

>PF00658 PABP: Poly-adenylate binding protein, unique domain; InterPro: IPR002004 The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (IPR000569 from INTERPRO) []

Probab=99.94  E-value=1.1e-27  Score=185.40  Aligned_cols=71  Identities=61%  Similarity=0.915  Sum_probs=69.4

Q ss_pred             ccchhhhhcCChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHH
Q 006282          556 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL  626 (652)
Q Consensus       556 ~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l  626 (652)
                      +.+++.|+++++++||++|||+|||+|..++|++|+||||||||||++||++||+|+++|++||+||++||
T Consensus         2 ~~~~~~la~~~~~~qk~~LGe~Ly~~V~~~~p~~A~KITGMLLe~~~~ell~ll~~~~~L~~kv~eA~~vL   72 (72)
T PF00658_consen    2 PLTASALASASPEQQKQILGERLYPLVQAIYPELAGKITGMLLEMDNSELLHLLEDPELLREKVQEAIEVL   72 (72)
T ss_dssp             STSHHHHHTSCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTSCHHHHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             cchHHHHhcCCHHHHHHHHhccccHHHHHhCcchhHHHHHHHhcCCHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999997

PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [].; GO: 0003723 RNA binding; PDB: 3KUR_E 1JH4_A 2RQH_B 3KUI_A 3KUS_A 3KUJ_A 3KTR_A 2X04_A 3PTH_A 1JGN_A ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.94  E-value=6.7e-26  Score=240.10  Aligned_cols=170  Identities=31%  Similarity=0.470  Sum_probs=151.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC--ceeEeec
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN--KSIRIMY  105 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G--~~i~i~~  105 (652)
                      ..++|||+|||.++++++|+++|+.||.|..+++++|..++.++|||||+|.+.++|++|++.||+..+.|  ++|+|.|
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            46789999999999999999999999999999999999999999999999999999999999999998877  5678877


Q ss_pred             ccCCccc------------------c------------------------------------------------------
Q 006282          106 SHRDPSI------------------R------------------------------------------------------  113 (652)
Q Consensus       106 s~~~~~~------------------~------------------------------------------------------  113 (652)
                      +......                  +                                                      
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            6432100                  0                                                      


Q ss_pred             ------------------cCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCC-CCCcccEEEEEEcCHHHHHHH
Q 006282          114 ------------------KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA  174 (652)
Q Consensus       114 ------------------~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~-~g~skG~afV~F~t~e~A~~A  174 (652)
                                        .....+|||+|||.++++++|+++|+.||.|.+|+|+.|. +|.++|||||+|.+.++|..|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence                              0011259999999999999999999999999999999995 999999999999999999999


Q ss_pred             HHHhcCceecCeeeeecccccch
Q 006282          175 IDKLNGMLINDKQVFVGHFLRKQ  197 (652)
Q Consensus       175 i~~lng~~l~g~~~~v~~~~~~~  197 (652)
                      ++.|||..+.|+.|.|.+...+.
T Consensus       328 i~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       328 ILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHhCCCEECCeEEEEEEccCCC
Confidence            99999999999999999877654

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

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

Probab=99.94  E-value=2.3e-25  Score=219.41  Aligned_cols=348  Identities=20%  Similarity=0.277  Sum_probs=259.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC--cccCCceeEe
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF--TPLNNKSIRI  103 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~--~~i~G~~i~i  103 (652)
                      ..++..|++||||++++|++|.+++.+||+|..+...+.+.      .||++|.+.++|...+.....  -.+.|++|.|
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yi   98 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYI   98 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcceee
Confidence            45789999999999999999999999999999999988654      699999999998874443222  2468899999


Q ss_pred             ecccCCc------------------------c-----c--cc-------CCCcceeecCCCccccHHHHHhhhccCCCee
Q 006282          104 MYSHRDP------------------------S-----I--RK-------SGTGNIFIKNLDKSIDHKALHDTFSSFGNIL  145 (652)
Q Consensus       104 ~~s~~~~------------------------~-----~--~~-------~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~  145 (652)
                      .|++...                        .     .  ..       +..-.++|.++-+.++-+-|+.+|++||.|+
T Consensus        99 q~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~Vl  178 (492)
T KOG1190|consen   99 QYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVL  178 (492)
T ss_pred             hhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeE
Confidence            8875210                        0     0  00       0112378899999999999999999999999


Q ss_pred             EEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCe--eeeecccc---------cchhhHHH------------
Q 006282          146 SCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDK--QVFVGHFL---------RKQERETV------------  202 (652)
Q Consensus       146 ~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~--~~~v~~~~---------~~~~~~~~------------  202 (652)
                      .|......++.   .|+|+|.+.+.|..|...|+|..|.+-  .+++.+..         ....|.-.            
T Consensus       179 KIiTF~Knn~F---QALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~  255 (492)
T KOG1190|consen  179 KIITFTKNNGF---QALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPS  255 (492)
T ss_pred             EEEEEecccch---hhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccc
Confidence            98887754443   589999999999999999988776432  33332221         00000000            


Q ss_pred             -----------------------------------hh-ccCcceEEecCCC-CCCCHHHHHHHhccCCCeeEEEEeeCCC
Q 006282          203 -----------------------------------AI-KTKFNNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGD  245 (652)
Q Consensus       203 -----------------------------------~~-~~~~~~l~V~nlp-~~~t~~~l~~~F~~~G~v~~~~i~~~~~  245 (652)
                                                         .. ...+..|.|.||. ..+|.+.|..+|+-||.|..|+|+.++.
T Consensus       256 l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk  335 (492)
T KOG1190|consen  256 LDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK  335 (492)
T ss_pred             cchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC
Confidence                                               00 0013557888886 5689999999999999999999997743


Q ss_pred             CCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchH-------HHHHHhHHHHHhhhhc---------cc-c
Q 006282          246 GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSE-------REQELKGQFEQAMKET---------VD-K  308 (652)
Q Consensus       246 g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~-------~~~~~~~~~~~~~~~~---------~~-~  308 (652)
                          .-+.|.+.+...|.-|++.|+|..+.|+.|+|..++...-       +...+...+....-.+         .. .
T Consensus       336 ----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~  411 (492)
T KOG1190|consen  336 ----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIF  411 (492)
T ss_pred             ----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccC
Confidence                3699999999999999999999999999999998865421       1111111111111111         11 2


Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC-eeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS-KPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g-~~l~v~~~  387 (652)
                      +++.+|+..|+|.+++||+|++.|..-|...+...+..   +.+.++++.+.+.|+|..|+..+|+..++. ..|+|+|.
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---CCcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence            35567999999999999999999999887766544432   235699999999999999999999999985 58999998


Q ss_pred             cc
Q 006282          388 QR  389 (652)
Q Consensus       388 ~~  389 (652)
                      +.
T Consensus       489 ks  490 (492)
T KOG1190|consen  489 KS  490 (492)
T ss_pred             cc
Confidence            64

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

Probab=99.94  E-value=2.5e-26  Score=203.18  Aligned_cols=172  Identities=34%  Similarity=0.614  Sum_probs=153.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ......+|||+||+..+|++.|+|+|-++|+|.+|++.+|+.+....|||||+|.+.|||+-|++-||...+.||+|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            34557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeE-EEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCce
Q 006282          105 YSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS-CKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGML  182 (652)
Q Consensus       105 ~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~-~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~  182 (652)
                      .+........ -..++||+||++.++++.|+++|+.||.+.+ -++..+ .+|.++|+|||.|++.|.+.+|+..+|+..
T Consensus        85 kas~~~~nl~-vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~  163 (203)
T KOG0131|consen   85 KASAHQKNLD-VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQY  163 (203)
T ss_pred             eccccccccc-ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccch
Confidence            8773322222 2378999999999999999999999998765 466666 468999999999999999999999999999


Q ss_pred             ecCeeeeecccccch
Q 006282          183 INDKQVFVGHFLRKQ  197 (652)
Q Consensus       183 l~g~~~~v~~~~~~~  197 (652)
                      +.++.+.|..+..+.
T Consensus       164 l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  164 LCNRPITVSYAFKKD  178 (203)
T ss_pred             hcCCceEEEEEEecC
Confidence            999999998876544

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

Probab=99.93  E-value=2.3e-25  Score=234.48  Aligned_cols=259  Identities=25%  Similarity=0.411  Sum_probs=217.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...+.|+|+|||..+..++|.+.|..||+|..|.+.+. .+     -|+|.|.++.+|..|+..|.++-++.-++.+.|+
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~-G~-----~aiv~fl~p~eAr~Afrklaysr~k~~plyle~a  456 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG-GT-----GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWA  456 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecCcc-cc-----eeeeeecCccchHHHHHHhchhhhccCccccccC
Confidence            34589999999999999999999999999998844422 11     4999999999999999999999999999988886


Q ss_pred             cCCccc------------------------------------------------ccCCCcceeecCCCccccHHHHHhhh
Q 006282          107 HRDPSI------------------------------------------------RKSGTGNIFIKNLDKSIDHKALHDTF  138 (652)
Q Consensus       107 ~~~~~~------------------------------------------------~~~~~~~lfV~nLp~~~t~~~L~~~F  138 (652)
                      ..+.-.                                                .......|||+||+++++.++|.+.|
T Consensus       457 P~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F  536 (725)
T KOG0110|consen  457 PEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLF  536 (725)
T ss_pred             hhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHH
Confidence            422000                                                00011229999999999999999999


Q ss_pred             ccCCCeeEEEEeeCCCCC----cccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchhh---HHHhhccCcceE
Q 006282          139 SSFGNILSCKIATDGSGQ----SKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER---ETVAIKTKFNNV  211 (652)
Q Consensus       139 s~fG~I~~~~v~~~~~g~----skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~~---~~~~~~~~~~~l  211 (652)
                      +..|.|++|.|....++.    |.|||||+|.+.++|..|++.|+|..+.|+.+.+..+......   .........+.|
T Consensus       537 ~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKI  616 (725)
T KOG0110|consen  537 SKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKI  616 (725)
T ss_pred             HhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCcccccccccccccccccee
Confidence            999999999998875543    5699999999999999999999999999999999887721111   111112335789


Q ss_pred             EecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHH
Q 006282          212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSER  290 (652)
Q Consensus       212 ~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~  290 (652)
                      +|+|+|+..+..+|+.+|+.||.+.++.+.+. ..+.++|||||.|-+..+|.+|+++|....+.||.|.+.|+.....-
T Consensus       617 lVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~~~  696 (725)
T KOG0110|consen  617 LVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDNTM  696 (725)
T ss_pred             eeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccchHH
Confidence            99999999999999999999999999999977 56778999999999999999999999999999999999999887663


Q ss_pred             H
Q 006282          291 E  291 (652)
Q Consensus       291 ~  291 (652)
                      +
T Consensus       697 e  697 (725)
T KOG0110|consen  697 E  697 (725)
T ss_pred             H
Confidence            3

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

Probab=99.93  E-value=2.6e-25  Score=215.50  Aligned_cols=166  Identities=23%  Similarity=0.496  Sum_probs=149.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      .|+||||.+..++.|+.|+..|..||+|++|....|..|++.+|||||+|+-+|.|.-|++.||+..+.||.|+|.....
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999986543


Q ss_pred             Cccc---------ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCC-CCCcccEEEEEEcCHHHHHHHHHHh
Q 006282          109 DPSI---------RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL  178 (652)
Q Consensus       109 ~~~~---------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~-~g~skG~afV~F~t~e~A~~Ai~~l  178 (652)
                      -+..         ....-.+|||..+.++.+++||+..|..||.|+.|++..+. .+..+||||++|.+..+-.+|+..+
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasM  272 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM  272 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhc
Confidence            3211         12234579999999999999999999999999999999995 5568999999999999999999999


Q ss_pred             cCceecCeeeeecccc
Q 006282          179 NGMLINDKQVFVGHFL  194 (652)
Q Consensus       179 ng~~l~g~~~~v~~~~  194 (652)
                      |-+.++|..++|+.+.
T Consensus       273 NlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  273 NLFDLGGQYLRVGKCV  288 (544)
T ss_pred             chhhcccceEeccccc
Confidence            9999999888886553

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

Probab=99.92  E-value=5.3e-25  Score=225.97  Aligned_cols=328  Identities=21%  Similarity=0.316  Sum_probs=227.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....+++|+--|.-.+++-+|+++|+.+|+|.+|+++.|..+++|+|.|||+|.+.+....|+. |.+..+.|-+|.|..
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQL  254 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecc
Confidence            4456788888888889999999999999999999999999999999999999999999999997 999999999999987


Q ss_pred             ccCCc--------ccc----cCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCC-CCCcccEEEEEEcCHHHHH
Q 006282          106 SHRDP--------SIR----KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQ  172 (652)
Q Consensus       106 s~~~~--------~~~----~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~-~g~skG~afV~F~t~e~A~  172 (652)
                      +....        .+.    ..+-..|+|+||..++++++|+.+|..||.|..+.+..|. +|.++||||++|.+.++|+
T Consensus       255 sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar  334 (549)
T KOG0147|consen  255 SEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDAR  334 (549)
T ss_pred             cHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHH
Confidence            65432        111    1111228999999999999999999999999999999994 9999999999999999999


Q ss_pred             HHHHHhcCceecCeeeeecccccchhhHHHhh-ccCcceEEecCCCCCC-CHHHHHHHhccCCCeeEEEEeeCCCCCcce
Q 006282          173 NAIDKLNGMLINDKQVFVGHFLRKQERETVAI-KTKFNNVFVKNLDEST-TDEDLKKIFGEYGTITSAVVMRDGDGKSKC  250 (652)
Q Consensus       173 ~Ai~~lng~~l~g~~~~v~~~~~~~~~~~~~~-~~~~~~l~V~nlp~~~-t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g  250 (652)
                      .|++.+||..+.|+.|.|.....+........ ...+...--.+|+.-. ...++..-|.+.-.+.   +          
T Consensus       335 ~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~---~----------  401 (549)
T KOG0147|consen  335 KALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRS---L----------  401 (549)
T ss_pred             HHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCcc---c----------
Confidence            99999999999999999887665544332100 0000000111222111 1122222222111000   0          


Q ss_pred             eEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCC-------C
Q 006282          251 FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDS-------I  323 (652)
Q Consensus       251 ~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-------~  323 (652)
                           -.+...+..++..+......+....+.-..+...             .... ....-|+.++|+=+.       |
T Consensus       402 -----~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~-------------~p~~-~i~t~C~lL~nMFdpstete~n~  462 (549)
T KOG0147|consen  402 -----PSTAISALLLLAKLASAAQFNGVVRVRSVDPADA-------------SPAF-DIPTQCLLLSNMFDPSTETEPNW  462 (549)
T ss_pred             -----cchhhhHHHhccccchHHhhcCCcCccccCcccc-------------cccc-CCccHHHHHhhcCCcccccCcch
Confidence                 0111122222221111111111000000000000             0000 145567888877222       2


Q ss_pred             C---HHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          324 D---DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       324 t---e~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +   .+++.+.+++||.|..|.|..+    |-||.||.|.+.+.|..|+++|||..|.||.|..+|-...
T Consensus       463 d~eI~edV~Eec~k~g~v~hi~vd~n----s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  463 DQEIREDVIEECGKHGKVCHIFVDKN----SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLE  528 (549)
T ss_pred             hhHHHHHHHHHHHhcCCeeEEEEccC----CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehh
Confidence            2   2688888899999999888665    4589999999999999999999999999999999987644

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

Probab=99.92  E-value=4.4e-24  Score=234.14  Aligned_cols=178  Identities=31%  Similarity=0.501  Sum_probs=152.4

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...++|||+|||..+++++|+++|+.||.|.+|.++.+ .+|+++|||||+|.+.++|.+|+. +++..+.|+.|.|...
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            34578999999999999999999999999999999988 568999999999999999999995 9999999999999876


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  363 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~  363 (652)
                      ...........      ..........++|||+||+..+++++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.+
T Consensus       166 ~~~~~~~~~~~------~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e  239 (457)
T TIGR01622       166 QAEKNRAAKAA------THQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE  239 (457)
T ss_pred             chhhhhhhhcc------cccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHH
Confidence            54332221100      0001111235789999999999999999999999999999999886 5689999999999999


Q ss_pred             HHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          364 EASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       364 ~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +|.+|+..|||..|.|+.|.|.|+...
T Consensus       240 ~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       240 EAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             HHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            999999999999999999999998843

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.

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

Probab=99.91  E-value=4.5e-24  Score=198.24  Aligned_cols=169  Identities=31%  Similarity=0.604  Sum_probs=154.1

Q ss_pred             ccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEc
Q 006282          205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  283 (652)
Q Consensus       205 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~  283 (652)
                      ....++|.|.-||..++.||++.+|+..|+|++|++++|+ +|.+-|||||+|.+++||++|+..|||-.+..+.+.|++
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            3456889999999999999999999999999999999995 799999999999999999999999999999999999999


Q ss_pred             cccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCH
Q 006282          284 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  362 (652)
Q Consensus       284 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~  362 (652)
                      +...+..                  ..+.+|||.+||..+|..||..+|++||.|..-+|..|. +|.|||.|||.|+..
T Consensus       118 ARPSs~~------------------Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr  179 (360)
T KOG0145|consen  118 ARPSSDS------------------IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKR  179 (360)
T ss_pred             ccCChhh------------------hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecch
Confidence            8665432                  235689999999999999999999999999998888886 899999999999999


Q ss_pred             HHHHHHHHHhcCcEecC--eeEEEEecccHH
Q 006282          363 EEASRALAEMNGKMIVS--KPLYVAVAQRKE  391 (652)
Q Consensus       363 ~~A~~A~~~lng~~~~g--~~l~v~~~~~~~  391 (652)
                      ++|+.||+.|||..--|  .+|.|+|+....
T Consensus       180 ~EAe~AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  180 IEAEEAIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             hHHHHHHHhccCCCCCCCCCCeEEEecCCcc
Confidence            99999999999987765  689999998763

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

Probab=99.91  E-value=3.1e-23  Score=201.09  Aligned_cols=270  Identities=23%  Similarity=0.467  Sum_probs=214.0

Q ss_pred             cceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccc
Q 006282          118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRK  196 (652)
Q Consensus       118 ~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~  196 (652)
                      ++|||+.|.+.+.++.|+..|..||.|.++.+.-| -+++.|||+||+|+-+|.|.-|++.+||..++||.+.|+....-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            46999999999999999999999999999999888 58999999999999999999999999999999999999866544


Q ss_pred             hhhHHHh-----hccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCC-CCcceeEEEeeCCHHHHHHHHHHHC
Q 006282          197 QERETVA-----IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALN  270 (652)
Q Consensus       197 ~~~~~~~-----~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-g~~~g~~fV~f~~~~~A~~Ai~~l~  270 (652)
                      .......     ....++++||..+..+.+++||+.+|+-||+|..|.+-++.+ +..|||||++|.+..+...|+..||
T Consensus       194 pQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             cccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence            3332222     236788999999999999999999999999999999999865 5689999999999999999999999


Q ss_pred             CCccCCceEEEEccccchH-------------------------------------------------------------
Q 006282          271 GKKFDDREWYVGKAQKKSE-------------------------------------------------------------  289 (652)
Q Consensus       271 ~~~~~g~~l~v~~a~~~~~-------------------------------------------------------------  289 (652)
                      -..++|..|+|+.+-....                                                             
T Consensus       274 lFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~  353 (544)
T KOG0124|consen  274 LFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLP  353 (544)
T ss_pred             hhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCcc
Confidence            9999999888886532210                                                             


Q ss_pred             --------------------------------------------------HH-HHHhHHHH--Hhh--------------
Q 006282          290 --------------------------------------------------RE-QELKGQFE--QAM--------------  302 (652)
Q Consensus       290 --------------------------------------------------~~-~~~~~~~~--~~~--------------  302 (652)
                                                                        ++ .++....+  ...              
T Consensus       354 qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sAR  433 (544)
T KOG0124|consen  354 QAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSAR  433 (544)
T ss_pred             ccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHH
Confidence                                                              00 00000000  000              


Q ss_pred             ----hhcccccccceeeecCC--CCCCCH---HHHHHHhhhcCCeeEEEEecCCCCCC-----ccEEEEEeCCHHHHHHH
Q 006282          303 ----KETVDKFQGLNLYIKNL--GDSIDD---EKLKELFSEFGTITSCKVMRDPSGIS-----KGSGFVAFSTPEEASRA  368 (652)
Q Consensus       303 ----~~~~~~~~~~~l~V~nl--p~~~te---~~L~~~F~~fG~I~~v~i~~~~~g~s-----~g~afV~F~s~~~A~~A  368 (652)
                          ..-.....++.+.++|+  |.+++|   .+|++.+++||.|.+|.|.....+..     ----||+|+...++.+|
T Consensus       434 hlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~ra  513 (544)
T KOG0124|consen  434 HLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRA  513 (544)
T ss_pred             HHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHHHH
Confidence                00011223556788887  445554   68999999999999998887653321     12369999999999999


Q ss_pred             HHHhcCcEecCeeEEEEec
Q 006282          369 LAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       369 ~~~lng~~~~g~~l~v~~~  387 (652)
                      ...|+|+.|+|+++...+.
T Consensus       514 k~ALdGRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  514 KQALDGRFFGGRKVVAEVY  532 (544)
T ss_pred             HHhhccceecCceeehhhh
Confidence            9999999999999876644

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

Probab=99.89  E-value=1.6e-23  Score=185.40  Aligned_cols=171  Identities=32%  Similarity=0.554  Sum_probs=153.1

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ....+|||+||+..++++-|.++|-+.|.|.++.+.+|. +...+|||||+|.++|+|.-|++-|+...+.|+.|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            345789999999999999999999999999999999984 5678999999999999999999999999999999999988


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEE-EEecCC-CCCCccEEEEEeCCH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDP-SGISKGSGFVAFSTP  362 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v-~i~~~~-~g~s~g~afV~F~s~  362 (652)
                      .....                 ....+.+|||+||+++++|.-|.+.|+.||.+.+. +|++++ +|.++|||||.|++.
T Consensus        87 s~~~~-----------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sf  149 (203)
T KOG0131|consen   87 SAHQK-----------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASF  149 (203)
T ss_pred             ccccc-----------------cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhH
Confidence            62211                 12245789999999999999999999999998775 888887 588999999999999


Q ss_pred             HHHHHHHHHhcCcEecCeeEEEEecccHHHH
Q 006282          363 EEASRALAEMNGKMIVSKPLYVAVAQRKEER  393 (652)
Q Consensus       363 ~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r  393 (652)
                      +.+.+|+..|||+.++.+++.|.++.+++.+
T Consensus       150 easd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  150 EASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             HHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            9999999999999999999999999887644

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

Probab=99.89  E-value=1.2e-21  Score=198.78  Aligned_cols=336  Identities=16%  Similarity=0.209  Sum_probs=239.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...-.|.+++|||++|++||.++|+.+ .|.++.+.|.  ++|..|-|||+|.+.+|+++||+ .+...+..+.|.|..+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            345678999999999999999999999 6888766664  68888999999999999999999 5777788899999877


Q ss_pred             cCCcc-------ccc--CCCcceeecCCCccccHHHHHhhhccCCCeeE-EEEeeCCCCCcccEEEEEEcCHHHHHHHHH
Q 006282          107 HRDPS-------IRK--SGTGNIFIKNLDKSIDHKALHDTFSSFGNILS-CKIATDGSGQSKGFGFVQFENKESAQNAID  176 (652)
Q Consensus       107 ~~~~~-------~~~--~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~-~~v~~~~~g~skG~afV~F~t~e~A~~Ai~  176 (652)
                      ..++.       -.+  .....|.+++||++|++++|.++|+..--|.. +.+..+..+++.|-|||+|++.+.|+.|+.
T Consensus        84 ~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~  163 (510)
T KOG4211|consen   84 GGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG  163 (510)
T ss_pred             CCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH
Confidence            54331       112  25667999999999999999999999854444 556777888899999999999999999997


Q ss_pred             HhcCceecCeeeeecccccchhhHHH------------------------------------------------------
Q 006282          177 KLNGMLINDKQVFVGHFLRKQERETV------------------------------------------------------  202 (652)
Q Consensus       177 ~lng~~l~g~~~~v~~~~~~~~~~~~------------------------------------------------------  202 (652)
                      +. ...|.-+-|.|-.+.....+...                                                      
T Consensus       164 rh-re~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~  242 (510)
T KOG4211|consen  164 RH-RENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSL  242 (510)
T ss_pred             HH-HHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccc
Confidence            63 33333333333221110000000                                                      


Q ss_pred             h----------------hc----------------cCc-ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcc
Q 006282          203 A----------------IK----------------TKF-NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK  249 (652)
Q Consensus       203 ~----------------~~----------------~~~-~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~  249 (652)
                      .                ..                ... ..++.++||+..++.++.++|+..-.+ .+.|-...+|+..
T Consensus       243 ~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~T  321 (510)
T KOG4211|consen  243 QDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRAT  321 (510)
T ss_pred             cccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccC
Confidence            0                00                000 237889999999999999999987655 6777778899999


Q ss_pred             eeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccch-HHHHHHh-------------------------------HH
Q 006282          250 CFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS-EREQELK-------------------------------GQ  297 (652)
Q Consensus       250 g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~-~~~~~~~-------------------------------~~  297 (652)
                      |-++|+|.+.++|..|+.. ++..+..+.+....-.... .......                               +.
T Consensus       322 GEAdveF~t~edav~Amsk-d~anm~hrYVElFln~~~ga~g~~~~s~~~g~~~~~~~~~~Gg~a~g~~~gG~~g~~~~~  400 (510)
T KOG4211|consen  322 GEADVEFATGEDAVGAMGK-DGANMGHRYVELFLNGAPGASGGGGPSGPGGVGSSGDRNGGGGYASGSYGGGGNGGGGRG  400 (510)
T ss_pred             CcceeecccchhhHhhhcc-CCcccCcceeeecccCCcccccCccCCCCCCccccccccCCCCccccccccCCCCCcccc
Confidence            9999999999999999853 4444544433322111000 0000000                               00


Q ss_pred             ------------------HHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEe
Q 006282          298 ------------------FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF  359 (652)
Q Consensus       298 ------------------~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F  359 (652)
                                        .+...-.......-.+|..+.+|+..++.++.++|.++ ....|.+.+|+.+...|-|=|.|
T Consensus       401 ~~~G~~~~~~~~~~~~Gy~g~~~~~~~~~~e~~~~~~rgap~~a~eadv~d~~~~~-~~a~~~~~yd~~~~~~~~a~~~~  479 (510)
T KOG4211|consen  401 SPYGRPSDGYSSPGGGGYSGPRGYGRGPQNEHFVIRMRGAPFRASEADVYDFFHPI-RPAQVELLYDHQFQRSGDARVIF  479 (510)
T ss_pred             CCCCCCcccccCCCCCCCcCcccCCCCccccccccCcCCCCccccccchhhccccc-CcccccccccccccccCceeEEE
Confidence                              00000000111223458888999999999999999999 45678899998887789999999


Q ss_pred             CCHHHHHHHHH
Q 006282          360 STPEEASRALA  370 (652)
Q Consensus       360 ~s~~~A~~A~~  370 (652)
                      .+.++++.|+.
T Consensus       480 ~~~~~~q~a~~  490 (510)
T KOG4211|consen  480 YNRKDYQDALM  490 (510)
T ss_pred             echhhhHHHHH
Confidence            99999999996

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

Probab=99.88  E-value=1.2e-22  Score=189.43  Aligned_cols=186  Identities=31%  Similarity=0.480  Sum_probs=157.5

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCcc---CCceEEEEc
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF---DDREWYVGK  283 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~---~g~~l~v~~  283 (652)
                      +.+.|||+-|.+.-+|||++.+|..||.|++|.+.+..+|.+|||+||.|.+..+|..||..||+...   -...|.|.+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            56789999999999999999999999999999999999999999999999999999999999998653   245788888


Q ss_pred             cccchHHHHHHhHHHH----------------------------------------------------------------
Q 006282          284 AQKKSEREQELKGQFE----------------------------------------------------------------  299 (652)
Q Consensus       284 a~~~~~~~~~~~~~~~----------------------------------------------------------------  299 (652)
                      +....||....-....                                                                
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A~  177 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAAA  177 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccccC
Confidence            8766544221100000                                                                


Q ss_pred             --------------------------------------------------------------------------------
Q 006282          300 --------------------------------------------------------------------------------  299 (652)
Q Consensus       300 --------------------------------------------------------------------------------  299 (652)
                                                                                                      
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence                                                                                            


Q ss_pred             ----------------HhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCH
Q 006282          300 ----------------QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  362 (652)
Q Consensus       300 ----------------~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~  362 (652)
                                      .......+...+|||||-.||.++.+.||-..|-+||.|.+.+|+.|. ++.||+||||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                            000001233468999999999999999999999999999999999886 899999999999999


Q ss_pred             HHHHHHHHHhcCcEecCeeEEEEecccHHH
Q 006282          363 EEASRALAEMNGKMIVSKPLYVAVAQRKEE  392 (652)
Q Consensus       363 ~~A~~A~~~lng~~~~g~~l~v~~~~~~~~  392 (652)
                      .+|..||..|||..|+-|+|+|.+.++|+.
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            999999999999999999999999998864

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

Probab=99.87  E-value=5.5e-20  Score=179.43  Aligned_cols=343  Identities=20%  Similarity=0.173  Sum_probs=254.3

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhh--cCCcccCCc
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV--LNFTPLNNK   99 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~--ln~~~i~G~   99 (652)
                      ....+.++..++|++|...++|.+|.|-++.||+|.-+.+...++      .|.|+|++.+.|+.++.-  -|...+.|+
T Consensus        24 dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r------~alvefedi~~akn~Vnfaa~n~i~i~gq   97 (494)
T KOG1456|consen   24 DPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKR------QALVEFEDIEGAKNCVNFAADNQIYIAGQ   97 (494)
T ss_pred             CCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccc------eeeeeeccccchhhheehhccCcccccCc
Confidence            444567789999999999999999999999999998888777654      699999999999998862  245567788


Q ss_pred             eeEeecccCCccccc-----CCCcc--eeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHH
Q 006282          100 SIRIMYSHRDPSIRK-----SGTGN--IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ  172 (652)
Q Consensus       100 ~i~i~~s~~~~~~~~-----~~~~~--lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~  172 (652)
                      ..-+.+|..+...|.     ..+..  +.|-|--+.+|.+-|+.++...|.|+.|.|.+. +|   -.|.|+|++.+.|.
T Consensus        98 ~Al~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ng---VQAmVEFdsv~~Aq  173 (494)
T KOG1456|consen   98 QALFNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NG---VQAMVEFDSVEVAQ  173 (494)
T ss_pred             hhhcccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cc---eeeEEeechhHHHH
Confidence            777777743322221     12222  345565678999999999999999999999875 43   37999999999999


Q ss_pred             HHHHHhcCceecC--eeeeecccccchhhHHHh-----------------------------------------------
Q 006282          173 NAIDKLNGMLIND--KQVFVGHFLRKQERETVA-----------------------------------------------  203 (652)
Q Consensus       173 ~Ai~~lng~~l~g--~~~~v~~~~~~~~~~~~~-----------------------------------------------  203 (652)
                      +|...|||..|-.  +.+.|+++.+.+-.....                                               
T Consensus       174 rAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~  253 (494)
T KOG1456|consen  174 RAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYY  253 (494)
T ss_pred             HHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCc
Confidence            9999999977632  345554443211000000                                               


Q ss_pred             -----------------------------hccCcceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEE
Q 006282          204 -----------------------------IKTKFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGF  253 (652)
Q Consensus       204 -----------------------------~~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~f  253 (652)
                                                   .......+.|.+|.. .++-+.|.++|..||.|..|++++.+.|    .++
T Consensus       254 sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~g----tam  329 (494)
T KOG1456|consen  254 SGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPG----TAM  329 (494)
T ss_pred             ccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccc----eeE
Confidence                                         000112377888874 5678889999999999999999998765    799


Q ss_pred             EeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHH----------HHh-------HHHHHh--hhhccccccccee
Q 006282          254 VNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ----------ELK-------GQFEQA--MKETVDKFQGLNL  314 (652)
Q Consensus       254 V~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~----------~~~-------~~~~~~--~~~~~~~~~~~~l  314 (652)
                      |+.-+....++|+..|++..+.|.+|.+..+....-...          ..+       .++...  ..+..-..+++.|
T Consensus       330 Vemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vL  409 (494)
T KOG1456|consen  330 VEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVL  409 (494)
T ss_pred             EEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCccee
Confidence            999999999999999999999999999988754311000          000       011111  1111223567889


Q ss_pred             eecCCCCCCCHHHHHHHhhhcCC-eeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          315 YIKNLGDSIDDEKLKELFSEFGT-ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       315 ~V~nlp~~~te~~L~~~F~~fG~-I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      +.-|.|..+||+.|.++|..-+. .++++|+.-++-+ ...|.++|++.++|..|+..+|...+.+
T Consensus       410 HffNaP~~vtEe~l~~i~nek~v~~~svkvFp~kser-SssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  410 HFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLKSER-SSSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             EEecCCCccCHHHHHHHhhhcCCCcceEEeecccccc-cccceeeeehHHHHHHHHHHhccccccC
Confidence            99999999999999999987753 4778888665333 3479999999999999999999999875

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

Probab=99.85  E-value=1.4e-21  Score=184.98  Aligned_cols=147  Identities=23%  Similarity=0.540  Sum_probs=138.0

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchH
Q 006282          210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSE  289 (652)
Q Consensus       210 ~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~  289 (652)
                      .|||+|||.++++.+|+.+|++||+|.+|.|+++       ||||..++...+..|+..||+..+.|..|.|.-+++++.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk   76 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSK   76 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEeccccCC
Confidence            5899999999999999999999999999999977       999999999999999999999999999999988766622


Q ss_pred             HHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHH
Q 006282          290 REQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL  369 (652)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~  369 (652)
                                          ..++|+|+||.+.++.+||+..|++||.|.+|+|++|       |+||.|.-.++|..|+
T Consensus        77 --------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~ai  129 (346)
T KOG0109|consen   77 --------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAI  129 (346)
T ss_pred             --------------------CccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHH
Confidence                                3568999999999999999999999999999999977       9999999999999999


Q ss_pred             HHhcCcEecCeeEEEEecccH
Q 006282          370 AEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       370 ~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +.|+|..|.|++++|.+..++
T Consensus       130 r~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  130 RGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             hcccccccccceeeeeeeccc
Confidence            999999999999999998754

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

Probab=99.85  E-value=2.4e-21  Score=183.44  Aligned_cols=150  Identities=24%  Similarity=0.479  Sum_probs=138.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      ..|||||||..+++.+|+.+|++||+|+++.|+++        |+||..++...|+.|+..|++..|+|..|.|+.++.+
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            47999999999999999999999999999999885        9999999999999999999999999999999988765


Q ss_pred             cccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeee
Q 006282          110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVF  189 (652)
Q Consensus       110 ~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~  189 (652)
                          ...+.+|+|+||.+.+++++|+..|.+||.|.+|+|++       +|+||+|...++|..|++.|++..+.|+++.
T Consensus        75 ----sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk-------dy~fvh~d~~eda~~air~l~~~~~~gk~m~  143 (346)
T KOG0109|consen   75 ----SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK-------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMH  143 (346)
T ss_pred             ----CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec-------ceeEEEEeeccchHHHHhcccccccccceee
Confidence                23456899999999999999999999999999999975       4999999999999999999999999999999


Q ss_pred             ecccccchh
Q 006282          190 VGHFLRKQE  198 (652)
Q Consensus       190 v~~~~~~~~  198 (652)
                      |....++..
T Consensus       144 vq~stsrlr  152 (346)
T KOG0109|consen  144 VQLSTSRLR  152 (346)
T ss_pred             eeeeccccc
Confidence            988766544

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

Probab=99.82  E-value=7.5e-20  Score=181.73  Aligned_cols=247  Identities=20%  Similarity=0.253  Sum_probs=208.1

Q ss_pred             cceeecCCCccccHHHHHhhhc-cCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccc
Q 006282          118 GNIFIKNLDKSIDHKALHDTFS-SFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRK  196 (652)
Q Consensus       118 ~~lfV~nLp~~~t~~~L~~~Fs-~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~  196 (652)
                      +.+||.|||+++.+.+|+++|. +.|.|.-|.++.|..|+++|+|.|+|+++|.+++|+++||.+.++|+.+.|.-....
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~  124 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDE  124 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCch
Confidence            4599999999999999999998 578999999999999999999999999999999999999999999999999765543


Q ss_pred             hhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCC
Q 006282          197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD  276 (652)
Q Consensus       197 ~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g  276 (652)
                      +.......-..-.+.|+.++....-..-|...|+--|.+..-.+.+|.++.+++..+++|++.-.+..++.-+.......
T Consensus       125 q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Fl  204 (608)
T KOG4212|consen  125 QRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFL  204 (608)
T ss_pred             hhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhh
Confidence            33222223345567999999999998999999998898888888899999999999999998877777775444443333


Q ss_pred             ceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEE
Q 006282          277 REWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF  356 (652)
Q Consensus       277 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~af  356 (652)
                      +.+.. +                       ..+....+||.||.+.+..+.|++.|.-.|.|+++.+-.|+.|.++||+.
T Consensus       205 r~~h~-f-----------------------~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~v  260 (608)
T KOG4212|consen  205 RSLHI-F-----------------------SPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAV  260 (608)
T ss_pred             hhccC-C-----------------------CCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeE
Confidence            33332 1                       11123359999999999999999999999999999999999999999999


Q ss_pred             EEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          357 VAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       357 V~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ++|..+-+|..||..+++..+..++..+++..
T Consensus       261 i~y~hpveavqaIsml~~~g~~~~~~~~Rl~~  292 (608)
T KOG4212|consen  261 IEYDHPVEAVQAISMLDRQGLFDRRMTVRLDR  292 (608)
T ss_pred             EEecchHHHHHHHHhhccCCCccccceeeccc
Confidence            99999999999999999988888888888754

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

Probab=99.77  E-value=1.6e-17  Score=168.94  Aligned_cols=260  Identities=18%  Similarity=0.249  Sum_probs=193.2

Q ss_pred             CcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccc
Q 006282          117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRK  196 (652)
Q Consensus       117 ~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~  196 (652)
                      ...|.+++||+++|++||.++|+.. .|.++++.+ .+|+..|-|||+|.++|++.+|+++ +.+.+..+-|.|-.....
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR-RNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec-cCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCCc
Confidence            3458889999999999999999998 677766555 5788999999999999999999966 666677777766544322


Q ss_pred             hhh---HHHh--hccCcceEEecCCCCCCCHHHHHHHhccCCCeeE-EEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHC
Q 006282          197 QER---ETVA--IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALN  270 (652)
Q Consensus       197 ~~~---~~~~--~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~-~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~  270 (652)
                      ...   ....  .....-.|.+++||+.++++||.++|+..-.|.. |.+..+..+++.|.+||+|++.+.|++|+. -|
T Consensus        87 e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rh  165 (510)
T KOG4211|consen   87 EADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RH  165 (510)
T ss_pred             cccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HH
Confidence            110   0001  1134566999999999999999999999887777 556677889999999999999999999996 47


Q ss_pred             CCccCCceEEEEccccchHHHHHHhH--------HHHH------------------------------------------
Q 006282          271 GKKFDDREWYVGKAQKKSEREQELKG--------QFEQ------------------------------------------  300 (652)
Q Consensus       271 ~~~~~g~~l~v~~a~~~~~~~~~~~~--------~~~~------------------------------------------  300 (652)
                      .+.|..|.|.|-++.....+......        .++.                                          
T Consensus       166 re~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~  245 (510)
T KOG4211|consen  166 RENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDY  245 (510)
T ss_pred             HHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccc
Confidence            78888888888777654433322000        0000                                          


Q ss_pred             ----------hh---hh----c-------c-cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEE
Q 006282          301 ----------AM---KE----T-------V-DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSG  355 (652)
Q Consensus       301 ----------~~---~~----~-------~-~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~a  355 (652)
                                ..   .+    .       . -...+..++-++||+..++-+|.++|+.. ....|.|-..++|+..|-|
T Consensus       246 ~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl-~p~~v~i~ig~dGr~TGEA  324 (510)
T KOG4211|consen  246 GNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPL-NPYRVHIEIGPDGRATGEA  324 (510)
T ss_pred             ccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCC-CceeEEEEeCCCCccCCcc
Confidence                      00   00    0       0 00112568889999999999999999987 4458888888899999999


Q ss_pred             EEEeCCHHHHHHHHHHhcCcEecCeeE
Q 006282          356 FVAFSTPEEASRALAEMNGKMIVSKPL  382 (652)
Q Consensus       356 fV~F~s~~~A~~A~~~lng~~~~g~~l  382 (652)
                      +|+|.|.++|..|+. -++..+..+-+
T Consensus       325 dveF~t~edav~Ams-kd~anm~hrYV  350 (510)
T KOG4211|consen  325 DVEFATGEDAVGAMG-KDGANMGHRYV  350 (510)
T ss_pred             eeecccchhhHhhhc-cCCcccCccee
Confidence            999999999999996 44444444433

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

Probab=99.77  E-value=8.2e-19  Score=175.58  Aligned_cols=171  Identities=29%  Similarity=0.473  Sum_probs=151.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..+.|+|++|+|+++|+.|++.|++||.|.++.|++|+.+++++||+||+|.+++...++|.. ....|+|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            678999999999999999999999999999999999999999999999999999999999984 4567899999998776


Q ss_pred             CCcccccCC----CcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCce
Q 006282          108 RDPSIRKSG----TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGML  182 (652)
Q Consensus       108 ~~~~~~~~~----~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~  182 (652)
                      ...+..+..    ...|||++|+.+++++++++.|..||.|..+.+..| ....++||+||.|.+++....++. ..-..
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~  162 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHD  162 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceee
Confidence            554443333    558999999999999999999999999999999988 678899999999999999988874 36678


Q ss_pred             ecCeeeeecccccchhhH
Q 006282          183 INDKQVFVGHFLRKQERE  200 (652)
Q Consensus       183 l~g~~~~v~~~~~~~~~~  200 (652)
                      ++++.+.|..+.++....
T Consensus       163 ~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             ecCceeeEeeccchhhcc
Confidence            899999999888776543

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

Probab=99.75  E-value=7.5e-17  Score=158.17  Aligned_cols=287  Identities=16%  Similarity=0.175  Sum_probs=199.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ..+..+..++|||.-+..+|..+|....-..-.++......++..|+|.|.|.+.|.-+-|++ .+...+.+++|.|..+
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka  136 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKA  136 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeecc
Confidence            346789999999999999999999876444444444444567777999999999999999999 4666778899999877


Q ss_pred             cCCccc--------------ccCCCcceeecCCCccccHHHHHhhhcc----CCCeeEEEEeeCCCCCcccEEEEEEcCH
Q 006282          107 HRDPSI--------------RKSGTGNIFIKNLDKSIDHKALHDTFSS----FGNILSCKIATDGSGQSKGFGFVQFENK  168 (652)
Q Consensus       107 ~~~~~~--------------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~----fG~I~~~~v~~~~~g~skG~afV~F~t~  168 (652)
                      ..+.-+              .+...-.|.+++||+++++.++.++|..    -|....+.+++..+|+..|-|||.|..+
T Consensus       137 ~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  137 TGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACE  216 (508)
T ss_pred             CchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCH
Confidence            654321              2223334788999999999999999962    2366788888888999999999999999


Q ss_pred             HHHHHHHHHhcCceecCeeeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCc
Q 006282          169 ESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS  248 (652)
Q Consensus       169 e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~  248 (652)
                      ++|..|+.+. ...++.|.|.+  +                         ..|..++......+-.-   -++.. .+. 
T Consensus       217 e~aq~aL~kh-rq~iGqRYIEl--F-------------------------RSTaaEvqqvlnr~~s~---pLi~~-~~s-  263 (508)
T KOG1365|consen  217 EDAQFALRKH-RQNIGQRYIEL--F-------------------------RSTAAEVQQVLNREVSE---PLIPG-LTS-  263 (508)
T ss_pred             HHHHHHHHHH-HHHHhHHHHHH--H-------------------------HHhHHHHHHHHHhhccc---cccCC-CCC-
Confidence            9999999873 33333332222  1                         11233333333222100   00000 000 


Q ss_pred             ceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHH
Q 006282          249 KCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL  328 (652)
Q Consensus       249 ~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L  328 (652)
                      -+-+-+                      ....+-..                        ...-||.+++||++.+.|+|
T Consensus       264 p~~p~~----------------------p~~~~p~~------------------------~~kdcvRLRGLPy~AtvEdI  297 (508)
T KOG1365|consen  264 PLLPGG----------------------PARLVPPT------------------------RSKDCVRLRGLPYEATVEDI  297 (508)
T ss_pred             CCCCCC----------------------ccccCCCC------------------------CCCCeeEecCCChhhhHHHH
Confidence            000000                      00000000                        01238999999999999999


Q ss_pred             HHHhhhcCC-eeE--EEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHH
Q 006282          329 KELFSEFGT-ITS--CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER  393 (652)
Q Consensus       329 ~~~F~~fG~-I~~--v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r  393 (652)
                      .++|..|-. |..  |.++.+..|+..|-|||+|.+.++|..|....|++...++.|.|--..-.+..
T Consensus       298 L~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eeln  365 (508)
T KOG1365|consen  298 LDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEELN  365 (508)
T ss_pred             HHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHHH
Confidence            999999963 444  78888989999999999999999999999988888777777777665555444

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

Probab=99.75  E-value=1.1e-17  Score=156.65  Aligned_cols=188  Identities=30%  Similarity=0.492  Sum_probs=151.5

Q ss_pred             CceeEeecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHH
Q 006282           98 NKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK  177 (652)
Q Consensus        98 G~~i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~  177 (652)
                      +|+|.|..+..  +.|....++|||+.|.+.-+|+|++.+|..||.|.+|.+....+|.+||++||.|.+.-+|..||..
T Consensus         2 nrpiqvkpads--esrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~a   79 (371)
T KOG0146|consen    2 NRPIQVKPADS--ESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINA   79 (371)
T ss_pred             CCCcccccccc--ccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHH
Confidence            36666655443  3455577899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCce-ecC--eeeeecccccchhhHHHhh--------------------------------------------------
Q 006282          178 LNGML-IND--KQVFVGHFLRKQERETVAI--------------------------------------------------  204 (652)
Q Consensus       178 lng~~-l~g--~~~~v~~~~~~~~~~~~~~--------------------------------------------------  204 (652)
                      |+|.. +.|  ..+.|.+.....+|....-                                                  
T Consensus        80 LHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~  159 (371)
T KOG0146|consen   80 LHGSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFA  159 (371)
T ss_pred             hcccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhH
Confidence            98854 222  3455544443333222110                                                  


Q ss_pred             --------------------------------------------------------------------------------
Q 006282          205 --------------------------------------------------------------------------------  204 (652)
Q Consensus       205 --------------------------------------------------------------------------------  204 (652)
                                                                                                      
T Consensus       160 ~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~v  239 (371)
T KOG0146|consen  160 AAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTV  239 (371)
T ss_pred             HHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccc
Confidence                                                                                            


Q ss_pred             ------------------------------------------ccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEee
Q 006282          205 ------------------------------------------KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR  242 (652)
Q Consensus       205 ------------------------------------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~  242 (652)
                                                                ..+.+||||..||.+..+.||..+|-.||.|.+.++..
T Consensus       240 a~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFv  319 (371)
T KOG0146|consen  240 ADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFV  319 (371)
T ss_pred             cchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeee
Confidence                                                      00113499999999999999999999999999999988


Q ss_pred             C-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccc
Q 006282          243 D-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  287 (652)
Q Consensus       243 ~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~  287 (652)
                      | .+..||+||||.|+++.+++.||.+|||..|+=++|.|..-..+
T Consensus       320 DRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPk  365 (371)
T KOG0146|consen  320 DRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPK  365 (371)
T ss_pred             hhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcc
Confidence            7 57889999999999999999999999999999888877554433

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

Probab=99.74  E-value=2.6e-18  Score=172.03  Aligned_cols=174  Identities=25%  Similarity=0.460  Sum_probs=150.5

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      +...+||++|++++++|.|++.|++||+|.++.+++| .+++++||+||+|.+.+....++. .....++++.+.+.++.
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            5577999999999999999999999999999999998 569999999999999998888885 46677899999988887


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHH
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  364 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~  364 (652)
                      +..+......            ......|||++|+..+++++++++|++||.|..+.++.|. +.+++||+||.|.+++.
T Consensus        84 ~r~~~~~~~~------------~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~s  151 (311)
T KOG4205|consen   84 SREDQTKVGR------------HLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDS  151 (311)
T ss_pred             Cccccccccc------------ccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccc
Confidence            7654332211            1134579999999999999999999999999999998875 78899999999999888


Q ss_pred             HHHHHHHhcCcEecCeeEEEEecccHHHHH
Q 006282          365 ASRALAEMNGKMIVSKPLYVAVAQRKEERR  394 (652)
Q Consensus       365 A~~A~~~lng~~~~g~~l~v~~~~~~~~r~  394 (652)
                      ..+++. ..-..|+++.+.|..|.+++...
T Consensus       152 Vdkv~~-~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  152 VDKVTL-QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             cceecc-cceeeecCceeeEeeccchhhcc
Confidence            888876 78889999999999999988764

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

Probab=99.73  E-value=3e-16  Score=155.48  Aligned_cols=252  Identities=20%  Similarity=0.276  Sum_probs=194.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC-C-cee
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN-N-KSI  101 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~-G-~~i  101 (652)
                      ..+..--.+.|+|+-+.||-+.|+.+|++||.|..|..+....+    -.|.|+|.+.+.|..|...|++..|. | ..+
T Consensus       145 ~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~----FQALvQy~d~~sAq~AK~aLdGqnIyngcCtL  220 (492)
T KOG1190|consen  145 DGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNG----FQALVQYTDAVSAQAAKLALDGQNIYNGCCTL  220 (492)
T ss_pred             CCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccc----hhhhhhccchhhHHHHHHhccCCcccCceeEE
Confidence            33445567889999999999999999999999999977765443    36999999999999999999998774 4 467


Q ss_pred             EeecccC-------------C---ccccc---------------------------------------------CCCcce
Q 006282          102 RIMYSHR-------------D---PSIRK---------------------------------------------SGTGNI  120 (652)
Q Consensus       102 ~i~~s~~-------------~---~~~~~---------------------------------------------~~~~~l  120 (652)
                      ||.||+-             |   +.+..                                             +.+..|
T Consensus       221 rId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vl  300 (492)
T KOG1190|consen  221 RIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVL  300 (492)
T ss_pred             EeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEE
Confidence            8877751             0   00000                                             012346


Q ss_pred             eecCC-CccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchhh
Q 006282          121 FIKNL-DKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER  199 (652)
Q Consensus       121 fV~nL-p~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~~  199 (652)
                      .|.|| +..+|.+.|+-+|..||+|..++|..+    .+-.|+|++.+...|.-|++.|+|..+.|++++|.......-.
T Consensus       301 lvsnln~~~VT~d~LftlFgvYGdVqRVkil~n----kkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  301 LVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYN----KKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             EEecCchhccchhHHHHHHhhhcceEEEEeeec----CCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            66666 567899999999999999999999986    3457999999999999999999999999999999776532211


Q ss_pred             HHHh----------------------hcc-------CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcce
Q 006282          200 ETVA----------------------IKT-------KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC  250 (652)
Q Consensus       200 ~~~~----------------------~~~-------~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g  250 (652)
                      -+..                      ...       ...++.+.|+|.++++|++++.|..-|-..+....--   +.+.
T Consensus       377 lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---kd~k  453 (492)
T KOG1190|consen  377 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---KDRK  453 (492)
T ss_pred             CCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---CCcc
Confidence            1110                      011       1234889999999999999999999987655544432   2355


Q ss_pred             eEEEeeCCHHHHHHHHHHHCCCccCCc-eEEEEcccc
Q 006282          251 FGFVNFENADDAAKAVEALNGKKFDDR-EWYVGKAQK  286 (652)
Q Consensus       251 ~~fV~f~~~~~A~~Ai~~l~~~~~~g~-~l~v~~a~~  286 (652)
                      ++++.+++.|+|..|+-.+|...+... .++|+++++
T Consensus       454 mal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  454 MALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             eeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            999999999999999999998888755 888887654

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

Probab=99.73  E-value=6.1e-17  Score=150.12  Aligned_cols=157  Identities=25%  Similarity=0.457  Sum_probs=135.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHH----HHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           29 TTSLYVGDLDFNVTDSQLYD----LFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~----~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      +.||||.||...+.-++|+.    +|++||.|++|.+++   |.+.+|.|||.|.+.+.|..|+..|++..|-|++++|.
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            44999999999999999877    999999999999986   67899999999999999999999999999999999999


Q ss_pred             cccCCcccc------------------------------------------------cCCCcceeecCCCccccHHHHHh
Q 006282          105 YSHRDPSIR------------------------------------------------KSGTGNIFIKNLDKSIDHKALHD  136 (652)
Q Consensus       105 ~s~~~~~~~------------------------------------------------~~~~~~lfV~nLp~~~t~~~L~~  136 (652)
                      +++.+.+..                                                ...+..+|+.|||..++.+.+.+
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHH
Confidence            998654221                                                12234589999999999999999


Q ss_pred             hhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceec-Ceeeeecc
Q 006282          137 TFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIN-DKQVFVGH  192 (652)
Q Consensus       137 ~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~-g~~~~v~~  192 (652)
                      +|..|.....++++..    ..+.|||+|.++..|..|...+.+..+. ...+.+..
T Consensus       166 lf~qf~g~keir~i~~----~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPP----RSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             HHhhCcccceeEeccC----CCceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            9999999999998875    5678999999999999999998888775 44554433

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

Probab=99.73  E-value=6.3e-17  Score=143.59  Aligned_cols=148  Identities=20%  Similarity=0.355  Sum_probs=125.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ..+++|||+|||.++.|.+|.++|.+||.|.+|.+..-   ...-+||||+|+++.||+.|+...++..++|..|+|++.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            45789999999999999999999999999999988543   344589999999999999999999999999999999998


Q ss_pred             cCCcc------------------------cccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEE
Q 006282          107 HRDPS------------------------IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGF  162 (652)
Q Consensus       107 ~~~~~------------------------~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~af  162 (652)
                      +.-.+                        ..+.....|.|.+||.+-++.+|++.....|.|--..+.+|      |++.
T Consensus        81 rggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~Gv  154 (241)
T KOG0105|consen   81 RGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGV  154 (241)
T ss_pred             cCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------ccee
Confidence            74311                        11223345999999999999999999999999966666553      5899


Q ss_pred             EEEcCHHHHHHHHHHhcCcee
Q 006282          163 VQFENKESAQNAIDKLNGMLI  183 (652)
Q Consensus       163 V~F~t~e~A~~Ai~~lng~~l  183 (652)
                      |+|...|+-+-|+.+|....+
T Consensus       155 V~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  155 VEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             eeeeehhhHHHHHHhhccccc
Confidence            999999999999999876554

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

Probab=99.72  E-value=7.3e-17  Score=146.05  Aligned_cols=90  Identities=30%  Similarity=0.565  Sum_probs=83.7

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      .+.....+++|||+|||+++||++|+++|++||+|.+|+|+.|+.|++++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus        27 ~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l  106 (144)
T PLN03134         27 LGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHI  106 (144)
T ss_pred             cccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34446678899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+...+.
T Consensus       107 ~V~~a~~~~~  116 (144)
T PLN03134        107 RVNPANDRPS  116 (144)
T ss_pred             EEEeCCcCCC
Confidence            9999876544

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

Probab=99.71  E-value=1.5e-17  Score=171.47  Aligned_cols=180  Identities=25%  Similarity=0.426  Sum_probs=149.5

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...+++|+-.+....+.-+|.++|+.+|.|.++.++.| ..+.++|.+||+|.+.++...|+ +|.|..+.|-.|.|...
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEeccc
Confidence            34567888888888999999999999999999999988 56889999999999999999999 79999999999999776


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  363 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~  363 (652)
                      .....+.+....    ...-..-..+...|||+||..++++++|+.+|++||.|+.|.++.|. +|+++|||||+|.+.+
T Consensus       256 Eaeknr~a~~s~----a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~  331 (549)
T KOG0147|consen  256 EAEKNRAANASP----ALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKE  331 (549)
T ss_pred             HHHHHHHHhccc----cccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHH
Confidence            443333111110    00000001122239999999999999999999999999999999997 9999999999999999


Q ss_pred             HHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          364 EASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       364 ~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +|.+|+..|||..+.|+.|.|.....+
T Consensus       332 ~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  332 DARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             HHHHHHHHhccceecCceEEEEEeeee
Confidence            999999999999999999999977654

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

Probab=99.70  E-value=2.4e-16  Score=165.28  Aligned_cols=256  Identities=21%  Similarity=0.409  Sum_probs=198.7

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhcc-----------C-CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQV-----------G-QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL   91 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~-----------G-~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l   91 (652)
                      ........+||+++|..++|+....+|+.-           | .|.++.++..+      ++||++|.+.++|..|+. +
T Consensus       170 ~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~------nfa~ie~~s~~~at~~~~-~  242 (500)
T KOG0120|consen  170 QATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEK------NFAFIEFRSISEATEAMA-L  242 (500)
T ss_pred             chhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccc------cceeEEecCCCchhhhhc-c
Confidence            345678899999999999999999999864           3 48888887764      499999999999999998 8


Q ss_pred             CCcccCCceeEeecccCCcc---------------------cccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEe
Q 006282           92 NFTPLNNKSIRIMYSHRDPS---------------------IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA  150 (652)
Q Consensus        92 n~~~i~G~~i~i~~s~~~~~---------------------~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~  150 (652)
                      +...+.|.++++...+..-.                     ..-.....+||++||..+++..+.++...||.+..+.++
T Consensus       243 ~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv  322 (500)
T KOG0120|consen  243 DGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLV  322 (500)
T ss_pred             cchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheee
Confidence            88999999998864432210                     011233459999999999999999999999999999999


Q ss_pred             eC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchhhHHHhh------------------ccCcceE
Q 006282          151 TD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAI------------------KTKFNNV  211 (652)
Q Consensus       151 ~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~~~~~~~------------------~~~~~~l  211 (652)
                      .| .+|.++||+|.+|.+......|+..+||+.+.++.+.+..+...........                  ......|
T Consensus       323 ~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl  402 (500)
T KOG0120|consen  323 KDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVL  402 (500)
T ss_pred             cccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhh
Confidence            99 5689999999999999999999999999999999998876543322211110                  0111122


Q ss_pred             EecCCC--CCC-C-------HHHHHHHhccCCCeeEEEEeeC-CC---CCcceeEEEeeCCHHHHHHHHHHHCCCccCCc
Q 006282          212 FVKNLD--EST-T-------DEDLKKIFGEYGTITSAVVMRD-GD---GKSKCFGFVNFENADDAAKAVEALNGKKFDDR  277 (652)
Q Consensus       212 ~V~nlp--~~~-t-------~~~l~~~F~~~G~v~~~~i~~~-~~---g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~  277 (652)
                      .+.|+=  .+. +       .|+++.-|++||.|.+|.+.++ .+   ....|..||+|.+.+++++|.++|+|..|.++
T Consensus       403 ~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nR  482 (500)
T KOG0120|consen  403 CLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANR  482 (500)
T ss_pred             hhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCc
Confidence            333321  000 1       2456677899999999999877 32   45577889999999999999999999999999


Q ss_pred             eEEEEcccc
Q 006282          278 EWYVGKAQK  286 (652)
Q Consensus       278 ~l~v~~a~~  286 (652)
                      .+...+...
T Consensus       483 tVvtsYyde  491 (500)
T KOG0120|consen  483 TVVASYYDE  491 (500)
T ss_pred             EEEEEecCH
Confidence            988877643

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

Probab=99.68  E-value=2e-16  Score=165.79  Aligned_cols=268  Identities=20%  Similarity=0.401  Sum_probs=199.7

Q ss_pred             CcceeecCCCccccHHHHHhhhccC-----------C-CeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceec
Q 006282          117 TGNIFIKNLDKSIDHKALHDTFSSF-----------G-NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIN  184 (652)
Q Consensus       117 ~~~lfV~nLp~~~t~~~L~~~Fs~f-----------G-~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~  184 (652)
                      ...+.+.+++..++++....+|..-           | .+++|.+..     .++++|++|.+.++|..++ .+++..+.
T Consensus       175 ~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~-----~~nfa~ie~~s~~~at~~~-~~~~~~f~  248 (500)
T KOG0120|consen  175 ARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL-----EKNFAFIEFRSISEATEAM-ALDGIIFE  248 (500)
T ss_pred             hhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc-----cccceeEEecCCCchhhhh-cccchhhC
Confidence            3458999999999999999988754           3 367777655     5779999999999999998 56788888


Q ss_pred             CeeeeecccccchhhHHHhh-----------------ccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CC
Q 006282          185 DKQVFVGHFLRKQERETVAI-----------------KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DG  246 (652)
Q Consensus       185 g~~~~v~~~~~~~~~~~~~~-----------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~g  246 (652)
                      |..+.+..............                 ......+||++||...++++++++.+.||.+....+.++. +|
T Consensus       249 g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g  328 (500)
T KOG0120|consen  249 GRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATG  328 (500)
T ss_pred             CCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccc
Confidence            87776654433221111100                 1122459999999999999999999999999999999884 58


Q ss_pred             CcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHH----HH--HhhhhcccccccceeeecCC-
Q 006282          247 KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQ----FE--QAMKETVDKFQGLNLYIKNL-  319 (652)
Q Consensus       247 ~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~----~~--~~~~~~~~~~~~~~l~V~nl-  319 (652)
                      .++||+|.+|.+......|+..|||..+.++.|.|..+.............    ..  .....+........|.+.|+ 
T Consensus       329 ~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~V  408 (500)
T KOG0120|consen  329 NSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVV  408 (500)
T ss_pred             cccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcC
Confidence            999999999999999999999999999999999999886654332221110    00  00001112223344555554 


Q ss_pred             -CCCC-CH-------HHHHHHhhhcCCeeEEEEecC-C---CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          320 -GDSI-DD-------EKLKELFSEFGTITSCKVMRD-P---SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       320 -p~~~-te-------~~L~~~F~~fG~I~~v~i~~~-~---~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                       +++. ++       |+++..+++||.|.+|.|.++ .   ...+.|..||+|.+.+++++|.++|+|.+|+++.+...+
T Consensus       409 t~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsY  488 (500)
T KOG0120|consen  409 TPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASY  488 (500)
T ss_pred             CHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEe
Confidence             1111 11       467777889999999999887 3   234678899999999999999999999999999999988


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ....
T Consensus       489 ydeD  492 (500)
T KOG0120|consen  489 YDED  492 (500)
T ss_pred             cCHH
Confidence            7754

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

Probab=99.64  E-value=1e-15  Score=138.57  Aligned_cols=82  Identities=33%  Similarity=0.581  Sum_probs=76.8

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ..+++|||+||++++++++|+++|++||.|++|+|+.|. +++++|||||+|.+.++|++|++.||+..|+|+.|+|.|+
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            356789999999999999999999999999999999875 7899999999999999999999999999999999999998


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus       112 ~~~  114 (144)
T PLN03134        112 NDR  114 (144)
T ss_pred             CcC
Confidence            753

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

Probab=99.62  E-value=6.8e-15  Score=136.58  Aligned_cols=175  Identities=23%  Similarity=0.409  Sum_probs=142.5

Q ss_pred             cceEEecCCCCCCCHHHHHH----HhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEc
Q 006282          208 FNNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  283 (652)
Q Consensus       208 ~~~l~V~nlp~~~t~~~l~~----~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~  283 (652)
                      +.+|||.||...+..++|+.    +|+.||.|.+|...+  +.+.+|-|||.|++.+.|..|+.+|+|..+.|+.+.+.+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            34899999999999999988    999999999988775  467899999999999999999999999999999999999


Q ss_pred             cccchHHHHHHhHHH---------HH------hhhh-----------------cccccccceeeecCCCCCCCHHHHHHH
Q 006282          284 AQKKSEREQELKGQF---------EQ------AMKE-----------------TVDKFQGLNLYIKNLGDSIDDEKLKEL  331 (652)
Q Consensus       284 a~~~~~~~~~~~~~~---------~~------~~~~-----------------~~~~~~~~~l~V~nlp~~~te~~L~~~  331 (652)
                      |.+++.--...+..+         +.      ....                 .....+...||+.|||.+++.+.|..+
T Consensus        87 A~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~l  166 (221)
T KOG4206|consen   87 AKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDL  166 (221)
T ss_pred             ccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHH
Confidence            987653222110000         00      0000                 011345678999999999999999999


Q ss_pred             hhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec-CeeEEEEecc
Q 006282          332 FSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQ  388 (652)
Q Consensus       332 F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~-g~~l~v~~~~  388 (652)
                      |+.|....+++++...    ++.|||+|.+...|..|...+.|..|- ...+.|.+++
T Consensus       167 f~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  167 FEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999999999998763    568999999999999999999999887 7788887764

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

Probab=99.58  E-value=3.7e-13  Score=132.11  Aligned_cols=244  Identities=21%  Similarity=0.277  Sum_probs=183.2

Q ss_pred             CCCCCCccEEEEcCCC--CCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC-C-
Q 006282           23 SGNQFLTTSLYVGDLD--FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN-N-   98 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp--~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~-G-   98 (652)
                      .+...++..|.+.=|.  +.+|.+.|+.++..+|+|..|-|++...     -.|.|+|.+.+.|++|.+.||+..|. | 
T Consensus       114 ~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkng-----VQAmVEFdsv~~AqrAk~alNGADIYsGC  188 (494)
T KOG1456|consen  114 DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNG-----VQAMVEFDSVEVAQRAKAALNGADIYSGC  188 (494)
T ss_pred             CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccc-----eeeEEeechhHHHHHHHhhcccccccccc
Confidence            3444556677766664  6699999999999999999999988633     37999999999999999999998874 3 


Q ss_pred             ceeEeecccCCc----------------cc--------------------------cc----------------------
Q 006282           99 KSIRIMYSHRDP----------------SI--------------------------RK----------------------  114 (652)
Q Consensus        99 ~~i~i~~s~~~~----------------~~--------------------------~~----------------------  114 (652)
                      .+++|.+++.+.                ..                          +.                      
T Consensus       189 CTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~  268 (494)
T KOG1456|consen  189 CTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRY  268 (494)
T ss_pred             eeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCC
Confidence            467777765210                00                          00                      


Q ss_pred             ----------------CCCcceeecCCCc-cccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHH
Q 006282          115 ----------------SGTGNIFIKNLDK-SIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK  177 (652)
Q Consensus       115 ----------------~~~~~lfV~nLp~-~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~  177 (652)
                                      ....-+.|.+|+. .++.+.|+++|..||+|+.+++++.    ..|.|.|+..+..+.++|+..
T Consensus       269 ~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkT----k~gtamVemgd~~aver~v~h  344 (494)
T KOG1456|consen  269 RDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKT----KPGTAMVEMGDAYAVERAVTH  344 (494)
T ss_pred             ccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeec----ccceeEEEcCcHHHHHHHHHH
Confidence                            0011278889974 4577899999999999999999986    456799999999999999999


Q ss_pred             hcCceecCeeeeecccccc------------------------hhh-------HHHhhccCcceEEecCCCCCCCHHHHH
Q 006282          178 LNGMLINDKQVFVGHFLRK------------------------QER-------ETVAIKTKFNNVFVKNLDESTTDEDLK  226 (652)
Q Consensus       178 lng~~l~g~~~~v~~~~~~------------------------~~~-------~~~~~~~~~~~l~V~nlp~~~t~~~l~  226 (652)
                      ||+..+.|.++.+......                        ..|       ........++.|..-|.|..+||+.|.
T Consensus       345 Lnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~  424 (494)
T KOG1456|consen  345 LNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLI  424 (494)
T ss_pred             hccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHH
Confidence            9999988888877544311                        000       001112334568889999999999999


Q ss_pred             HHhccCCC-eeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCC
Q 006282          227 KIFGEYGT-ITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD  276 (652)
Q Consensus       227 ~~F~~~G~-v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g  276 (652)
                      ++|...+. -.++++...++-+ ...|.++|++.++|..|+-.+|...+.+
T Consensus       425 ~i~nek~v~~~svkvFp~kser-SssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  425 GICNEKDVPPTSVKVFPLKSER-SSSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             HHhhhcCCCcceEEeecccccc-cccceeeeehHHHHHHHHHHhccccccC
Confidence            99987763 4556665544433 3368999999999999999999887754

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

Probab=99.56  E-value=4.5e-13  Score=143.10  Aligned_cols=80  Identities=23%  Similarity=0.451  Sum_probs=74.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      -+++|||+.|+..+++.+|.++|+.||+|.+|.++..     +|||||++....+|.+|+.+|++..+.++.|+|.|+..
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            4678999999999999999999999999999998765     89999999999999999999999999999999999987


Q ss_pred             HHHHH
Q 006282          390 KEERR  394 (652)
Q Consensus       390 ~~~r~  394 (652)
                      +..+.
T Consensus       495 ~G~ks  499 (894)
T KOG0132|consen  495 KGPKS  499 (894)
T ss_pred             CCcch
Confidence            65444

>PF00076 RRM_1: RNA recognition motif

Probab=99.56  E-value=1.3e-14  Score=114.96  Aligned_cols=70  Identities=43%  Similarity=0.742  Sum_probs=67.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        32 L~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      |||+|||+++|+++|+++|+.||.|..+++.++ .++++.|||||.|.+.++|++|++.+++..+.|+.||
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 7789999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>PF00076 RRM_1: RNA recognition motif

Probab=99.54  E-value=2.8e-14  Score=113.08  Aligned_cols=70  Identities=47%  Similarity=0.797  Sum_probs=67.6

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEE
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  383 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~  383 (652)
                      |||+|||.++++++|+++|+.||.|..++++.+..+.++|+|||+|.+.++|.+|++.++|..++|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999999999999988889999999999999999999999999999999885

(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 ....

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

Probab=99.53  E-value=1.2e-13  Score=122.99  Aligned_cols=172  Identities=20%  Similarity=0.318  Sum_probs=132.7

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      ..+.+||+|||.++.+.+|.++|-+||.|..|.++....  .-+|+||+|++..+|+.||..-++..++|..|.|.++..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g--~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPG--PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCC--CCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            457799999999999999999999999999998875432  246999999999999999999999999999999998765


Q ss_pred             chHHHHHHhHHHH--------HhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEE
Q 006282          287 KSEREQELKGQFE--------QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA  358 (652)
Q Consensus       287 ~~~~~~~~~~~~~--------~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~  358 (652)
                      -......-.....        -...-...+-....|.|.+||.+-++.+|+++..+-|.|....+.+|      |++.|.
T Consensus        83 gr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV~  156 (241)
T KOG0105|consen   83 GRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVVE  156 (241)
T ss_pred             CCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceeee
Confidence            4211000000000        00000011112346999999999999999999999999999999887      379999


Q ss_pred             eCCHHHHHHHHHHhcCcEec--CeeEEEEe
Q 006282          359 FSTPEEASRALAEMNGKMIV--SKPLYVAV  386 (652)
Q Consensus       359 F~s~~~A~~A~~~lng~~~~--g~~l~v~~  386 (652)
                      |...|+-+-|+..|...++.  |-..++.+
T Consensus       157 ~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  157 YLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             eeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            99999999999999888775  44444443

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

Probab=99.51  E-value=4.8e-13  Score=130.67  Aligned_cols=180  Identities=19%  Similarity=0.272  Sum_probs=139.4

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCee--------EEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTIT--------SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR  277 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~--------~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~  277 (652)
                      ..+++|||+|||.++|.+++.++|+++|.|.        .|.+.++..|+.+|-|.|.|-..+++.-|+..|++..+.|+
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            4567899999999999999999999999875        46788889999999999999999999999999999999999


Q ss_pred             eEEEEccccchH--H---------HHHHhHHHHHhh---------hhcccccccceeeecCCC----CCCC-------HH
Q 006282          278 EWYVGKAQKKSE--R---------EQELKGQFEQAM---------KETVDKFQGLNLYIKNLG----DSID-------DE  326 (652)
Q Consensus       278 ~l~v~~a~~~~~--~---------~~~~~~~~~~~~---------~~~~~~~~~~~l~V~nlp----~~~t-------e~  326 (652)
                      .+.|.+|+-...  .         ....++......         ......-..++|.++|+=    ...+       .+
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            999999863210  0         000000000000         011112235678888871    1222       36


Q ss_pred             HHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       327 ~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      +|++-+++||.|.+|.|...   ...|.+-|.|.+.++|..+|+.|+|+.|+|+.|...+..
T Consensus       292 dl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence            78888999999999988744   246789999999999999999999999999999888654

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

Probab=99.50  E-value=3.3e-14  Score=137.59  Aligned_cols=81  Identities=28%  Similarity=0.507  Sum_probs=76.1

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .....|||.|||+...|-||+.+|++||.|.+|.|+.++.| |||||||+|++.+||++|..+|||..+.||+|.|+.+-
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            34567999999999999999999999999999999999887 79999999999999999999999999999999999887


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            55

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

Probab=99.50  E-value=6.1e-14  Score=130.70  Aligned_cols=84  Identities=27%  Similarity=0.397  Sum_probs=80.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ...+++|.|.||+.+++|++|.+||..||.|..|.|.+|+.||.++|||||.|.+.+||.+|++.||+.-++.--|+|.|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            44688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 006282          106 SHRD  109 (652)
Q Consensus       106 s~~~  109 (652)
                      ++..
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9863

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

Probab=99.49  E-value=3.8e-14  Score=131.69  Aligned_cols=79  Identities=29%  Similarity=0.461  Sum_probs=71.9

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .-++|||++|+|++..|+|+++|++||+|+++.|+.|+ +|+|||||||+|++.++|.+|++.- +-.|+||+-.|++|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchhh
Confidence            34689999999999999999999999999999999886 8999999999999999999999844 458899999999886


Q ss_pred             c
Q 006282          389 R  389 (652)
Q Consensus       389 ~  389 (652)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

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

Probab=99.49  E-value=1.8e-14  Score=135.50  Aligned_cols=168  Identities=27%  Similarity=0.438  Sum_probs=133.2

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchH
Q 006282          210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSE  289 (652)
Q Consensus       210 ~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~  289 (652)
                      .+||++|++.+.+.+|..+|..||.+..+.+..       ||+||.|.+..+|..|+..++++.+.+..+.+.++.....
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMKN-------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceeec-------ccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            589999999999999999999999999998764       4999999999999999999999999998888888764321


Q ss_pred             HHHHHhHHH-H-HhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHH
Q 006282          290 REQELKGQF-E-QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASR  367 (652)
Q Consensus       290 ~~~~~~~~~-~-~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~  367 (652)
                      ......... . .........-..+.|.|.|+..++.+.+|.++|+.+|.++...++       ++++||+|.+.++|.+
T Consensus        76 ~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~~da~r  148 (216)
T KOG0106|consen   76 GRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQEDAKR  148 (216)
T ss_pred             ccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehhhhhhhh
Confidence            110000000 0 011111123356789999999999999999999999999666553       5599999999999999


Q ss_pred             HHHHhcCcEecCeeEEEEecccHH
Q 006282          368 ALAEMNGKMIVSKPLYVAVAQRKE  391 (652)
Q Consensus       368 A~~~lng~~~~g~~l~v~~~~~~~  391 (652)
                      |+..+++..+.++.|.+.......
T Consensus       149 a~~~l~~~~~~~~~l~~~~~~~d~  172 (216)
T KOG0106|consen  149 ALEKLDGKKLNGRRISVEKNSRDR  172 (216)
T ss_pred             cchhccchhhcCceeeecccCcch
Confidence            999999999999999995444433

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

Probab=99.49  E-value=6.5e-14  Score=117.21  Aligned_cols=84  Identities=30%  Similarity=0.504  Sum_probs=79.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      -..+++||||||+..++|+.|+|||+.+|+|..|.+=.|+.+.+.-|||||+|.+.+||+.|+..+|++.++.++|+|-|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 006282          106 SHRD  109 (652)
Q Consensus       106 s~~~  109 (652)
                      ..--
T Consensus       113 D~GF  116 (153)
T KOG0121|consen  113 DAGF  116 (153)
T ss_pred             cccc
Confidence            7643

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

Probab=99.49  E-value=4.3e-14  Score=132.94  Aligned_cols=150  Identities=23%  Similarity=0.484  Sum_probs=128.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      ..+||++||+.+.+.+|.+||..||.|.++.+..        ||+||+|.+..||..|+..+|+..|.|..+.++|....
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            5799999999999999999999999999998865        69999999999999999999999999988888887731


Q ss_pred             ------c------c-cc-----cCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHH
Q 006282          110 ------P------S-IR-----KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESA  171 (652)
Q Consensus       110 ------~------~-~~-----~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A  171 (652)
                            +      . .+     ......+++.++...+.+.+|.+.|+.+|.+.....       ..+++||+|++.++|
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da  146 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDA  146 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhh
Confidence                  0      0 11     123445899999999999999999999998844333       567899999999999


Q ss_pred             HHHHHHhcCceecCeeeeecccc
Q 006282          172 QNAIDKLNGMLINDKQVFVGHFL  194 (652)
Q Consensus       172 ~~Ai~~lng~~l~g~~~~v~~~~  194 (652)
                      ..|+..+++..+.++.+.+....
T Consensus       147 ~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  147 KRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             hhcchhccchhhcCceeeecccC
Confidence            99999999999999999884433

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

Probab=99.48  E-value=7.1e-14  Score=129.93  Aligned_cols=78  Identities=27%  Similarity=0.469  Sum_probs=72.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      -+.||||+|+|+++.+.|+++|++||.|++..|+.|+.|+||+||+||.|.+.++|.+|++.-| -.|+||+..|.++.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhh
Confidence            5899999999999999999999999999999999999999999999999999999999999654 67899998887654

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

Probab=99.48  E-value=9.2e-13  Score=128.71  Aligned_cols=165  Identities=19%  Similarity=0.348  Sum_probs=136.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~--------i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      +.-+++|||+|||.++|.+++.++|+.||-|..        |++.++.. |+.+|=|.+.|...++.+-|+..|+...|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCccccc
Confidence            445788999999999999999999999997744        78899866 899999999999999999999999999999


Q ss_pred             CceeEeecccCC------------------------------------cccccCCCcceeecCCC----cccc-------
Q 006282           98 NKSIRIMYSHRD------------------------------------PSIRKSGTGNIFIKNLD----KSID-------  130 (652)
Q Consensus        98 G~~i~i~~s~~~------------------------------------~~~~~~~~~~lfV~nLp----~~~t-------  130 (652)
                      |+.|+|..++-.                                    ...+....++|.++|+=    ...+       
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            999999876510                                    11233445668888871    1111       


Q ss_pred             HHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccc
Q 006282          131 HKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFL  194 (652)
Q Consensus       131 ~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~  194 (652)
                      .++|.+-+++||.|.++.|...   .+.|.+-|.|.+.++|..||+.|+|..+.|+.|......
T Consensus       290 kedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence            4677788999999999988743   467889999999999999999999999999999876543

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

Probab=99.47  E-value=2.7e-13  Score=142.60  Aligned_cols=357  Identities=18%  Similarity=0.186  Sum_probs=237.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...+.+-+.+++.+..+.+++++|-.. .|-++.+..+...+.-.|-+||.|....++.+|+. .|...+..|.+.|...
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTGPP  386 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeecCC
Confidence            346777788999999999999999765 56666777776655557999999999999999998 5777778888877533


Q ss_pred             cCC----------------------------cc---------cccCCCcceeecCCCccccHHHHHhhhccCCCeeE-EE
Q 006282          107 HRD----------------------------PS---------IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS-CK  148 (652)
Q Consensus       107 ~~~----------------------------~~---------~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~-~~  148 (652)
                      -.+                            ..         ........|+|..||..+++.++.++|++.-.|++ |.
T Consensus       387 g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~  466 (944)
T KOG4307|consen  387 GNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIE  466 (944)
T ss_pred             CccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeE
Confidence            211                            00         11123446999999999999999999999877777 66


Q ss_pred             EeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchh-------------------hHHHhh-----
Q 006282          149 IATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQE-------------------RETVAI-----  204 (652)
Q Consensus       149 v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~-------------------~~~~~~-----  204 (652)
                      +....++..++-|||.|.+++++..|...-+..++..+.|.|....+...                   ++....     
T Consensus       467 lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m~~ek~~~~~~~lq~~~~dqre~~l~~p~~~  546 (944)
T KOG4307|consen  467 LTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAMMMEKNGEQGIKLQQSDKDQRETALDGPIPS  546 (944)
T ss_pred             eccCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhHHHHHHHhHHHHHHHhhhhhHHHHHhhcCCccc
Confidence            66668899999999999998888888765555566656666643321110                   000000     


Q ss_pred             -----------c-cCc---------------------------------------------------ceEEecCCCCCCC
Q 006282          205 -----------K-TKF---------------------------------------------------NNVFVKNLDESTT  221 (652)
Q Consensus       205 -----------~-~~~---------------------------------------------------~~l~V~nlp~~~t  221 (652)
                                 . ..+                                                   -++-|.|+++...
T Consensus       547 v~~~~~~~~~~~~~~F~~~~rr~~~e~~~~~~~~n~~p~~~dN~~~~~~~~~v~~~n~p~~r~~~~~~~~~vnn~pF~m~  626 (944)
T KOG4307|consen  547 VSMVPSKEQRSHEDDFDKKSRRSRWENTSPIRSPNRSPLRRDNRDRSRSRSPVRRRNSPRRREEHTRWCVQVNNVPFRMK  626 (944)
T ss_pred             hhhhhhhhhhccCcccccchHHHHhhhcCCccCccccccccccCCcccccCccccCCCccccchhhhhhhcccCcceeec
Confidence                       0 000                                                   0145666666665


Q ss_pred             HHHHHHHhccC------------CCee-----EE---EEe------------------------eCCCCCcceeEEEeeC
Q 006282          222 DEDLKKIFGEY------------GTIT-----SA---VVM------------------------RDGDGKSKCFGFVNFE  257 (652)
Q Consensus       222 ~~~l~~~F~~~------------G~v~-----~~---~i~------------------------~~~~g~~~g~~fV~f~  257 (652)
                      .+++.+.|+.-            |.+.     ++   .++                        ....-.+.|.-+++|.
T Consensus       627 ~~~~~~~~sekn~Pa~~~~~~~~gv~~~p~v~~~~~~~l~~~r~~~~g~l~tg~~lr~~~i~~~~~~~~~~~g~~~~e~~  706 (944)
T KOG4307|consen  627 DEELLEWFSEKNRPAKLTRTFYDGVASDPWVAEFSSESLMKRRSFGIGTLCTGRTLRLRYIDNAKADEILKIGDVYGEGK  706 (944)
T ss_pred             chhhhhhhcccCCcccccccccCCCCCCcccccccccccccccCCCccccccCcccccchhhhhhhccccccccceeccC
Confidence            55555544321            0000     00   000                        0011123455688999


Q ss_pred             CHHHHHHHHHHHCCCccCCceEEEEccccchH---------------------------------------H--------
Q 006282          258 NADDAAKAVEALNGKKFDDREWYVGKAQKKSE---------------------------------------R--------  290 (652)
Q Consensus       258 ~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~---------------------------------------~--------  290 (652)
                      +.-..+.|+...+.+...++.+.+..+.....                                       +        
T Consensus       707 ~~~~ee~a~~~~~~~~an~~~~fn~p~~~~gs~~~~p~~p~p~~~gg~nG~~~p~pn~~NdGapg~g~~vp~~f~~gp~~  786 (944)
T KOG4307|consen  707 RQMNEEAALQHEVAEKANPPSFFNAPAATRGSGPMPPLNPAPLPSGGQNGMNVPPPNGFNDGAPGRGGFVPRGFSQGPGM  786 (944)
T ss_pred             CccchhHHHHHHhhhhccCCCcccccccccccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCcCCcCCccccCCCCC
Confidence            99888899888777766555544443321100                                       0        


Q ss_pred             -----------------HHHHh----HHHH---------------------------------------Hhhhhcccccc
Q 006282          291 -----------------EQELK----GQFE---------------------------------------QAMKETVDKFQ  310 (652)
Q Consensus       291 -----------------~~~~~----~~~~---------------------------------------~~~~~~~~~~~  310 (652)
                                       ...+.    ..+.                                       ....+ ..+..
T Consensus       787 ~~gp~g~gggP~~~qngP~sl~~~p~~~f~sn~p~~~gf~pg~rggpp~~g~gpg~~~g~~p~~~~~P~~~~~~-~~~~p  865 (944)
T KOG4307|consen  787 GRGPHGGGGGPNFYQNGPNSLNNGPQGQFRSNQPNDGGFRPGFRGGPPGRGGGPGGFQGGSPGDDSQPSQELME-LIKSP  865 (944)
T ss_pred             CCCCCCCCCCccccccCCcccCCCCccccCCCCCCcCCcCCccCCCCCCCCCCCCCCCCCCCCCCCCChHHHHH-hcCCC
Confidence                             00000    0000                                       00000 01123


Q ss_pred             cc-eeeecCCCCCCCHHHHHHHhhhcCCe-eEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          311 GL-NLYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       311 ~~-~l~V~nlp~~~te~~L~~~F~~fG~I-~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ++ .|-+.|+|++++-+||.++|..|-.+ .+|.+.++++|...|.|.|.|++.++|..|...++++.|..+.++|.+
T Consensus       866 Gp~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  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            44 79999999999999999999999544 567777888999999999999999999999999999999999999875

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.47  E-value=1.7e-13  Score=108.58  Aligned_cols=70  Identities=30%  Similarity=0.607  Sum_probs=65.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        32 L~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      |||+|||+++++++|+++|+.+|.|..+++.+++. ++++|+|||+|.+.++|.+|++.+++..|+|+.|+
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            79999999999999999999999999999999977 89999999999999999999999988999999875

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 ....

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.46  E-value=2.9e-13  Score=107.25  Aligned_cols=70  Identities=40%  Similarity=0.701  Sum_probs=65.2

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEE
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  383 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~  383 (652)
                      |||+|||+++++++|+++|+.||.|..+++..+++|.++|+|||+|.|.++|.+|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999999987789999999999999999999999999999999874

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 ....

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

Probab=99.45  E-value=1.4e-12  Score=119.75  Aligned_cols=157  Identities=18%  Similarity=0.295  Sum_probs=119.2

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEE-eeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc---CCc
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC-RDLSTRRSLGYGYVNYANPADAARALDVLNFTPL---NNK   99 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~-~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i---~G~   99 (652)
                      +.+..-++|||.+||.++...+|+.+|..|--.....+. .++...-..-+|||.|.+..+|..|++.||+..|   .+.
T Consensus        29 ~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~s  108 (284)
T KOG1457|consen   29 DEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGS  108 (284)
T ss_pred             ccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCc
Confidence            345568999999999999999999999988433333332 2222223346999999999999999999999887   578


Q ss_pred             eeEeecccCCcccc------------------------------------------------------------------
Q 006282          100 SIRIMYSHRDPSIR------------------------------------------------------------------  113 (652)
Q Consensus       100 ~i~i~~s~~~~~~~------------------------------------------------------------------  113 (652)
                      .++|.+++.++...                                                                  
T Consensus       109 tLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~  188 (284)
T KOG1457|consen  109 TLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDS  188 (284)
T ss_pred             eeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhh
Confidence            99998775321100                                                                  


Q ss_pred             ------------------cCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHH
Q 006282          114 ------------------KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI  175 (652)
Q Consensus       114 ------------------~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai  175 (652)
                                        .+...+|||.||..++++++|+.+|+.|-.....+|.. ..  ....+|+.|++.+.|..|+
T Consensus       189 ~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~~--g~~vaf~~~~~~~~at~am  265 (284)
T KOG1457|consen  189 KAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-RG--GMPVAFADFEEIEQATDAM  265 (284)
T ss_pred             cCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-CC--CcceEeecHHHHHHHHHHH
Confidence                              01122499999999999999999999997766666543 22  2347999999999999999


Q ss_pred             HHhcCcee
Q 006282          176 DKLNGMLI  183 (652)
Q Consensus       176 ~~lng~~l  183 (652)
                      ..+.|..+
T Consensus       266 ~~lqg~~~  273 (284)
T KOG1457|consen  266 NHLQGNLL  273 (284)
T ss_pred             HHhhccee
Confidence            99988776

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

Probab=99.45  E-value=7.7e-13  Score=135.06  Aligned_cols=147  Identities=27%  Similarity=0.498  Sum_probs=117.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc-
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH-  107 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~-  107 (652)
                      .++|||+|||.++|+++|+++|..||.|..|++..|+.+++++|||||.|.+.++|..|++.+++..|.|++|+|.+.. 
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            6999999999999999999999999999999999999999999999999999999999999999999999999999953 


Q ss_pred             ---CCcc------------------cccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCC-cccEEEEEE
Q 006282          108 ---RDPS------------------IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQF  165 (652)
Q Consensus       108 ---~~~~------------------~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~-skG~afV~F  165 (652)
                         ....                  ........+++.+++..++..++...|..+|.+....+.....+. .....++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence               1111                  112234558999999999999999999999999666665553222 333333444


Q ss_pred             cCHHHHHHHH
Q 006282          166 ENKESAQNAI  175 (652)
Q Consensus       166 ~t~e~A~~Ai  175 (652)
                      .....+....
T Consensus       275 ~~~~~~~~~~  284 (306)
T COG0724         275 EASKDALESN  284 (306)
T ss_pred             hHHHhhhhhh
Confidence            4444444433

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

Probab=99.45  E-value=2.2e-13  Score=126.96  Aligned_cols=82  Identities=33%  Similarity=0.541  Sum_probs=77.8

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|.|.||+.++++++|+++|.+||.|.++.|.+|. +|.+||||||.|.+.++|.+||..|||.-++.-.|.|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            356789999999999999999999999999999999886 8999999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      +++
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            875

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

Probab=99.43  E-value=3e-13  Score=119.82  Aligned_cols=80  Identities=31%  Similarity=0.488  Sum_probs=73.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...+.||||||+..+++.||...|..||+|.+|+|-+.     .-|||||+|+++.||+.|+..|++..|.|..|+|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            34789999999999999999999999999999999874     3389999999999999999999999999999999998


Q ss_pred             cCCcc
Q 006282          107 HRDPS  111 (652)
Q Consensus       107 ~~~~~  111 (652)
                      .-.+.
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            86543

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.43  E-value=5.3e-13  Score=128.97  Aligned_cols=76  Identities=20%  Similarity=0.336  Sum_probs=71.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      .++|||+||++++||++|+++|+.||+|.+|+|++|..   ++|||||+|.+.++|+.||. ||+..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999999864   45899999999999999996 999999999999998764

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.40  E-value=1.2e-12  Score=126.66  Aligned_cols=75  Identities=23%  Similarity=0.362  Sum_probs=69.6

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .++|||+||++.+++++|+++|+.||.|++|+|..+.  .++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~--~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN--ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC--CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            4689999999999999999999999999999999885  357999999999999999996 99999999999999754

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

Probab=99.39  E-value=4.3e-12  Score=116.53  Aligned_cols=170  Identities=21%  Similarity=0.364  Sum_probs=124.1

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCC--CCCcceeEEEeeCCHHHHHHHHHHHCCCccC---CceEE
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEALNGKKFD---DREWY  280 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~---g~~l~  280 (652)
                      ...++|||.+||.++...+|..+|..|---+.+.+....  +...+.+||+.|.+..+|..|++.|||..|+   +..|.
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            456889999999999999999999999766666666543  2346689999999999999999999999885   55666


Q ss_pred             EEccccchHHHHH--------------------Hh-HHHH----------------------------------Hh----
Q 006282          281 VGKAQKKSEREQE--------------------LK-GQFE----------------------------------QA----  301 (652)
Q Consensus       281 v~~a~~~~~~~~~--------------------~~-~~~~----------------------------------~~----  301 (652)
                      +..+++...+...                    .+ ...+                                  ..    
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            6666533211000                    00 0000                                  00    


Q ss_pred             ------hhh---cccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh
Q 006282          302 ------MKE---TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM  372 (652)
Q Consensus       302 ------~~~---~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l  372 (652)
                            .+.   ........+|||-||..+++|++|+.+|+.|-....++|... .|  ...|||.|++.+.|..|+..|
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~g--~~vaf~~~~~~~~at~am~~l  268 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-GG--MPVAFADFEEIEQATDAMNHL  268 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-CC--cceEeecHHHHHHHHHHHHHh
Confidence                  000   000012345999999999999999999999988888877543 23  568999999999999999999


Q ss_pred             cCcEec
Q 006282          373 NGKMIV  378 (652)
Q Consensus       373 ng~~~~  378 (652)
                      .|..+-
T Consensus       269 qg~~~s  274 (284)
T KOG1457|consen  269 QGNLLS  274 (284)
T ss_pred             hcceec
Confidence            998764

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

Probab=99.38  E-value=6.5e-14  Score=124.44  Aligned_cols=80  Identities=25%  Similarity=0.494  Sum_probs=76.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .++-|||||||.++||-+|.-+||+||.|++|.++||+.||+|.||||+.|++..+-.-|++.||+..|.||.|||-...
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999997543

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

Probab=99.38  E-value=5.3e-15  Score=159.69  Aligned_cols=323  Identities=18%  Similarity=0.182  Sum_probs=240.2

Q ss_pred             CccEEEEcCCCCCCCHHHHH-HHHhccCCeEE-EEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           28 LTTSLYVGDLDFNVTDSQLY-DLFSQVGQVLS-VRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~-~~Fs~~G~V~~-i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++++|.|.+..-+...|. .+|+.|+-+.. ++.   ...++.+-.||+.-.+++++..++..+.......-++-+.-
T Consensus       478 md~~R~iWn~imty~~~~iag~Wle~~~lE~~~g~~---~~~R~~~R~ay~~~~~~~~~~ev~~~~~r~Ere~gtl~~~~  554 (881)
T KOG0128|consen  478 MDKAREIWNFIMTYGGGSIAGKWLEAINLEREYGDG---PSARKVLRKAYSQVVDPEDALEVLEFFRRFEREYGTLESFD  554 (881)
T ss_pred             hhhhhHhhhccccCCcchHHHHHHHHHhHHHHhCCc---hhHHHHHHHHHhcCcCchhHHHHHHHHHHHHhccccHHHHh
Confidence            34678888998888888888 78877753322 221   22344667899999999999999998876555444443322


Q ss_pred             ccCCc-----ccccCCCcceeecCCCccccHH-HHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHh
Q 006282          106 SHRDP-----SIRKSGTGNIFIKNLDKSIDHK-ALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL  178 (652)
Q Consensus       106 s~~~~-----~~~~~~~~~lfV~nLp~~~t~~-~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~l  178 (652)
                      +....     ....-......+.++.+....+ ..+..|..+|+|..+++... ..-....++++.++...++..|. ..
T Consensus       555 ~~~~~~~pr~~~~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat-~p  633 (881)
T KOG0128|consen  555 LCPEKVLPRVYEAPLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESAT-VP  633 (881)
T ss_pred             hhHHhhcchhhhhhhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcc-cc
Confidence            11111     1111123345667776666555 56788999999999998873 22223337889999999998887 44


Q ss_pred             cCceecCeeeeecccccchhhHHHhhc----cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEe-eCCCCCcceeEE
Q 006282          179 NGMLINDKQVFVGHFLRKQERETVAIK----TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGF  253 (652)
Q Consensus       179 ng~~l~g~~~~v~~~~~~~~~~~~~~~----~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~-~~~~g~~~g~~f  253 (652)
                      .+..+.++...+....++.........    .....+|++||+..+.+++|...|..+|.+..+.+. ...+++-+|+|+
T Consensus       634 a~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y  713 (881)
T KOG0128|consen  634 AGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAY  713 (881)
T ss_pred             cccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhcccccccee
Confidence            677777888877777665533322221    223458999999999999999999999988877766 446788899999


Q ss_pred             EeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhh
Q 006282          254 VNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFS  333 (652)
Q Consensus       254 V~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~  333 (652)
                      +.|...+++.+|+.. ....+.|+                                  ..|+|.|.|...|+++|+.+|+
T Consensus       714 ~~F~~~~~~~aaV~f-~d~~~~gK----------------------------------~~v~i~g~pf~gt~e~~k~l~~  758 (881)
T KOG0128|consen  714 VEFLKPEHAGAAVAF-RDSCFFGK----------------------------------ISVAISGPPFQGTKEELKSLAS  758 (881)
T ss_pred             eEeecCCchhhhhhh-hhhhhhhh----------------------------------hhhheeCCCCCCchHHHHhhcc
Confidence            999999999999964 43333331                                  1599999999999999999999


Q ss_pred             hcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          334 EFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       334 ~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .+|++++++++....|+.+|-+||.|.+..+|.+++.......+..+.+.|++.++
T Consensus       759 ~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  759 KTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             ccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            99999999999989999999999999999999999988888777777777776554

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

Probab=99.36  E-value=2.5e-12  Score=103.68  Aligned_cols=85  Identities=27%  Similarity=0.491  Sum_probs=76.4

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      .--++..++.|||+|||.++|.++.+++|..||+|..|||=..+.|+   |-|||-|++..||.+|++.|++..+.++.+
T Consensus        11 ~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~Tr---GTAFVVYedi~dAk~A~dhlsg~n~~~ryl   87 (124)
T KOG0114|consen   11 IRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETR---GTAFVVYEDIFDAKKACDHLSGYNVDNRYL   87 (124)
T ss_pred             CCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcC---ceEEEEehHhhhHHHHHHHhcccccCCceE
Confidence            33456678999999999999999999999999999999998776665   899999999999999999999999999999


Q ss_pred             EeecccCC
Q 006282          102 RIMYSHRD  109 (652)
Q Consensus       102 ~i~~s~~~  109 (652)
                      .|.+-+..
T Consensus        88 ~vlyyq~~   95 (124)
T KOG0114|consen   88 VVLYYQPE   95 (124)
T ss_pred             EEEecCHH
Confidence            99876643

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

Probab=99.36  E-value=1.1e-12  Score=119.00  Aligned_cols=84  Identities=29%  Similarity=0.445  Sum_probs=79.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      +-.-+++|.|-||-+-+|.++|+.+|++||.|.+|.|.+|..|+.++|||||.|....||++|++.|++..++|+.|+|.
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            34457999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccC
Q 006282          105 YSHR  108 (652)
Q Consensus       105 ~s~~  108 (652)
                      ++.-
T Consensus        89 ~ary   92 (256)
T KOG4207|consen   89 MARY   92 (256)
T ss_pred             hhhc
Confidence            7753

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

Probab=99.35  E-value=1.7e-12  Score=115.04  Aligned_cols=78  Identities=28%  Similarity=0.517  Sum_probs=72.2

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...+.|||+||+..+++.||..+|..||.|.+|.|..+    ..|||||+|+++.+|..|+..|+|+.|+|..|.|++..
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            34688999999999999999999999999999999886    47799999999999999999999999999999999876


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      -.
T Consensus        84 G~   85 (195)
T KOG0107|consen   84 GR   85 (195)
T ss_pred             CC
Confidence            43

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

Probab=99.34  E-value=3.3e-12  Score=122.48  Aligned_cols=83  Identities=22%  Similarity=0.388  Sum_probs=78.3

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      +...+-+||||+-|+++++|..|++.|+.||+|..|++++|+.|++|+|||||+|++..|-..|.+..++..|+|+.|-|
T Consensus        96 a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~V  175 (335)
T KOG0113|consen   96 AIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILV  175 (335)
T ss_pred             ccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEE
Confidence            34467899999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ecc
Q 006282          104 MYS  106 (652)
Q Consensus       104 ~~s  106 (652)
                      -+.
T Consensus       176 DvE  178 (335)
T KOG0113|consen  176 DVE  178 (335)
T ss_pred             Eec
Confidence            643

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

Probab=99.34  E-value=1.3e-12  Score=118.57  Aligned_cols=78  Identities=27%  Similarity=0.467  Sum_probs=74.6

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .+.|.|.||.+.++.++|+.+|++||.|-+|.|.+|. ++.++|||||.|.+..+|+.|++.|+|.+++|+.|.|.+++
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            4679999999999999999999999999999999996 88999999999999999999999999999999999999876

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.34  E-value=4.3e-12  Score=120.59  Aligned_cols=76  Identities=20%  Similarity=0.237  Sum_probs=69.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .+.+|||+||++++||++|+++|+.||+|.+|++.+|.   ++.|+|||+|.++++|+.|+. ||+..|.+++|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            46799999999999999999999999999999999994   445899999999999999997 99999999999997533

>PLN03213 repressor of silencing 3; Provisional

Probab=99.33  E-value=6.6e-12  Score=127.43  Aligned_cols=81  Identities=22%  Similarity=0.421  Sum_probs=73.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCH--HHHHHHHHHhcCcEecCeeEEEEe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP--EEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~--~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ..+.+|||+||++.+++++|+.+|+.||.|.+|.|+++ +|  ||||||+|.+.  .++.+||..|||..+.|+.|+|..
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            34678999999999999999999999999999999954 55  99999999987  789999999999999999999999


Q ss_pred             cccHHH
Q 006282          387 AQRKEE  392 (652)
Q Consensus       387 ~~~~~~  392 (652)
                      |++.-.
T Consensus        85 AKP~YL   90 (759)
T PLN03213         85 AKEHYL   90 (759)
T ss_pred             ccHHHH
Confidence            987643

>smart00362 RRM_2 RNA recognition motif

Probab=99.32  E-value=1e-11  Score=98.17  Aligned_cols=72  Identities=43%  Similarity=0.746  Sum_probs=67.8

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      +|||+|||..+++++|+++|+.||.|..+++..+. +.++|+|||+|.+.++|.+|+..+++..+.|+.|.|+
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            48999999999999999999999999999999887 7789999999999999999999999999999998873

>smart00362 RRM_2 RNA recognition motif

Probab=99.32  E-value=7.5e-12  Score=98.98  Aligned_cols=71  Identities=35%  Similarity=0.678  Sum_probs=67.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      +|||+|||.++++++|+++|+.||+|..+++.++.  +.++|+|||+|.+.++|++|++.+++..|.|+.|+|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            58999999999999999999999999999999886  678899999999999999999999999999999876

>PLN03213 repressor of silencing 3; Provisional

Probab=99.32  E-value=5.1e-12  Score=128.22  Aligned_cols=116  Identities=16%  Similarity=0.206  Sum_probs=88.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCH--HHHHHHHhhcCCcccCCceeEee
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP--ADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~--e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ..+.+||||||++++|+++|..+|+.||.|.+|.|+|+  |+  +|||||+|.+.  +++.+|++.||+..++|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            34689999999999999999999999999999999965  55  79999999987  78999999999999999999998


Q ss_pred             cccCCc----------ccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEE
Q 006282          105 YSHRDP----------SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI  149 (652)
Q Consensus       105 ~s~~~~----------~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v  149 (652)
                      .++..-          .... ....+.+-..  ..+...|.-+|-.++.|.++-+
T Consensus        84 KAKP~YLeRLkrEReea~s~-~~~~~kl~k~--~~e~~qLnifFPrLrKvKslPf  135 (759)
T PLN03213         84 KAKEHYLARLKREWEAASST-SDNTIKAPSD--SPPATHLNIFFPRLRKVKAMPL  135 (759)
T ss_pred             eccHHHHHHHHHHHHHhhcc-cccccccccc--CCccceeeEecccccccccccc
Confidence            776321          0000 1111211111  1345677788888887766544

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

Probab=99.31  E-value=3.9e-12  Score=123.39  Aligned_cols=103  Identities=27%  Similarity=0.447  Sum_probs=88.2

Q ss_pred             cCCcccCCceeEeecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHH
Q 006282           91 LNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKES  170 (652)
Q Consensus        91 ln~~~i~G~~i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~  170 (652)
                      -++....|.++....+.+  +..+.+.++|.|.|||+...+-||+.+|.+||.|++++|+.++.| |||||||+|++.+|
T Consensus        72 ~~~~~t~g~~~~~~~st~--s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~d  148 (376)
T KOG0125|consen   72 SNGAPTDGQPIQTQPSTN--SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPAD  148 (376)
T ss_pred             cCCCCCCCCccccCCCCc--CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhh
Confidence            345556666665544333  344566778999999999999999999999999999999999887 89999999999999


Q ss_pred             HHHHHHHhcCceecCeeeeecccccc
Q 006282          171 AQNAIDKLNGMLINDKQVFVGHFLRK  196 (652)
Q Consensus       171 A~~Ai~~lng~~l~g~~~~v~~~~~~  196 (652)
                      |++|.++|||..+.||+|.|.....+
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchh
Confidence            99999999999999999999887655

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

Probab=99.31  E-value=1.3e-11  Score=125.90  Aligned_cols=164  Identities=32%  Similarity=0.469  Sum_probs=124.0

Q ss_pred             cceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       208 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      ..+|||+||+.++++++|.++|..||.|..+.+..+ .+|.++|||||.|.+.+++..|+..+++..+.|+.+.|.++..
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            588999999999999999999999999999999998 5899999999999999999999999999999999999999653


Q ss_pred             ----chHHHHH--HhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCC-CccEEEEEe
Q 006282          287 ----KSEREQE--LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAF  359 (652)
Q Consensus       287 ----~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~-s~g~afV~F  359 (652)
                          .......  ....................+++.+++..++..++...|..+|.+....+.....+. ...+.++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence                2111100  000001111122334567789999999999999999999999999777776554332 334444555


Q ss_pred             CCHHHHHHHHHH
Q 006282          360 STPEEASRALAE  371 (652)
Q Consensus       360 ~s~~~A~~A~~~  371 (652)
                      .....+......
T Consensus       275 ~~~~~~~~~~~~  286 (306)
T COG0724         275 EASKDALESNSR  286 (306)
T ss_pred             hHHHhhhhhhcc
Confidence            555555554443

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.30  E-value=9.6e-12  Score=118.21  Aligned_cols=76  Identities=20%  Similarity=0.379  Sum_probs=69.9

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .+.+|||+||++.+|+++|+++|+.||+|.+|+|++|  +.++|||||+|.++++|..|+. |+|..|.+++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            4679999999999999999999999999999999988  5667899999999999999996 99999999999988443

>smart00360 RRM RNA recognition motif

Probab=99.30  E-value=1e-11  Score=97.74  Aligned_cols=70  Identities=37%  Similarity=0.683  Sum_probs=67.0

Q ss_pred             EcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           34 VGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        34 V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      |+|||.++++++|+++|+.||.|..++++.+..+++++|||||.|.+.++|.+|++.+++..+.|+.|+|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            6899999999999999999999999999999888999999999999999999999999999999999887

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

Probab=99.30  E-value=4.9e-12  Score=106.89  Aligned_cols=84  Identities=20%  Similarity=0.319  Sum_probs=79.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      +-.+=.|||.+++.+.||++|.+.|..||+|++|.+-.|..|+-.+|||+|+|.+.++|..|++.+|+..+.|..|.|-|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 006282          106 SHRD  109 (652)
Q Consensus       106 s~~~  109 (652)
                      +-..
T Consensus       149 ~Fv~  152 (170)
T KOG0130|consen  149 CFVK  152 (170)
T ss_pred             EEec
Confidence            7543

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

Probab=99.29  E-value=7.5e-12  Score=131.27  Aligned_cols=81  Identities=31%  Similarity=0.615  Sum_probs=78.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      ++|||||+|++++|++|.++|+..|+|.++++..|+.||+++||||++|.+.++|++|++.||+.++.|++|+|.|...+
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            89999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             c
Q 006282          110 P  110 (652)
Q Consensus       110 ~  110 (652)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            4

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

Probab=99.28  E-value=4.5e-13  Score=119.13  Aligned_cols=76  Identities=25%  Similarity=0.479  Sum_probs=72.6

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      +.-|||+|||++.||.+|..+|++||+|..|.+++|. +|+|+||||+||.+..+..-|+..|||..|.|+.|+|.-
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            4569999999999999999999999999999999996 899999999999999999999999999999999999974

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

Probab=99.27  E-value=2.7e-11  Score=97.75  Aligned_cols=81  Identities=26%  Similarity=0.417  Sum_probs=73.1

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..+.|||+|||+.+|.|+..++|.+||.|..++|=...  ..+|.|||.|++..+|.+|++.|+|..++++.|.|-+.+.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            34579999999999999999999999999999986653  3588999999999999999999999999999999999886


Q ss_pred             HHH
Q 006282          390 KEE  392 (652)
Q Consensus       390 ~~~  392 (652)
                      .+.
T Consensus        95 ~~~   97 (124)
T KOG0114|consen   95 EDA   97 (124)
T ss_pred             HHH
Confidence            543

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

Probab=99.26  E-value=1.5e-11  Score=117.98  Aligned_cols=83  Identities=23%  Similarity=0.440  Sum_probs=77.4

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ..+=++|||..|+++++|.+|+..|+.||.|+.|+|+.|. +|+++|||||+|.+..+-..|.+..+|.+|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            3456789999999999999999999999999999999995 999999999999999999999999999999999999997


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      -.-.
T Consensus       178 ERgR  181 (335)
T KOG0113|consen  178 ERGR  181 (335)
T ss_pred             cccc
Confidence            6643

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

Probab=99.25  E-value=5.1e-10  Score=118.37  Aligned_cols=167  Identities=15%  Similarity=0.016  Sum_probs=125.0

Q ss_pred             eeecCCCccccHHHHHhhhccCCCeeEEEEeeCC-CCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchh
Q 006282          120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQE  198 (652)
Q Consensus       120 lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~-~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~  198 (652)
                      +-+++++.+.++.+++++|... .|.+..+..+. .+...|-++|.|....++.+|+.+ |.+..-++.+.+...-....
T Consensus       314 ~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~~~~  391 (944)
T KOG4307|consen  314 NNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGNLGR  391 (944)
T ss_pred             eeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCcccc
Confidence            6678889999999999999876 56666666663 444588999999999999999976 44444455555543321110


Q ss_pred             --------hHH------------------H-------hhccCcceEEecCCCCCCCHHHHHHHhccCCCeeE-EEEeeCC
Q 006282          199 --------RET------------------V-------AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDG  244 (652)
Q Consensus       199 --------~~~------------------~-------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~-~~i~~~~  244 (652)
                              ...                  .       .......+|||..||..+++.++.++|...-.|++ |.+.+..
T Consensus       392 ~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P  471 (944)
T KOG4307|consen  392 NGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP  471 (944)
T ss_pred             ccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC
Confidence                    000                  0       00112246999999999999999999999888887 6666778


Q ss_pred             CCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccch
Q 006282          245 DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  288 (652)
Q Consensus       245 ~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~  288 (652)
                      +++.++.|||.|..++++..|...-+...+..+.|.|..+.++.
T Consensus       472 ~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~  515 (944)
T KOG4307|consen  472 TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYA  515 (944)
T ss_pred             cccccchhhheeccccccchhhhcccccccCceEEEeechhhHH
Confidence            88999999999999988888887777778888899998876653

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

Probab=99.24  E-value=1.5e-11  Score=103.23  Aligned_cols=82  Identities=23%  Similarity=0.337  Sum_probs=73.9

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .+++|||+||+..++||.|.++|+++|+|..|.+=.|. +-..=|||||+|.+.++|..|++.++|..++.++|.+.|.-
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            46899999999999999999999999999999776665 44567999999999999999999999999999999999987


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      --.
T Consensus       115 GF~  117 (153)
T KOG0121|consen  115 GFV  117 (153)
T ss_pred             cch
Confidence            543

>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=99.23  E-value=5.3e-11  Score=94.57  Aligned_cols=74  Identities=39%  Similarity=0.722  Sum_probs=69.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      +|+|+|||+.+++++|+++|+.+|.|..+.+..+..+ ++.|+|||.|.+.++|..|++.+++..++|+.+.|.|
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            5899999999999999999999999999999998765 6789999999999999999999999999999998864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>smart00360 RRM RNA recognition motif

Probab=99.23  E-value=4.4e-11  Score=94.15  Aligned_cols=70  Identities=44%  Similarity=0.763  Sum_probs=65.4

Q ss_pred             ecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       316 V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      |+|||..+++++|+++|+.||.|..+++..+. ++.++|+|||+|.+.++|.+|+..+++..+.|+.|.|+
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            68999999999999999999999999998876 58889999999999999999999999999999998873

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

Probab=99.22  E-value=6.7e-12  Score=114.79  Aligned_cols=84  Identities=27%  Similarity=0.490  Sum_probs=80.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++||||+|-.+|+|..|...|-+||.|++|.+..|..+++.+|||||+|...|||..|++.||..++.||.|||.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCc
Q 006282          107 HRDP  110 (652)
Q Consensus       107 ~~~~  110 (652)
                      ....
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            8653

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

Probab=99.22  E-value=1.4e-11  Score=128.04  Aligned_cols=154  Identities=21%  Similarity=0.243  Sum_probs=106.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      .-+..+|+|-|||.+|++++|+++|+.||.|.+|+-.+.     ..|..||+|.+..+|++|+++||+..|.|+.|+.-.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~  146 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPG  146 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCC
Confidence            345789999999999999999999999999999766543     448999999999999999999999999999987322


Q ss_pred             ccCCcc--------------------cccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEE
Q 006282          106 SHRDPS--------------------IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF  165 (652)
Q Consensus       106 s~~~~~--------------------~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F  165 (652)
                      +.+...                    .-......+|+- |++..+..-+..+|+-+|.+.. ..    ++.-+..-|+.|
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~----~~~~~hq~~~~~  220 (549)
T KOG4660|consen  147 GARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RE----TPLLNHQRFVEF  220 (549)
T ss_pred             cccccchhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-cc----ccchhhhhhhhh
Confidence            211100                    000112234433 8887777666667777776644 21    222222567888


Q ss_pred             cCHHHHHHHHHHhcCceecCeeeeec
Q 006282          166 ENKESAQNAIDKLNGMLINDKQVFVG  191 (652)
Q Consensus       166 ~t~e~A~~Ai~~lng~~l~g~~~~v~  191 (652)
                      .+..++..+.... |+.+.+......
T Consensus       221 ~~~~s~a~~~~~~-G~~~s~~~~v~t  245 (549)
T KOG4660|consen  221 ADNRSYAFSEPRG-GFLISNSSGVIT  245 (549)
T ss_pred             ccccchhhcccCC-ceecCCCCceEE
Confidence            8888875555433 666666554443

>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=99.22  E-value=8.8e-11  Score=93.29  Aligned_cols=74  Identities=41%  Similarity=0.719  Sum_probs=69.8

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+..+.++|+|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999887777899999999999999999999999999999999874

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).

>PF13893 RRM_5: RNA recognition motif

Probab=99.20  E-value=9.3e-11  Score=88.23  Aligned_cols=56  Identities=36%  Similarity=0.711  Sum_probs=51.6

Q ss_pred             HHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          328 LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       328 L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      |+++|++||+|+++++..+.    +++|||+|.+.++|.+|++.|||..++|++|+|.|+
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            78999999999999998874    589999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=99.16  E-value=1.6e-11  Score=112.38  Aligned_cols=83  Identities=29%  Similarity=0.485  Sum_probs=77.8

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||++|.++++|.-|...|-+||.|+.|.+..|. +++.||||||+|.-.|+|..|+..||+..+.|+.|+|++++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            46789999999999999999999999999999999884 78899999999999999999999999999999999999998


Q ss_pred             cHHH
Q 006282          389 RKEE  392 (652)
Q Consensus       389 ~~~~  392 (652)
                      +..-
T Consensus        89 P~ki   92 (298)
T KOG0111|consen   89 PEKI   92 (298)
T ss_pred             Cccc
Confidence            7643

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

Probab=99.16  E-value=6.2e-11  Score=124.43  Aligned_cols=84  Identities=27%  Similarity=0.476  Sum_probs=79.2

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +++||+|||+++++++|.++|+..|.|.+++++.|. +|+++|||||+|.+.++|.+|++.|||..+.|++|+|.|+...
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            789999999999999999999999999999999885 8999999999999999999999999999999999999999876


Q ss_pred             HHHHH
Q 006282          391 EERRA  395 (652)
Q Consensus       391 ~~r~~  395 (652)
                      ..+..
T Consensus        99 ~~~~~  103 (435)
T KOG0108|consen   99 KNAER  103 (435)
T ss_pred             chhHH
Confidence            65543

>PF13893 RRM_5: RNA recognition motif

Probab=99.14  E-value=1e-10  Score=87.97  Aligned_cols=56  Identities=30%  Similarity=0.688  Sum_probs=51.4

Q ss_pred             HHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           46 LYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        46 L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      |+++|++||+|.+|++.++.     .++|||+|.+.++|++|++.||+..+.|++|+|.||
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            78999999999999998765     479999999999999999999999999999999986

(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 ....

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

Probab=99.14  E-value=8.2e-10  Score=118.58  Aligned_cols=111  Identities=21%  Similarity=0.346  Sum_probs=90.7

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ..+++|||+.|+.++++.||.++|+.||.|.+|+++..     ++||||+..+..+|.+|+.+|+...+.++.+.+.|+.
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            34578999999999999999999999999999998854     7899999999999999999999999999999999998


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhh
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSE  334 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~  334 (652)
                      .+..+. +++..++            ..+=|.-||++--.++|+.+++.
T Consensus       494 g~G~ks-e~k~~wD------------~~lGVt~IP~~kLt~dl~~~~eg  529 (894)
T KOG0132|consen  494 GKGPKS-EYKDYWD------------VELGVTYIPWEKLTDDLEAWCEG  529 (894)
T ss_pred             cCCcch-hhhhhhh------------cccCeeEeehHhcCHHHHHhhhh
Confidence            887665 4444333            23556667876544446666543

>smart00361 RRM_1 RNA recognition motif

Probab=99.13  E-value=2e-10  Score=90.64  Aligned_cols=60  Identities=25%  Similarity=0.534  Sum_probs=53.6

Q ss_pred             HHHHHHHhh----hcCCeeEEE-EecC-CC--CCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          325 DEKLKELFS----EFGTITSCK-VMRD-PS--GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       325 e~~L~~~F~----~fG~I~~v~-i~~~-~~--g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      +++|+++|+    .||.|.++. |..+ .+  |.++|||||+|.+.++|.+|+..|||+.+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578899998    999999995 5544 34  889999999999999999999999999999999976

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

Probab=99.13  E-value=1.1e-10  Score=115.24  Aligned_cols=160  Identities=19%  Similarity=0.275  Sum_probs=121.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccC----CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVG----QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G----~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      --.|.+++||.++++.++.++|..--    -+..|-.++ +-.+|.+|-|||.|..+++|..||.+ |...+.-|.|.+.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~-rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElF  238 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVT-RPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELF  238 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEE-CCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHH
Confidence            45788999999999999999996322    223343333 23578899999999999999999984 5555666677665


Q ss_pred             cccCC-----------------------------cccccCCCcceeecCCCccccHHHHHhhhccCC-Ce--eEEEEeeC
Q 006282          105 YSHRD-----------------------------PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG-NI--LSCKIATD  152 (652)
Q Consensus       105 ~s~~~-----------------------------~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG-~I--~~~~v~~~  152 (652)
                      .|...                             -..+.....+|.+++||++.+.++|.++|..|- .|  ..+.+..+
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N  318 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN  318 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc
Confidence            54310                             011223367899999999999999999999886 23  34778888


Q ss_pred             CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeee
Q 006282          153 GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV  190 (652)
Q Consensus       153 ~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v  190 (652)
                      ..|...|-|||+|.+.|+|..|..+.+.+....+.+.|
T Consensus       319 ~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEv  356 (508)
T KOG1365|consen  319 GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEV  356 (508)
T ss_pred             CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEE
Confidence            89999999999999999999999988777765555444

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

Probab=99.13  E-value=8e-11  Score=99.65  Aligned_cols=83  Identities=22%  Similarity=0.448  Sum_probs=77.1

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...+..|||.++..+.++++|.+.|..||+|+.+.+-.|. +|..+|||+|+|.+.++|.+|+..+||..+.|..|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            3457789999999999999999999999999999998775 899999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      .-.+
T Consensus       149 ~Fv~  152 (170)
T KOG0130|consen  149 CFVK  152 (170)
T ss_pred             EEec
Confidence            8654

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

Probab=99.11  E-value=1.3e-11  Score=133.86  Aligned_cols=234  Identities=18%  Similarity=0.140  Sum_probs=186.7

Q ss_pred             CCCccEEEEcCCCCCCCHH-HHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           26 QFLTTSLYVGDLDFNVTDS-QLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~-~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      +.....+++.++-+..... ..+..|..+|.|..|++........+-.++++.++...+++.|.. ..+.-+.++.+.+.
T Consensus       568 ~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~  646 (881)
T KOG0128|consen  568 PLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVG  646 (881)
T ss_pred             hhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCC
Confidence            3445677888887777665 578899999999999987643333444489999999999999998 67777888888887


Q ss_pred             cccCCcccccCC--------CcceeecCCCccccHHHHHhhhccCCCeeEEEEe-eCCCCCcccEEEEEEcCHHHHHHHH
Q 006282          105 YSHRDPSIRKSG--------TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA-TDGSGQSKGFGFVQFENKESAQNAI  175 (652)
Q Consensus       105 ~s~~~~~~~~~~--------~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~-~~~~g~skG~afV~F~t~e~A~~Ai  175 (652)
                      .+...+......        ..++|+.||+..+.+.+|.+.|..+|.+..+.+. ....+.-+|+|||.|..++++.+|+
T Consensus       647 ~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV  726 (881)
T KOG0128|consen  647 LADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAV  726 (881)
T ss_pred             CCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhh
Confidence            776554332222        2358999999999999999999999988777666 3357778999999999999999999


Q ss_pred             HHhcCceecCeeeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEe
Q 006282          176 DKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVN  255 (652)
Q Consensus       176 ~~lng~~l~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~  255 (652)
                      .....+.+.                       ...|+|+|.|+..|+++++.+|..+|.+++..+....+|+.+|-++|.
T Consensus       727 ~f~d~~~~g-----------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~  783 (881)
T KOG0128|consen  727 AFRDSCFFG-----------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVD  783 (881)
T ss_pred             hhhhhhhhh-----------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceecc
Confidence            764444432                       234899999999999999999999999999999888999999999999


Q ss_pred             eCCHHHHHHHHHHHCCCccCCceEEEEc
Q 006282          256 FENADDAAKAVEALNGKKFDDREWYVGK  283 (652)
Q Consensus       256 f~~~~~A~~Ai~~l~~~~~~g~~l~v~~  283 (652)
                      |.+..++..++...+...+..+.+.+..
T Consensus       784 y~~ea~~s~~~~s~d~~~~rE~~~~v~v  811 (881)
T KOG0128|consen  784 YNTEADASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             CCCcchhhhhcccchhhhhhhcCccccc
Confidence            9999999998876666555544444433

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

Probab=99.10  E-value=2.6e-11  Score=111.18  Aligned_cols=153  Identities=24%  Similarity=0.358  Sum_probs=125.1

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ++...++|||+||...|+|+-|.|+|-+.|+|..|.|..++.. +-+ ||||+|.+.-+..-|++-+|+..+.++++.|.
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~-~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQ-EQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccC-CCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            3456789999999999999999999999999999988777553 333 99999999999999999999999999999885


Q ss_pred             cccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceec
Q 006282          105 YSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIN  184 (652)
Q Consensus       105 ~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~  184 (652)
                      +-....-           .-|+..++++.++..|+..|.+..+++..+.+|.++.++|+.+--....-.++....++...
T Consensus        83 ~r~G~sh-----------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~  151 (267)
T KOG4454|consen   83 LRCGNSH-----------APLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELF  151 (267)
T ss_pred             cccCCCc-----------chhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcC
Confidence            4321100           12777889999999999999999999999988999999999888777777777766666554


Q ss_pred             Ceeeee
Q 006282          185 DKQVFV  190 (652)
Q Consensus       185 g~~~~v  190 (652)
                      -+++.+
T Consensus       152 ~~~~~~  157 (267)
T KOG4454|consen  152 QKKVTI  157 (267)
T ss_pred             CCCccc
Confidence            444444

>smart00361 RRM_1 RNA recognition motif

Probab=99.10  E-value=3e-10  Score=89.70  Aligned_cols=61  Identities=25%  Similarity=0.355  Sum_probs=56.2

Q ss_pred             HHHHHHHHh----ccCCeEEEE-EEeeCCC--CCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           43 DSQLYDLFS----QVGQVLSVR-VCRDLST--RRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        43 e~~L~~~Fs----~~G~V~~i~-v~~d~~t--~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      +++|+++|+    .||.|.+|. |..|+.+  ++++|||||.|.+.++|.+|++.||+..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678999998    999999995 7777776  899999999999999999999999999999999976

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

Probab=98.99  E-value=4.2e-10  Score=105.81  Aligned_cols=169  Identities=27%  Similarity=0.439  Sum_probs=129.7

Q ss_pred             EEecCCCCCCCHHH---HHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccc
Q 006282          211 VFVKNLDESTTDED---LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  287 (652)
Q Consensus       211 l~V~nlp~~~t~~~---l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~  287 (652)
                      .++.++-..+..+-   +...|+.+-.+....+.++..+.-++++|+.|.....-.++-..-+++.+....+....++..
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtsw  178 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSW  178 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecccccc
Confidence            44555544444333   256677777777778888888888999999999888777777666777777776666665543


Q ss_pred             hHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHH
Q 006282          288 SEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEAS  366 (652)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~  366 (652)
                      .....            ..-+.....||++.|..+++++.|-..|.+|-.....++++|. +|+++||+||.|.++.++.
T Consensus       179 edPsl------------~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~  246 (290)
T KOG0226|consen  179 EDPSL------------AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYV  246 (290)
T ss_pred             CCccc------------ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHH
Confidence            21110            0111233479999999999999999999999999999999886 8999999999999999999


Q ss_pred             HHHHHhcCcEecCeeEEEEecccHH
Q 006282          367 RALAEMNGKMIVSKPLYVAVAQRKE  391 (652)
Q Consensus       367 ~A~~~lng~~~~g~~l~v~~~~~~~  391 (652)
                      .|+.+|+|+.++.++|.++-..-++
T Consensus       247 rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  247 RAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             HHHHhhcccccccchhHhhhhhHHh
Confidence            9999999999999999887554443

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

Probab=98.95  E-value=2.4e-10  Score=104.96  Aligned_cols=138  Identities=25%  Similarity=0.359  Sum_probs=120.9

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      ..++|||.|+...++++-|.++|=.-|.|..+.|..+.++..+ |+||+|+++.+..-|++-+||..+.+..+.+     
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~-----   81 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQR-----   81 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhc-----
Confidence            3467999999999999999999999999999999998888888 9999999999999999999999888776554     


Q ss_pred             chHHHHHHhHHHHHhhhhcccccccceeeecC----CCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCH
Q 006282          287 KSEREQELKGQFEQAMKETVDKFQGLNLYIKN----LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP  362 (652)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----lp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~  362 (652)
                                                +++.++    |+..++++.+...|+.-|.+..+++..+.+|+.+.++|+++.-.
T Consensus        82 --------------------------~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~  135 (267)
T KOG4454|consen   82 --------------------------TLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRL  135 (267)
T ss_pred             --------------------------ccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhh
Confidence                                      355666    77889999999999999999999999998999999999999887


Q ss_pred             HHHHHHHHHhcCcE
Q 006282          363 EEASRALAEMNGKM  376 (652)
Q Consensus       363 ~~A~~A~~~lng~~  376 (652)
                      ...-.++....+..
T Consensus       136 ~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen  136 CAVPFALDLYQGLE  149 (267)
T ss_pred             hcCcHHhhhhcccC
Confidence            77777776555433

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

Probab=98.94  E-value=1.4e-09  Score=106.57  Aligned_cols=86  Identities=24%  Similarity=0.384  Sum_probs=81.1

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ...++...|||=.|.+-+|.++|.-+||.||+|.++.|+||..|+-|+.||||+|.+.++.++|.=+|++..|+.+.|+|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCC
Q 006282          104 MYSHRD  109 (652)
Q Consensus       104 ~~s~~~  109 (652)
                      -||+.-
T Consensus       314 DFSQSV  319 (479)
T KOG0415|consen  314 DFSQSV  319 (479)
T ss_pred             ehhhhh
Confidence            998853

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

Probab=98.93  E-value=2.1e-09  Score=98.54  Aligned_cols=82  Identities=22%  Similarity=0.341  Sum_probs=74.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhcc-CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQV-GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~-G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ......+||..+|..+.|.+|..+|.++ |.|..+|+.|.+.||.|+|||||+|++.+.|+-|-++||+..+.|+.+.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3456789999999999999999999988 799999999999999999999999999999999999999999999988776


Q ss_pred             ccc
Q 006282          105 YSH  107 (652)
Q Consensus       105 ~s~  107 (652)
                      +-.
T Consensus       126 vmp  128 (214)
T KOG4208|consen  126 VMP  128 (214)
T ss_pred             EeC
Confidence            533

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

Probab=98.91  E-value=1.3e-08  Score=105.36  Aligned_cols=152  Identities=22%  Similarity=0.340  Sum_probs=115.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCC--Cccc---EEEEEeCCHHHHHHHHhhcCCc------
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR--RSLG---YGYVNYANPADAARALDVLNFT------   94 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~--~s~g---~AfV~F~~~e~A~~Al~~ln~~------   94 (652)
                      +.-++.||||+||++++|+.|...|..||++.-=.-.+....+  ..+|   |+|+.|+++.+...-++.+...      
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf  335 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYF  335 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEE
Confidence            4458899999999999999999999999977432221221111  2345   9999999999988877766421      


Q ss_pred             -----ccCCceeEee-cccC------CcccccCCCcceeecCCCccccHHHHHhhhc-cCCCeeEEEEeeC-CCCCcccE
Q 006282           95 -----PLNNKSIRIM-YSHR------DPSIRKSGTGNIFIKNLDKSIDHKALHDTFS-SFGNILSCKIATD-GSGQSKGF  160 (652)
Q Consensus        95 -----~i~G~~i~i~-~s~~------~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs-~fG~I~~~~v~~~-~~g~skG~  160 (652)
                           .++.+.+.|. |--.      +.+..-...++|||++||.-++.++|..+|+ -||.|.-+-|-+| +.+..+|-
T Consensus       336 ~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGa  415 (520)
T KOG0129|consen  336 KVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGA  415 (520)
T ss_pred             EEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCc
Confidence                 1233333332 2221      2233445678999999999999999999999 7999999999999 78889999


Q ss_pred             EEEEEcCHHHHHHHHHH
Q 006282          161 GFVQFENKESAQNAIDK  177 (652)
Q Consensus       161 afV~F~t~e~A~~Ai~~  177 (652)
                      |-|+|.+...-.+||..
T Consensus       416 GRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  416 GRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ceeeecccHHHHHHHhh
Confidence            99999999999999974

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

Probab=98.89  E-value=3.9e-09  Score=103.79  Aligned_cols=79  Identities=27%  Similarity=0.437  Sum_probs=70.5

Q ss_pred             ccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh-cCcEecCeeEEE
Q 006282          306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYV  384 (652)
Q Consensus       306 ~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l-ng~~~~g~~l~v  384 (652)
                      .++..-.+|||++|.+.++|.+|+++|.+||+|.+++++..     ++||||+|.|.++|++|..+. |...|+|.+|.|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            33445678999999999999999999999999999999876     679999999999999998864 666778999999


Q ss_pred             Eeccc
Q 006282          385 AVAQR  389 (652)
Q Consensus       385 ~~~~~  389 (652)
                      .|.+.
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99998

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.87  E-value=1.9e-07  Score=91.59  Aligned_cols=76  Identities=18%  Similarity=0.237  Sum_probs=64.5

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcC--CeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG--~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ..++||+||-|++|+++|.+....-|  .+.+++++.+. +|+|||||+|...+..+.++.++.|-.+.|+|..-.|.-
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            35899999999999999999998776  46677777664 899999999999999999999999999999986554443

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

Probab=98.84  E-value=6.6e-09  Score=95.32  Aligned_cols=79  Identities=27%  Similarity=0.435  Sum_probs=72.9

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhc-CCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEF-GTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~f-G~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..+||+.+|.-+.+.+|..+|.+| |.|+.+++-++ .+|.|+|||||+|.+.+.|.-|.+.||++.+.++.|.|.+-.+
T Consensus        50 g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen   50 GVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             cceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence            469999999999999999999999 77888888666 4999999999999999999999999999999999999998887


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      .
T Consensus       130 e  130 (214)
T KOG4208|consen  130 E  130 (214)
T ss_pred             h
Confidence            6

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

Probab=98.81  E-value=4.7e-09  Score=98.86  Aligned_cols=154  Identities=22%  Similarity=0.329  Sum_probs=123.0

Q ss_pred             HhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccchhhHHHhhccCcceEEec
Q 006282          135 HDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVK  214 (652)
Q Consensus       135 ~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~  214 (652)
                      ...|+.+-.+...+++.+..+.-.+++|+.|.....-.++-..-+++++....|++.-...........-....-.||.+
T Consensus       117 ~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcg  196 (290)
T KOG0226|consen  117 PVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCG  196 (290)
T ss_pred             hhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecc
Confidence            56777777777788888877788999999999888877777666777776665665544444333333334555679999


Q ss_pred             CCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccch
Q 006282          215 NLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  288 (652)
Q Consensus       215 nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~  288 (652)
                      .|..+++++.|...|.+|-.-...++++| .+|+++||+||.|.+..++..|+..|+++.++.+.+.+.....+.
T Consensus       197 dlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  197 DLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             cccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            99999999999999999988888888888 579999999999999999999999999999999988776555444

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

Probab=98.78  E-value=1.3e-08  Score=100.18  Aligned_cols=76  Identities=24%  Similarity=0.412  Sum_probs=68.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc-CCcccCCceeEeec
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL-NFTPLNNKSIRIMY  105 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l-n~~~i~G~~i~i~~  105 (652)
                      ...++|||++|-..++|.+|+++|-+||.|.+|++....      ++|||+|.+.++|++|.++. |...|+|++|.|.|
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~W  299 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKW  299 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEEEEe
Confidence            457899999999999999999999999999999998753      49999999999999998754 56778999999999


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      ...
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            987

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

Probab=98.77  E-value=9.6e-09  Score=100.79  Aligned_cols=86  Identities=30%  Similarity=0.459  Sum_probs=79.9

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ..++...|||--|.+-+++++|.-+|+.||.|.+|.|++|. +|-|-.||||+|.+.+++++|.-.|.+..|+.++|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            34567789999999999999999999999999999999985 89999999999999999999999999999999999999


Q ss_pred             ecccHHH
Q 006282          386 VAQRKEE  392 (652)
Q Consensus       386 ~~~~~~~  392 (652)
                      |+++...
T Consensus       315 FSQSVsk  321 (479)
T KOG0415|consen  315 FSQSVSK  321 (479)
T ss_pred             hhhhhhh
Confidence            9987644

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

Probab=98.69  E-value=1.2e-08  Score=111.69  Aligned_cols=161  Identities=20%  Similarity=0.293  Sum_probs=135.6

Q ss_pred             ccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       205 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...+++||++||+..+++.+|+..|..+|.|.++.|....-+.-.-|+||.|.+...+..|+..+.+..|....+.+...
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            34567899999999999999999999999999999987765666669999999999999999888888887665555554


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE  364 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~  364 (652)
                      ..+                    ....+.++|++|..++....|...|..||.|..|.+-..     --|++|.|.+...
T Consensus       449 ~~k--------------------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~  503 (975)
T KOG0112|consen  449 QPK--------------------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPA  503 (975)
T ss_pred             ccc--------------------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCcc
Confidence            332                    123456999999999999999999999999998776433     3499999999999


Q ss_pred             HHHHHHHhcCcEecC--eeEEEEecccH
Q 006282          365 ASRALAEMNGKMIVS--KPLYVAVAQRK  390 (652)
Q Consensus       365 A~~A~~~lng~~~~g--~~l~v~~~~~~  390 (652)
                      |..|++.|.|..|++  +++.|.|+...
T Consensus       504 aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  504 AQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             chhhHHHHhcCcCCCCCcccccccccCC
Confidence            999999999999985  77888888754

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

Probab=98.69  E-value=1.3e-07  Score=98.28  Aligned_cols=162  Identities=17%  Similarity=0.296  Sum_probs=113.4

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC----CCCCcce---eEEEeeCCHHHHHHHHHHHCCCccCCce
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD----GDGKSKC---FGFVNFENADDAAKAVEALNGKKFDDRE  278 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~----~~g~~~g---~~fV~f~~~~~A~~Ai~~l~~~~~~g~~  278 (652)
                      .-++.|||++||++++|+.|...|..||.+.. .....    ..-..+|   |.|+-|+++.++...+.++..   ....
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~V-dWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~  332 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKV-DWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGN  332 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEe-ecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccc
Confidence            44567999999999999999999999997652 22211    1223566   999999999999888776654   3333


Q ss_pred             EEEEccccchHHH-HHH---h-HHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhh-hcCCeeEEEEecC-CCCCC
Q 006282          279 WYVGKAQKKSERE-QEL---K-GQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFS-EFGTITSCKVMRD-PSGIS  351 (652)
Q Consensus       279 l~v~~a~~~~~~~-~~~---~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~-~fG~I~~v~i~~~-~~g~s  351 (652)
                      ++........... ..+   . ...+-.......-.+.++|||++||--++.++|-.+|+ -||.|..+-|-.| +-+..
T Consensus       333 ~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYP  412 (520)
T KOG0129|consen  333 YYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYP  412 (520)
T ss_pred             eEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCC
Confidence            3332222111000 000   0 00000001112234567899999999999999999999 7999999999998 56778


Q ss_pred             ccEEEEEeCCHHHHHHHHHH
Q 006282          352 KGSGFVAFSTPEEASRALAE  371 (652)
Q Consensus       352 ~g~afV~F~s~~~A~~A~~~  371 (652)
                      +|-|-|+|.+..+=.+||.+
T Consensus       413 kGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  413 KGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCcceeeecccHHHHHHHhh
Confidence            99999999999999999984

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

Probab=98.64  E-value=5e-08  Score=101.19  Aligned_cols=82  Identities=27%  Similarity=0.465  Sum_probs=74.0

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...++||||.+|...+...+|+.+|++||.|+..+|+.+. +--.++|+||++.+.++|.++|..||...++|+.|.|.-
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            3457899999999999999999999999999999999875 233589999999999999999999999999999999987


Q ss_pred             ccc
Q 006282          387 AQR  389 (652)
Q Consensus       387 ~~~  389 (652)
                      ++.
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            654

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

Probab=98.61  E-value=1e-07  Score=92.34  Aligned_cols=79  Identities=30%  Similarity=0.508  Sum_probs=75.3

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +.|+|.||+..|++++|+++|..||.++.+-+.+++.|.|.|.|-|.|...++|..|++.+||..++|+.+.+.+....
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            6799999999999999999999999999999999999999999999999999999999999999999999999877654

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.61  E-value=8.2e-08  Score=102.42  Aligned_cols=83  Identities=30%  Similarity=0.449  Sum_probs=74.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCC---CCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS---TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~---t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      -+.++.|||+||+++++|+.|...|..||+|.+|+|+....   .++-..|+||-|-+..||++|+++|++..+.+..++
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            44578999999999999999999999999999999986533   245668999999999999999999999999999999


Q ss_pred             eecccC
Q 006282          103 IMYSHR  108 (652)
Q Consensus       103 i~~s~~  108 (652)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999974

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

Probab=98.59  E-value=8.9e-08  Score=99.34  Aligned_cols=85  Identities=25%  Similarity=0.465  Sum_probs=78.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..-++.|||++|..-+--.+|..||++||+|+..+|+.+..+---+||+||.+.+.++|.+||+.|+.+.+.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34578899999999999999999999999999999999888777889999999999999999999999999999999998


Q ss_pred             ccCCc
Q 006282          106 SHRDP  110 (652)
Q Consensus       106 s~~~~  110 (652)
                      ++..+
T Consensus       482 aKNEp  486 (940)
T KOG4661|consen  482 AKNEP  486 (940)
T ss_pred             cccCc
Confidence            87654

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.58  E-value=3.7e-07  Score=75.63  Aligned_cols=79  Identities=22%  Similarity=0.355  Sum_probs=68.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcc--CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC----CceeEe
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQV--GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN----NKSIRI  103 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~--G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~----G~~i~i  103 (652)
                      +||.|+|+|...|.++|.+++...  |..--+-+.-|-.++.++|||||+|.++++|.+..+.+++..+.    .|.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            699999999999999999988653  67777888889899999999999999999999999999987764    567777


Q ss_pred             ecccC
Q 006282          104 MYSHR  108 (652)
Q Consensus       104 ~~s~~  108 (652)
                      .|++-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77653

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.57  E-value=6.7e-08  Score=97.31  Aligned_cols=169  Identities=24%  Similarity=0.308  Sum_probs=135.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...+++|++++.+.+.+.++..+|..+|.+.............++|+++|.|...+.+..|+.......+.++.+..-..
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            35789999999999999999999999998888888776677889999999999999999999944323444444433332


Q ss_pred             cCCc--------ccccCCCccee-ecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHH
Q 006282          107 HRDP--------SIRKSGTGNIF-IKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID  176 (652)
Q Consensus       107 ~~~~--------~~~~~~~~~lf-V~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~  176 (652)
                      +...        ........+++ +.+++.+++.++|+..|..+|.|..+++..+ ..+..+|++||.|.+...+..++.
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~  245 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALN  245 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhh
Confidence            2211        12223344455 9999999999999999999999999999988 688999999999999999999997


Q ss_pred             HhcCceecCeeeeecccccc
Q 006282          177 KLNGMLINDKQVFVGHFLRK  196 (652)
Q Consensus       177 ~lng~~l~g~~~~v~~~~~~  196 (652)
                      . ....+.++.+.+....++
T Consensus       246 ~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  246 D-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             c-ccCcccCcccccccCCCC
Confidence            7 777888887777665554

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.56  E-value=4.2e-08  Score=98.77  Aligned_cols=175  Identities=23%  Similarity=0.253  Sum_probs=132.8

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEee-CCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR-DGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~-~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ..+.+|++++.+.+.+.+...++..+|......+.. .....++|++.+.|...+.+..++.........++.+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            457799999999999998999999999777666655 4678899999999999999999996433344444443332222


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceee-ecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHH
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLY-IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  363 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~  363 (652)
                      ....+.        .............++| |++++..+++++|+.+|..+|.|+.+++..++ .|.++|||+|+|.+..
T Consensus       167 ~~~~~~--------~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~  238 (285)
T KOG4210|consen  167 RRGLRP--------KNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGN  238 (285)
T ss_pred             cccccc--------cchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhch
Confidence            211000        0000111222333455 99999999999999999999999999998765 7899999999999999


Q ss_pred             HHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          364 EASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       364 ~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .+..++.. ....+.+.++.+......
T Consensus       239 ~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  239 SKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             hHHHHhhc-ccCcccCcccccccCCCC
Confidence            99999987 888999999998877655

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

Probab=98.53  E-value=5.3e-08  Score=106.73  Aligned_cols=160  Identities=20%  Similarity=0.271  Sum_probs=134.0

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      .+...+.+|++|||+..+++.+|+..|..+|.|.+|.+.+-... +-.-||||.|.+...+-+|+-++....|....+++
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~-~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIK-TESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCC-cccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            44567899999999999999999999999999999999776543 34469999999999999999999888887778888


Q ss_pred             ecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCcee
Q 006282          104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLI  183 (652)
Q Consensus       104 ~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l  183 (652)
                      .+.+.    ....+..+|+++|...+....|...|..||.|..|.+-.     ...|+||.|++.+.+..|++.+.+..+
T Consensus       446 glG~~----kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h-----gq~yayi~yes~~~aq~a~~~~rgap~  516 (975)
T KOG0112|consen  446 GLGQP----KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH-----GQPYAYIQYESPPAAQAATHDMRGAPL  516 (975)
T ss_pred             ccccc----ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc-----CCcceeeecccCccchhhHHHHhcCcC
Confidence            77654    233456799999999999999999999999998877644     456999999999999999999999988


Q ss_pred             cC--eeeeeccc
Q 006282          184 ND--KQVFVGHF  193 (652)
Q Consensus       184 ~g--~~~~v~~~  193 (652)
                      .+  +.+.|.+.
T Consensus       517 G~P~~r~rvdla  528 (975)
T KOG0112|consen  517 GGPPRRLRVDLA  528 (975)
T ss_pred             CCCCcccccccc
Confidence            65  44555444

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

Probab=98.47  E-value=4.2e-07  Score=88.10  Aligned_cols=81  Identities=30%  Similarity=0.440  Sum_probs=73.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      -.+.|+|.|||+.|++++|.|+|..||.+..+-|..|. .++|+|.|-|.|...+||++|++.+|+..++|++++|....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34789999999999999999999999988888887774 58999999999999999999999999999999999887655


Q ss_pred             CC
Q 006282          108 RD  109 (652)
Q Consensus       108 ~~  109 (652)
                      ..
T Consensus       161 ~~  162 (243)
T KOG0533|consen  161 SP  162 (243)
T ss_pred             Cc
Confidence            43

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.43  E-value=5.6e-07  Score=94.36  Aligned_cols=83  Identities=14%  Similarity=0.273  Sum_probs=71.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      +.....+|||+|||.++++++|+++|..||+|...+|..-...+++-+||||+|.+.++++.|+++ +...+.++.+.|.
T Consensus       284 ~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Ve  362 (419)
T KOG0116|consen  284 PRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVE  362 (419)
T ss_pred             eeecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEE
Confidence            344567799999999999999999999999999999988665566669999999999999999995 5788899999997


Q ss_pred             cccC
Q 006282          105 YSHR  108 (652)
Q Consensus       105 ~s~~  108 (652)
                      .-..
T Consensus       363 ek~~  366 (419)
T KOG0116|consen  363 EKRP  366 (419)
T ss_pred             eccc
Confidence            5443

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.38  E-value=1.3e-06  Score=93.51  Aligned_cols=83  Identities=31%  Similarity=0.503  Sum_probs=75.4

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC----CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  383 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~----~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~  383 (652)
                      ++..+||||+||+..++++.|...|..||.|.+++||.-.    .-+.+.||||.|-+..+|.+|++.|+|.++.+..+.
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            4567899999999999999999999999999999999643    455688999999999999999999999999999999


Q ss_pred             EEecccH
Q 006282          384 VAVAQRK  390 (652)
Q Consensus       384 v~~~~~~  390 (652)
                      +.|++..
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9998743

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.36  E-value=2e-06  Score=67.50  Aligned_cols=70  Identities=27%  Similarity=0.373  Sum_probs=49.5

Q ss_pred             cEEEEcCCCCCCCHHHH----HHHHhccC-CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           30 TSLYVGDLDFNVTDSQL----YDLFSQVG-QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L----~~~Fs~~G-~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      +.|||.|||.+.+-..|    +.++..|| +|.+|.       +   +.|+|.|.+.+.|++|.+.|++..+-|+.|.|.
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-------G---GTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------T---T-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-------C---CEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            57999999999887765    66777886 888872       1   579999999999999999999999999999999


Q ss_pred             cccCC
Q 006282          105 YSHRD  109 (652)
Q Consensus       105 ~s~~~  109 (652)
                      +....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            88544

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.31  E-value=7.1e-07  Score=86.92  Aligned_cols=82  Identities=22%  Similarity=0.346  Sum_probs=76.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....+++||+|+...+|.+++..+|+.||.|..|.|..|+.++.++|||||+|.+.+.++.|+. ||+..|.|+.|.+.|
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3457899999999999999999999999999999999999999999999999999999999999 999999999999986


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      -..
T Consensus       177 ~r~  179 (231)
T KOG4209|consen  177 KRT  179 (231)
T ss_pred             eee
Confidence            543

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.24  E-value=6.1e-06  Score=68.39  Aligned_cols=79  Identities=24%  Similarity=0.322  Sum_probs=68.2

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhc--CCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEec----CeeEEE
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV----SKPLYV  384 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~f--G~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~----g~~l~v  384 (652)
                      ++|.|+|||...|.++|.+++...  |....+.+..|- ++.+.|||||.|.+++.|.+..+.++|+.+.    .|...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            689999999999999999999654  677777777774 6678999999999999999999999999886    578888


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .+|+-.
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            888754

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.22  E-value=2.2e-06  Score=89.99  Aligned_cols=79  Identities=25%  Similarity=0.424  Sum_probs=68.1

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ....|||+|||.+++.++|+++|..||.|+...|.... .+++.+||||+|.+.+++..|+.+ +-..+++++|.|.-.+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            34559999999999999999999999999999987654 455569999999999999999984 4778899999998655


Q ss_pred             c
Q 006282          389 R  389 (652)
Q Consensus       389 ~  389 (652)
                      .
T Consensus       366 ~  366 (419)
T KOG0116|consen  366 P  366 (419)
T ss_pred             c
Confidence            3

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

Probab=98.09  E-value=1.8e-06  Score=90.62  Aligned_cols=70  Identities=27%  Similarity=0.439  Sum_probs=63.8

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  383 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~  383 (652)
                      ...+|+|-|||..|++++|+.+|+.||+|.+|+.-..    .+|.+||+|.|..+|+.|+++||+..+.|+.|.
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4457999999999999999999999999999776555    467899999999999999999999999999887

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.07  E-value=4.8e-06  Score=81.12  Aligned_cols=80  Identities=23%  Similarity=0.349  Sum_probs=73.5

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      .....+||+|++..++.+++..+|+.||.|..+.|..|. .|.++||+||.|.+.+.+.+|+. |+|..|.|+.+.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            445679999999999999999999999999999998886 56799999999999999999999 9999999999999977


Q ss_pred             cc
Q 006282          388 QR  389 (652)
Q Consensus       388 ~~  389 (652)
                      +-
T Consensus       178 r~  179 (231)
T KOG4209|consen  178 RT  179 (231)
T ss_pred             ee
Confidence            63

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.06  E-value=9.2e-07  Score=89.07  Aligned_cols=154  Identities=23%  Similarity=0.357  Sum_probs=119.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc-ccCCceeEeecccC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT-PLNNKSIRIMYSHR  108 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~-~i~G~~i~i~~s~~  108 (652)
                      ..||++||.+.++.++|..+|...-.-.+-.++.      -.|||||++.+..-|.+|++++++. .+.|+++.+..+-.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4699999999999999999997651111111111      1279999999999999999999875 68999999887654


Q ss_pred             CcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeee
Q 006282          109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV  188 (652)
Q Consensus       109 ~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~  188 (652)
                      ..    ..++.+-|+|+|....++-|..+...||++..|....-..  -.-..-|+|.+.+.++.|+.++++..+.+..+
T Consensus        76 kk----qrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~--etavvnvty~~~~~~~~ai~kl~g~Q~en~~~  149 (584)
T KOG2193|consen   76 KK----QRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDS--ETAVVNVTYSAQQQHRQAIHKLNGPQLENQHL  149 (584)
T ss_pred             HH----HHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccch--HHHHHHHHHHHHHHHHHHHHhhcchHhhhhhh
Confidence            32    2234599999999999999999999999999998854321  11223468899999999999999999988888


Q ss_pred             eeccccc
Q 006282          189 FVGHFLR  195 (652)
Q Consensus       189 ~v~~~~~  195 (652)
                      .+.+..+
T Consensus       150 k~~YiPd  156 (584)
T KOG2193|consen  150 KVGYIPD  156 (584)
T ss_pred             hcccCch
Confidence            8876643

>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=97.86  E-value=5e-05  Score=59.80  Aligned_cols=69  Identities=26%  Similarity=0.442  Sum_probs=47.7

Q ss_pred             eeeecCCCCCCCHHH----HHHHhhhcC-CeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          313 NLYIKNLGDSIDDEK----LKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       313 ~l~V~nlp~~~te~~----L~~~F~~fG-~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      -|||.|||.+.+...    |+.++..+| .|.+|.         .+.|+|.|.+.+.|.+|.+.|+|..+.|.+|.|++.
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~   74 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFS   74 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEc
Confidence            599999999988764    556666775 677662         468999999999999999999999999999999998


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ...
T Consensus        75 ~~~   77 (90)
T PF11608_consen   75 PKN   77 (90)
T ss_dssp             --S
T ss_pred             CCc
Confidence            543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.83  E-value=4.2e-05  Score=65.04  Aligned_cols=78  Identities=33%  Similarity=0.541  Sum_probs=49.1

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcC-----cEecCeeEEEE
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG-----KMIVSKPLYVA  385 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng-----~~~~g~~l~v~  385 (652)
                      |+.|+|.+++..++.++|++.|+.||.|..|.+....     ..|+|.|.+.+.|.+|+..+.-     ..+.+..+.+.
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-----~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-----TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-----CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            4679999999999999999999999999999887653     3799999999999999997743     46677778777


Q ss_pred             ecccHHHH
Q 006282          386 VAQRKEER  393 (652)
Q Consensus       386 ~~~~~~~r  393 (652)
                      +-.-.++.
T Consensus        76 vLeGeeE~   83 (105)
T PF08777_consen   76 VLEGEEEE   83 (105)
T ss_dssp             ---HHHHH
T ss_pred             ECCCHHHH
Confidence            76554443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.70  E-value=1e-05  Score=81.68  Aligned_cols=155  Identities=23%  Similarity=0.436  Sum_probs=121.3

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCC-eeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCc-cCCceEEEEcccc
Q 006282          209 NNVFVKNLDESTTDEDLKKIFGEYGT-ITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK-FDDREWYVGKAQK  286 (652)
Q Consensus       209 ~~l~V~nlp~~~t~~~l~~~F~~~G~-v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~-~~g~~l~v~~a~~  286 (652)
                      +.+|++||.+.++..++..+|...-. ...-++++      .||+||.+.+..-|.+|++.++++. +.|+.+.+...-.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            35899999999999999999987532 12222322      4699999999999999999998764 6788877766554


Q ss_pred             chHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEe-cCCCCCCccEEEEEeCCHHHH
Q 006282          287 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEA  365 (652)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~-~~~~g~s~g~afV~F~s~~~A  365 (652)
                      +..+.                    +.+-|+|+|.-.-++-|..+...||+++.|... .+..   .-..-|+|.+.+.+
T Consensus        76 kkqrs--------------------rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e---tavvnvty~~~~~~  132 (584)
T KOG2193|consen   76 KKQRS--------------------RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE---TAVVNVTYSAQQQH  132 (584)
T ss_pred             HHHHh--------------------hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH---HHHHHHHHHHHHHH
Confidence            44332                    237899999999999999999999999999754 3321   22345789999999


Q ss_pred             HHHHHHhcCcEecCeeEEEEecccHHH
Q 006282          366 SRALAEMNGKMIVSKPLYVAVAQRKEE  392 (652)
Q Consensus       366 ~~A~~~lng~~~~g~~l~v~~~~~~~~  392 (652)
                      ..|+..++|..+....+.|.+....+.
T Consensus       133 ~~ai~kl~g~Q~en~~~k~~YiPdeq~  159 (584)
T KOG2193|consen  133 RQAIHKLNGPQLENQHLKVGYIPDEQN  159 (584)
T ss_pred             HHHHHhhcchHhhhhhhhcccCchhhh
Confidence            999999999999999999988765543

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.69  E-value=2.6e-05  Score=78.21  Aligned_cols=172  Identities=17%  Similarity=0.189  Sum_probs=121.7

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCC----CCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD----GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       210 ~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~----g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      .|.|.||.+.++.+++..+|+..|.|.++.++...+    ......|||.|.+..++..|. .|....+-++.|.|.+..
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            688999999999999999999999999999886422    344668999999999998887 588888888888887765


Q ss_pred             cchHHHH-HHh---HHHH--------------------Hhhhhcc------------ccc--ccceeeecCCCCCCCHHH
Q 006282          286 KKSEREQ-ELK---GQFE--------------------QAMKETV------------DKF--QGLNLYIKNLGDSIDDEK  327 (652)
Q Consensus       286 ~~~~~~~-~~~---~~~~--------------------~~~~~~~------------~~~--~~~~l~V~nlp~~~te~~  327 (652)
                      ....... .+.   ....                    .......            .+.  -..+++|.+|...|...+
T Consensus        88 ~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e  167 (479)
T KOG4676|consen   88 DEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPE  167 (479)
T ss_pred             CCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchh
Confidence            4322111 110   0000                    0000000            000  124599999999999999


Q ss_pred             HHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          328 LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       328 L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      +.+.|..+|+|...++.-..   ..-+|-|.|........|+. ++|+.+.-....+.+
T Consensus       168 ~~e~f~r~Gev~ya~~ask~---~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai  222 (479)
T KOG4676|consen  168 SGESFERKGEVSYAHTASKS---RSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAI  222 (479)
T ss_pred             hhhhhhhcchhhhhhhhccC---CCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhh
Confidence            99999999999988776443   23467799998888888887 777766533333333

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.69  E-value=7.6e-05  Score=63.51  Aligned_cols=60  Identities=28%  Similarity=0.395  Sum_probs=40.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      ++.|+|.+++.+++.++|+++|+.||.|..|.+.++..      .|||.|.+.++|++|++.+...
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHT
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhc
Confidence            36799999999999999999999999999999877643      6999999999999999987543

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.67  E-value=0.0024  Score=63.44  Aligned_cols=78  Identities=22%  Similarity=0.232  Sum_probs=63.7

Q ss_pred             cceEEecCCCCCCCHHHHHHHhccCCC--eeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          208 FNNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       208 ~~~l~V~nlp~~~t~~~l~~~F~~~G~--v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      .-++||+||-|.+|++||.+.....|.  +.+++++.+ .+|.+|||++|...+..+.++-++-|-.+.+.|..-.|...
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            346999999999999999998877773  556666655 57999999999999999999999988888888876665444


Q ss_pred             c
Q 006282          285 Q  285 (652)
Q Consensus       285 ~  285 (652)
                      .
T Consensus       160 N  160 (498)
T KOG4849|consen  160 N  160 (498)
T ss_pred             c
Confidence            3

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.64  E-value=8.5e-05  Score=74.50  Aligned_cols=86  Identities=19%  Similarity=0.302  Sum_probs=77.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVL--------SVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL   96 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~--------~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i   96 (652)
                      ......+|||..|+..+++.+|.++|.+||.|.        -|.|.+|+.|++++|-|.|.|.+...|+.|+.-++...|
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            345578999999999999999999999999873        588999999999999999999999999999999999999


Q ss_pred             CCceeEeecccCCc
Q 006282           97 NNKSIRIMYSHRDP  110 (652)
Q Consensus        97 ~G~~i~i~~s~~~~  110 (652)
                      .|.+|+|..+...+
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999998776543

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.62  E-value=7.1e-05  Score=75.21  Aligned_cols=203  Identities=13%  Similarity=0.153  Sum_probs=120.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEee---CCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD---LSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d---~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .|.|.||.+++|.++++.||...|+|-+++|+..   ...-..+-.|||.|.+...+..|-. |.++.|-++.|.|...-
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEecC
Confidence            8999999999999999999999999999999763   2222345689999999999998887 66677777766553222


Q ss_pred             CCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCee
Q 006282          108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQ  187 (652)
Q Consensus       108 ~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~  187 (652)
                      ..                +  +....   .|..+++-..+--....+|       |-|.+.--  .-+..++...|.-  
T Consensus        88 ~~----------------~--~p~r~---af~~l~~~navprll~pdg-------~Lp~~~~l--t~~nh~p~ailkt--  135 (479)
T KOG4676|consen   88 DE----------------V--IPDRF---AFVELADQNAVPRLLPPDG-------VLPGDRPL--TKINHSPNAILKT--  135 (479)
T ss_pred             CC----------------C--CccHH---HHHhcCcccccccccCCCC-------ccCCCCcc--ccccCCccceecC--
Confidence            11                0  11111   2322222111110000111       00100000  0011111111111  


Q ss_pred             eeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHH
Q 006282          188 VFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE  267 (652)
Q Consensus       188 ~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~  267 (652)
                          +..+..--... ...-.++++|.+|...|...++.+.|..+|.|....+-.   +....+|.+.|....+...|+.
T Consensus       136 ----P~Lp~~~~A~k-leeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as---k~~s~~c~~sf~~qts~~halr  207 (479)
T KOG4676|consen  136 ----PELPPQAAAKK-LEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTAS---KSRSSSCSHSFRKQTSSKHALR  207 (479)
T ss_pred             ----CCCChHhhhhh-hHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc---cCCCcchhhhHhhhhhHHHHHH
Confidence                11111100000 111226799999999999999999999999887665433   3334578899999888888886


Q ss_pred             HHCCCccC
Q 006282          268 ALNGKKFD  275 (652)
Q Consensus       268 ~l~~~~~~  275 (652)
                       +++..+.
T Consensus       208 -~~gre~k  214 (479)
T KOG4676|consen  208 -SHGRERK  214 (479)
T ss_pred             -hcchhhh
Confidence             5666655

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=97.56  E-value=0.00049  Score=75.11  Aligned_cols=19  Identities=16%  Similarity=0.564  Sum_probs=11.0

Q ss_pred             CCCHHHHHHHHhccCCeEE
Q 006282           40 NVTDSQLYDLFSQVGQVLS   58 (652)
Q Consensus        40 ~vte~~L~~~Fs~~G~V~~   58 (652)
                      +++++++.++|...|.=.+
T Consensus        82 ~ls~~e~~~~F~~~~~dmn  100 (1102)
T KOG1924|consen   82 SLSSNEVLELFELMGEDMN  100 (1102)
T ss_pred             hccHHHHHHHHHHHhhhcc
Confidence            3566666666666654333

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.53  E-value=0.00015  Score=69.29  Aligned_cols=93  Identities=25%  Similarity=0.296  Sum_probs=82.3

Q ss_pred             HHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeE
Q 006282          261 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS  340 (652)
Q Consensus       261 ~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~  340 (652)
                      -|..|...|++....++.+.|.++.++                         .|||.||...++-+.|...|+.||.|..
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~a-------------------------~l~V~nl~~~~sndll~~~f~~fg~~e~   60 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMHA-------------------------ELYVVNLMQGASNDLLEQAFRRFGPIER   60 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeeccc-------------------------eEEEEecchhhhhHHHHHhhhhcCccch
Confidence            466777788999999999999998652                         4999999999999999999999999999


Q ss_pred             EEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          341 CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       341 v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      ..+..|..++..+-++|.|...-.|.+|+...+-.-|.
T Consensus        61 av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~   98 (275)
T KOG0115|consen   61 AVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFG   98 (275)
T ss_pred             heeeecccccccccchhhhhcchhHHHHHHHhccCccc
Confidence            99999999999999999999999999999977544443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.41  E-value=0.00025  Score=74.64  Aligned_cols=78  Identities=22%  Similarity=0.296  Sum_probs=65.0

Q ss_pred             ccceeeecCCCCCCC------HHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec-CeeE
Q 006282          310 QGLNLYIKNLGDSID------DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPL  382 (652)
Q Consensus       310 ~~~~l~V~nlp~~~t------e~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~-g~~l  382 (652)
                      -..+|+|.|+|---.      ..-|.++|+++|.|..+.+..++.|.++||.|++|.+..+|..|++.+||+.++ .+..
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            345799999985221      245678999999999999998998889999999999999999999999999998 4666


Q ss_pred             EEEec
Q 006282          383 YVAVA  387 (652)
Q Consensus       383 ~v~~~  387 (652)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            66643

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.36  E-value=0.00016  Score=72.62  Aligned_cols=83  Identities=23%  Similarity=0.415  Sum_probs=72.4

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeE--------EEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~--------v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      ....+|||.+|++.+++.+|.++|..+|.|..        +.|.+| +++.+||-|.|.|.+...|+.|+.-++++.|.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            34567999999999999999999999998865        334444 378999999999999999999999999999999


Q ss_pred             eeEEEEecccHH
Q 006282          380 KPLYVAVAQRKE  391 (652)
Q Consensus       380 ~~l~v~~~~~~~  391 (652)
                      ..|.|.++..+.
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999999888664

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.36  E-value=0.00037  Score=68.72  Aligned_cols=82  Identities=23%  Similarity=0.398  Sum_probs=64.4

Q ss_pred             CCccEEEEcCCCCCCCHHH----H--HHHHhccCCeEEEEEEeeCCCCCcc-cEE--EEEeCCHHHHHHHHhhcCCcccC
Q 006282           27 FLTTSLYVGDLDFNVTDSQ----L--YDLFSQVGQVLSVRVCRDLSTRRSL-GYG--YVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~----L--~~~Fs~~G~V~~i~v~~d~~t~~s~-g~A--fV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      -...-+||-+|++.+-.++    |  .++|.+||+|..|-|-+......|. +.+  ||.|.+.|||.+|+.+.++..++
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            3456789999999886555    3  7899999999988776653222222 224  99999999999999999999999


Q ss_pred             CceeEeecccC
Q 006282           98 NKSIRIMYSHR  108 (652)
Q Consensus        98 G~~i~i~~s~~  108 (652)
                      ||.|+..+...
T Consensus       192 Gr~lkatYGTT  202 (480)
T COG5175         192 GRVLKATYGTT  202 (480)
T ss_pred             CceEeeecCch
Confidence            99999987553

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.36  E-value=0.00043  Score=50.82  Aligned_cols=52  Identities=23%  Similarity=0.451  Sum_probs=42.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHH
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL   88 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al   88 (652)
                      +.|-|.+.+.+.. ++++++|+.||.|..+.+-.      ...++||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            5788999998855 45556899999999988752      2248999999999999996

>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]

Probab=97.29  E-value=9.9e-05  Score=83.05  Aligned_cols=67  Identities=25%  Similarity=0.353  Sum_probs=62.3

Q ss_pred             HHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHH--HHHHHHHHhhcCC
Q 006282          570 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAM--EVLRSVAQQQANN  636 (652)
Q Consensus       570 ~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~--~~l~~~~~~~~~~  636 (652)
                      -+|.|||+||+.++.+.|.+|.||||||||.....+|..|..++.|+..|++|+  +++..|.++..++
T Consensus      2607 e~Q~la~l~wgqhe~~l~a~~s~~sGfL~dek~~g~llgi~ce~p~eafVdaa~ndd~i~~H~qei~Ad 2675 (3015)
T KOG0943|consen 2607 ERQALAELLWGQHEAMLPAFASKISGFLLDEKPAGLLLGIACEDPLEAFVDAAMNDDLIIAHGQEIGAD 2675 (3015)
T ss_pred             hhccchhhcchhhhhHHHHHHHhhhhhhhccchHHHHHHHhhcCcHHHHHHHhcchHHHHHHHHHhhhH
Confidence            578999999999999999999999999999999999999999999999999999  8999988765443

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.24  E-value=0.00055  Score=65.50  Aligned_cols=89  Identities=22%  Similarity=0.343  Sum_probs=80.4

Q ss_pred             HHHHHHHhhcCCcccCCceeEeecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEE
Q 006282           82 ADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFG  161 (652)
Q Consensus        82 e~A~~Al~~ln~~~i~G~~i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~a  161 (652)
                      .-|+.|..+|++...+|+.++|.|+..         ..|+|.||..-++++.+..-|+.||.|....++.|..+...+-+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~---------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg   75 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH---------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREG   75 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc---------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccc
Confidence            346777778889999999999999875         36999999999999999999999999999999999899999999


Q ss_pred             EEEEcCHHHHHHHHHHhc
Q 006282          162 FVQFENKESAQNAIDKLN  179 (652)
Q Consensus       162 fV~F~t~e~A~~Ai~~ln  179 (652)
                      +|.|...-.|.+|...++
T Consensus        76 ~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   76 IVEFAKKPNARKAARRCR   93 (275)
T ss_pred             hhhhhcchhHHHHHHHhc
Confidence            999999999999998764

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.10  E-value=0.00045  Score=70.52  Aligned_cols=67  Identities=22%  Similarity=0.450  Sum_probs=57.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEee---CCCCC----------cccEEEEEeCCHHHHHHHHhhcC
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD---LSTRR----------SLGYGYVNYANPADAARALDVLN   92 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d---~~t~~----------s~g~AfV~F~~~e~A~~Al~~ln   92 (652)
                      .-++++|.+-|||.+-.-+.|.++|+.+|.|++||||..   ....+          ..-+|+|+|...+.|.+|.+.+|
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            347999999999999888999999999999999999987   22111          14589999999999999999775

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.00  E-value=0.0014  Score=48.15  Aligned_cols=52  Identities=21%  Similarity=0.365  Sum_probs=41.4

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL  369 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~  369 (652)
                      +.|-|.+.+.+.. +.+..+|..||+|+.+.+-.     .+.+.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            3577888876654 45666999999999988762     2458999999999999985

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=96.99  E-value=0.0035  Score=68.75  Aligned_cols=11  Identities=0%  Similarity=0.087  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHh
Q 006282          168 KESAQNAIDKL  178 (652)
Q Consensus       168 ~e~A~~Ai~~l  178 (652)
                      ..++.+|++.+
T Consensus       209 ~~eiIrClka~  219 (1102)
T KOG1924|consen  209 LQEIIRCLKAF  219 (1102)
T ss_pred             HHHHHHHHHHH
Confidence            34455555544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.96  E-value=0.0023  Score=63.25  Aligned_cols=82  Identities=26%  Similarity=0.461  Sum_probs=65.3

Q ss_pred             ccceeeecCCCCCCCHHH----H--HHHhhhcCCeeEEEEecCC-C-CCCcc-E-EEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          310 QGLNLYIKNLGDSIDDEK----L--KELFSEFGTITSCKVMRDP-S-GISKG-S-GFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~----L--~~~F~~fG~I~~v~i~~~~-~-g~s~g-~-afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      +..-+||-+|+..+-+|+    |  .++|.+||.|..+.|-+.. . +...+ + .+|+|.+.++|.++|.+.+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            344589999999887666    2  4899999999999887654 1 11122 2 3999999999999999999999999


Q ss_pred             eeEEEEecccHH
Q 006282          380 KPLYVAVAQRKE  391 (652)
Q Consensus       380 ~~l~v~~~~~~~  391 (652)
                      +.|+..+.-.|-
T Consensus       193 r~lkatYGTTKY  204 (480)
T COG5175         193 RVLKATYGTTKY  204 (480)
T ss_pred             ceEeeecCchHH
Confidence            999999887664

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.90  E-value=0.00049  Score=66.03  Aligned_cols=71  Identities=21%  Similarity=0.349  Sum_probs=59.6

Q ss_pred             HHHHHHhh-hcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHHHHH
Q 006282          326 EKLKELFS-EFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR  396 (652)
Q Consensus       326 ~~L~~~F~-~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r~~~  396 (652)
                      ++|...|+ +||+|++++|..+-.-.-+|-++|.|...++|.+|+..|||..+.|++|+..+..-.+-+.+.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~rea~  154 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFREAI  154 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchhhhh
Confidence            45666666 999999998876654456889999999999999999999999999999999998876655543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.88  E-value=0.00045  Score=66.29  Aligned_cols=63  Identities=25%  Similarity=0.422  Sum_probs=52.6

Q ss_pred             HHHHHHHh-ccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           44 SQLYDLFS-QVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        44 ~~L~~~Fs-~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ++|+.-|+ +||.|.++.||... .-.-.|-+||.|...++|++|++.||+..|.|++|...++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34444444 89999999888753 34667999999999999999999999999999999887765

>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=96.79  E-value=0.0048  Score=51.65  Aligned_cols=76  Identities=24%  Similarity=0.287  Sum_probs=52.3

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEE-EecC-------CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee-
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCK-VMRD-------PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP-  381 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~-i~~~-------~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~-  381 (652)
                      .+.|.|-+.|.. ....|.++|++||+|.+.. +.++       +.-....+.-|+|+++.+|.+|+. .||..+.|.- 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456889999988 5567889999999998875 1111       011235699999999999999998 8999998754 


Q ss_pred             EEEEecc
Q 006282          382 LYVAVAQ  388 (652)
Q Consensus       382 l~v~~~~  388 (652)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4465553

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.

>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=96.76  E-value=0.0045  Score=51.83  Aligned_cols=77  Identities=22%  Similarity=0.191  Sum_probs=52.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEE-eeC------CCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC-RDL------STRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~-~d~------~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ..+.|.|-+.|++ ....|.+.|++||.|++..-+ ++.      ......++..|.|.++.+|.+||. .|+..|.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            4578999999988 677788999999999887511 100      001122589999999999999999 6999998864


Q ss_pred             e-Eeecc
Q 006282          101 I-RIMYS  106 (652)
Q Consensus       101 i-~i~~s  106 (652)
                      + -|.++
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4 45555

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.75  E-value=0.0013  Score=62.99  Aligned_cols=73  Identities=23%  Similarity=0.347  Sum_probs=62.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCC--------CCcc----cEEEEEeCCHHHHHHHHhhcCCcc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLST--------RRSL----GYGYVNYANPADAARALDVLNFTP   95 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t--------~~s~----g~AfV~F~~~e~A~~Al~~ln~~~   95 (652)
                      .+-.||+++||+.+.-..|+++|+.||.|-.|-+.....+        +.+.    --++|+|.+...|.+..+.||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3468999999999999999999999999999888776555        2222    346799999999999999999999


Q ss_pred             cCCce
Q 006282           96 LNNKS  100 (652)
Q Consensus        96 i~G~~  100 (652)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99974

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

Probab=96.68  E-value=0.0057  Score=59.53  Aligned_cols=82  Identities=20%  Similarity=0.339  Sum_probs=62.9

Q ss_pred             eeeecCC--CCCCC---HHHHHHHhhhcCCeeEEEEecCCCC--CCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          313 NLYIKNL--GDSID---DEKLKELFSEFGTITSCKVMRDPSG--ISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       313 ~l~V~nl--p~~~t---e~~L~~~F~~fG~I~~v~i~~~~~g--~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      .|.++|.  +..++   ++++++.+++||.|..|.|+.++.-  ..----||+|...++|.+|+-.|||+.|+|+.+...
T Consensus       283 vlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~  362 (378)
T KOG1996|consen  283 VLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSAC  362 (378)
T ss_pred             HHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeehe
Confidence            3555555  23444   4588999999999999999876421  012247999999999999999999999999999988


Q ss_pred             ecccHHHHH
Q 006282          386 VAQRKEERR  394 (652)
Q Consensus       386 ~~~~~~~r~  394 (652)
                      |.+...-+.
T Consensus       363 Fyn~ekfs~  371 (378)
T KOG1996|consen  363 FYNLEKFSN  371 (378)
T ss_pred             eccHHhhhh
Confidence            887655443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.65  E-value=0.00075  Score=71.14  Aligned_cols=77  Identities=29%  Similarity=0.397  Sum_probs=62.4

Q ss_pred             CcceEEecCCCCCCC------HHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEE
Q 006282          207 KFNNVFVKNLDESTT------DEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  280 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t------~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~  280 (652)
                      ..+.|+|.|+|.--.      ..-|..+|+++|++....+..+..|..+||.|++|.+..+|..|++.+||+.+....-.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            446788999884221      23467789999999999999898888999999999999999999999999998765444


Q ss_pred             EEc
Q 006282          281 VGK  283 (652)
Q Consensus       281 v~~  283 (652)
                      ..+
T Consensus       137 ~v~  139 (698)
T KOG2314|consen  137 FVR  139 (698)
T ss_pred             Eee
Confidence            333

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.58  E-value=0.0081  Score=53.37  Aligned_cols=58  Identities=19%  Similarity=0.369  Sum_probs=47.1

Q ss_pred             HHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHH
Q 006282          327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEE  392 (652)
Q Consensus       327 ~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~  392 (652)
                      +|-+.|+.||+|.=+|+..+       .-+|+|.+-+.|.+|+. ++|..++|+.|.|++..+.-.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpdW~  109 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPDWL  109 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE------
T ss_pred             HHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCccHH
Confidence            77888999999998888765       58999999999999998 999999999999998876543

; PDB: 1UFW_A 2DNR_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.51  E-value=0.0017  Score=66.56  Aligned_cols=68  Identities=24%  Similarity=0.395  Sum_probs=57.7

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC---C---CCC--------CccEEEEEeCCHHHHHHHHHHhcC
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD---P---SGI--------SKGSGFVAFSTPEEASRALAEMNG  374 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~---~---~g~--------s~g~afV~F~s~~~A~~A~~~lng  374 (652)
                      .++++|.+-|||.+-.-+.|.++|+.+|.|.+|+|..-   +   .|.        .+-||||+|...+.|.+|.+.+|.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46789999999999999999999999999999999865   2   222        267899999999999999998765


Q ss_pred             cE
Q 006282          375 KM  376 (652)
Q Consensus       375 ~~  376 (652)
                      ..
T Consensus       309 e~  310 (484)
T KOG1855|consen  309 EQ  310 (484)
T ss_pred             hh
Confidence            43

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.34  E-value=0.008  Score=53.41  Aligned_cols=72  Identities=24%  Similarity=0.312  Sum_probs=52.7

Q ss_pred             CccEEEEcCCCCC-----CCH----HHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC
Q 006282           28 LTTSLYVGDLDFN-----VTD----SQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN   98 (652)
Q Consensus        28 ~~~sL~V~nLp~~-----vte----~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G   98 (652)
                      +-.||.|.=+.++     .-.    .+|.+.|+.||.|.-||+..+        .-+|.|.+-++|.+|++ +++..|.|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g   96 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNG   96 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETT
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECC
Confidence            4556766655511     222    257888999999998888765        46999999999999999 89999999


Q ss_pred             ceeEeecccC
Q 006282           99 KSIRIMYSHR  108 (652)
Q Consensus        99 ~~i~i~~s~~  108 (652)
                      +.|+|.....
T Consensus        97 ~~l~i~LKtp  106 (146)
T PF08952_consen   97 RTLKIRLKTP  106 (146)
T ss_dssp             EEEEEEE---
T ss_pred             EEEEEEeCCc
Confidence            9999986544

; PDB: 1UFW_A 2DNR_A.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.25  E-value=0.0026  Score=60.94  Aligned_cols=70  Identities=23%  Similarity=0.369  Sum_probs=59.3

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC---------CCCcc----EEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS---------GISKG----SGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~---------g~s~g----~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      -.||+.+||+.++...||++|+.||.|-.|.+-....         |..++    -|+|+|.+-..|......|||..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            3699999999999999999999999999998875531         22222    3689999999999999999999999


Q ss_pred             Cee
Q 006282          379 SKP  381 (652)
Q Consensus       379 g~~  381 (652)
                      |+.
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            864

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.93  E-value=0.034  Score=44.14  Aligned_cols=56  Identities=25%  Similarity=0.351  Sum_probs=41.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF   93 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~   93 (652)
                      .-..||+ +|..+...||+++|+.||.|. |.-+.|  |     -|||...+.+.|..|+..++.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d--T-----SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND--T-----SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT--T-----EEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC--C-----cEEEEeecHHHHHHHHHHhcc
Confidence            4566777 999999999999999999883 333333  2     699999999999999998864

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.86  E-value=0.036  Score=41.75  Aligned_cols=54  Identities=26%  Similarity=0.383  Sum_probs=45.2

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhc---CCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM  372 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~f---G~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l  372 (652)
                      ..|+|++++ +++-++|+.+|..|   .....|..+.|.      .|-|.|.+.+.|.+|+..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            369999995 58888999999999   246788888884      4899999999999999754

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.77  E-value=0.04  Score=48.17  Aligned_cols=75  Identities=17%  Similarity=0.244  Sum_probs=60.8

Q ss_pred             CCCccEEEEcCCCCCC-CHHHH---HHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           26 QFLTTSLYVGDLDFNV-TDSQL---YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~v-te~~L---~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ..+.++|.|+=|..++ ..+||   ...++.||+|.+|..|-.       -.|.|.|.+..+|-+|+..+.. ..-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            4568999999998876 34444   445688999999999853       2599999999999999998764 6678999


Q ss_pred             EeecccC
Q 006282          102 RIMYSHR  108 (652)
Q Consensus       102 ~i~~s~~  108 (652)
                      ++.|-++
T Consensus       155 qCsWqqr  161 (166)
T PF15023_consen  155 QCSWQQR  161 (166)
T ss_pred             Eeecccc
Confidence            9999875

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.61  E-value=0.034  Score=59.52  Aligned_cols=83  Identities=24%  Similarity=0.243  Sum_probs=67.6

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhh-cCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEe---cCeeEEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VSKPLYV  384 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~-fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~---~g~~l~v  384 (652)
                      ..+..|||.||---+|.-.|+.++.+ .|.|++. +|..    =+.-|||.|.+.++|...+.+|||..+   +.|.|.+
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHH-HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            34667999999999999999999994 5666766 4432    134699999999999999999999988   5799999


Q ss_pred             EecccHHHHHHH
Q 006282          385 AVAQRKEERRAR  396 (652)
Q Consensus       385 ~~~~~~~~r~~~  396 (652)
                      .|+...+....+
T Consensus       517 df~~~deld~hr  528 (718)
T KOG2416|consen  517 DFVRADELDKHR  528 (718)
T ss_pred             eecchhHHHHHh
Confidence            999887766443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.97  E-value=0.063  Score=47.01  Aligned_cols=74  Identities=19%  Similarity=0.230  Sum_probs=56.2

Q ss_pred             cccceeeecCCCCCC----CHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          309 FQGLNLYIKNLGDSI----DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~----te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      .+-.+|.|+-|..++    +-..+-..++.||.|.+|....      +..|.|.|.+..+|-+|+.++.. ..-|..+.+
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qC  156 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQC  156 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEEe
Confidence            344567777666555    2234555668899999998763      45799999999999999998887 667888888


Q ss_pred             Eeccc
Q 006282          385 AVAQR  389 (652)
Q Consensus       385 ~~~~~  389 (652)
                      +|-.+
T Consensus       157 sWqqr  161 (166)
T PF15023_consen  157 SWQQR  161 (166)
T ss_pred             ecccc
Confidence            88654

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

Probab=94.95  E-value=0.064  Score=52.46  Aligned_cols=81  Identities=15%  Similarity=0.123  Sum_probs=60.1

Q ss_pred             CccEEEEcCC--CCCCC---HHHHHHHHhccCCeEEEEEEeeCCCCCc-ccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           28 LTTSLYVGDL--DFNVT---DSQLYDLFSQVGQVLSVRVCRDLSTRRS-LGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        28 ~~~sL~V~nL--p~~vt---e~~L~~~Fs~~G~V~~i~v~~d~~t~~s-~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ++..|.++|+  +-.+.   |+++.+-+.+||+|..|.|+.+...-.. .--.||+|...++|.+|+-.||+..|.|+.+
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v  359 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVV  359 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceee
Confidence            3444666665  23343   4567888999999999998877432111 1237999999999999999999999999999


Q ss_pred             EeecccC
Q 006282          102 RIMYSHR  108 (652)
Q Consensus       102 ~i~~s~~  108 (652)
                      +..|-+-
T Consensus       360 ~A~Fyn~  366 (378)
T KOG1996|consen  360 SACFYNL  366 (378)
T ss_pred             eheeccH
Confidence            8877553

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=94.79  E-value=0.67  Score=45.88  Aligned_cols=182  Identities=13%  Similarity=0.171  Sum_probs=113.9

Q ss_pred             cceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCC--------CCCcceeEEEeeCCHHHHHHHHH----HHC--CCc
Q 006282          208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--------DGKSKCFGFVNFENADDAAKAVE----ALN--GKK  273 (652)
Q Consensus       208 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~--------~g~~~g~~fV~f~~~~~A~~Ai~----~l~--~~~  273 (652)
                      .+.|...|+..+++-..+-.-|-+||.|++|.++.+.        +.+......+.|-+.+.+.....    .|.  ...
T Consensus        15 TRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~~   94 (309)
T PF10567_consen   15 TRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKTK   94 (309)
T ss_pred             eHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHHh
Confidence            3568889999999999999999999999999998765        33455678999999988775433    222  233


Q ss_pred             cCCceEEEEccccchHH----HH--HHhH-H-HHHhhhhcccccccceeeecCCCCCCCHHHHHHHhh--------hcCC
Q 006282          274 FDDREWYVGKAQKKSER----EQ--ELKG-Q-FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFS--------EFGT  337 (652)
Q Consensus       274 ~~g~~l~v~~a~~~~~~----~~--~~~~-~-~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~--------~fG~  337 (652)
                      +....|.+.+..-+...    ..  .... . .....-+-......++|.|.--.+...++-+.+.+.        +| .
T Consensus        95 L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~~~~~~~dl~~~kL~fL~~~~n~RY-V  173 (309)
T PF10567_consen   95 LKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFKDPVDKDDLIEKKLPFLKNSNNKRY-V  173 (309)
T ss_pred             cCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEecCccchhHHHHHhhhhhccCCCceE-E
Confidence            55666666665421110    00  0000 0 011111223344556777765433334443333331        34 5


Q ss_pred             eeEEEEecCC---CCCCccEEEEEeCCHHHHHHHHHHhc--CcEec-CeeEEEEecccH
Q 006282          338 ITSCKVMRDP---SGISKGSGFVAFSTPEEASRALAEMN--GKMIV-SKPLYVAVAQRK  390 (652)
Q Consensus       338 I~~v~i~~~~---~g~s~g~afV~F~s~~~A~~A~~~ln--g~~~~-g~~l~v~~~~~~  390 (652)
                      +++|.++...   +.-++.||.++|-+..-|...++.+.  +...+ .+..+|.+....
T Consensus       174 lEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs~~~~~  232 (309)
T PF10567_consen  174 LESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVSVQPHA  232 (309)
T ss_pred             EEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEeccCcc
Confidence            7888888543   34568899999999999999888765  44443 677788876644

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.44  E-value=0.036  Score=52.04  Aligned_cols=71  Identities=15%  Similarity=0.198  Sum_probs=46.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhc-cCCe---EEEEEEeeCCC-C-CcccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQ-VGQV---LSVRVCRDLST-R-RSLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~-~G~V---~~i~v~~d~~t-~-~s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      .....|.||+||+++||+++.+.++. ++.-   ..+.-+.+... . ....-|||.|.+.+++....+.+++..|.
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            34579999999999999999997776 6655   33332222221 1 12356999999999999999999886653

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.

>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=94.15  E-value=0.082  Score=49.78  Aligned_cols=61  Identities=28%  Similarity=0.330  Sum_probs=46.9

Q ss_pred             CHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhc--CcEecCeeEEEEeccc
Q 006282          324 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN--GKMIVSKPLYVAVAQR  389 (652)
Q Consensus       324 te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~ln--g~~~~g~~l~v~~~~~  389 (652)
                      ..+.|+++|..|+.+....+++.     -+-..|.|.+.++|.+|...++  +..+.|+.++|.+++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999999999888764     4468999999999999999999  9999999999999853

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.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.04  E-value=0.2  Score=39.88  Aligned_cols=53  Identities=23%  Similarity=0.409  Sum_probs=40.7

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhc
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN  373 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~ln  373 (652)
                      ..||. .|.+|-..||.++|++||.|. |..+.|.      .|||.....+.|..|+..+.
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT------EEEEEECCCHHHHHHHHHHT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC------cEEEEeecHHHHHHHHHHhc
Confidence            45665 999999999999999999875 5555553      69999999999999998775

; 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.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=93.89  E-value=0.14  Score=48.24  Aligned_cols=62  Identities=24%  Similarity=0.342  Sum_probs=46.7

Q ss_pred             CHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC--CcccCCceeEeecccCC
Q 006282           42 TDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN--FTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        42 te~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln--~~~i~G~~i~i~~s~~~  109 (652)
                      ..+.|+++|+.++.+.++.+.+      |.+=..|.|.+.++|.+|...|+  +..|.|+.++|.+.+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~------sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK------SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET------TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcC------CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            4578999999999998887775      33458999999999999999999  89999999999998543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=93.80  E-value=0.32  Score=36.66  Aligned_cols=53  Identities=23%  Similarity=0.351  Sum_probs=42.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcc----CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQV----GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL   91 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~----G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l   91 (652)
                      ..|+|+++. +++.++|+.+|+.|    ++ ..|.=+-|.       .|=|.|.+.+.|.+||..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            479999996 68999999999998    53 355555553       3779999999999999864

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=93.68  E-value=0.046  Score=57.06  Aligned_cols=79  Identities=22%  Similarity=0.285  Sum_probs=65.2

Q ss_pred             CCCCccEEEEcCCCCCC-CHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           25 NQFLTTSLYVGDLDFNV-TDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~v-te~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      .....+.|-+.-.|... +-++|..+|.+||.|..|.|-..      .--|.|.|.+..+|-+|.. .....|+++.|++
T Consensus       368 ~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl  440 (526)
T KOG2135|consen  368 AVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKL  440 (526)
T ss_pred             hhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEE
Confidence            34456788888888776 78899999999999999988443      1258999999999977777 5788999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|.+..+
T Consensus       441 ~whnps~  447 (526)
T KOG2135|consen  441 FWHNPSP  447 (526)
T ss_pred             EEecCCc
Confidence            9998754

>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=93.51  E-value=0.93  Score=38.81  Aligned_cols=75  Identities=12%  Similarity=0.186  Sum_probs=53.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC---ceeEee
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVG-QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN---KSIRIM  104 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G-~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G---~~i~i~  104 (652)
                      +..+.+...|+-++-++|..+.+.+- .|..+||.||...  ++-.+.+.|.+.++|.......|+..|..   ..++|.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p--nrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvv   90 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP--NRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVV   90 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC--ceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEE
Confidence            33444444445556666766666653 7889999998654  45689999999999999999999887643   455554


Q ss_pred             c
Q 006282          105 Y  105 (652)
Q Consensus       105 ~  105 (652)
                      |
T Consensus        91 f   91 (110)
T PF07576_consen   91 F   91 (110)
T ss_pred             E
Confidence            4

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.29  E-value=0.049  Score=60.68  Aligned_cols=73  Identities=26%  Similarity=0.308  Sum_probs=62.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc--CCceeEeecccC
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL--NNKSIRIMYSHR  108 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i--~G~~i~i~~s~~  108 (652)
                      ..++.|.+-+.+-.-|..+|+.||.|.+++..||-.      .|.|.|.+.+.|..|++.+.+.++  .|-+.+|++++.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            445666677788888999999999999999988744      799999999999999999999875  688999999875


Q ss_pred             C
Q 006282          109 D  109 (652)
Q Consensus       109 ~  109 (652)
                      -
T Consensus       374 ~  374 (1007)
T KOG4574|consen  374 L  374 (1007)
T ss_pred             c
Confidence            3

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=92.98  E-value=0.08  Score=56.79  Aligned_cols=80  Identities=23%  Similarity=0.228  Sum_probs=63.0

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHh-ccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc---CCc
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFS-QVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL---NNK   99 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs-~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i---~G~   99 (652)
                      .....+..|||.||=.-.|+-.|++++. .+|.|.+.++  |++    +..|||.|.+.++|......|++..+   +++
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--DkI----KShCyV~yss~eEA~atr~AlhnV~WP~sNPK  512 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DKI----KSHCYVSYSSVEEAAATREALHNVQWPPSNPK  512 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HHh----hcceeEecccHHHHHHHHHHHhccccCCCCCc
Confidence            3566789999999999999999999998 5677777744  222    23799999999999999999998655   567


Q ss_pred             eeEeecccCC
Q 006282          100 SIRIMYSHRD  109 (652)
Q Consensus       100 ~i~i~~s~~~  109 (652)
                      .|.|.|...+
T Consensus       513 ~L~adf~~~d  522 (718)
T KOG2416|consen  513 HLIADFVRAD  522 (718)
T ss_pred             eeEeeecchh
Confidence            7777665543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=92.76  E-value=0.33  Score=47.94  Aligned_cols=65  Identities=22%  Similarity=0.217  Sum_probs=51.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ..=|-|-++|+. .-..|..+|++||.|+....-      +.-.+-+|.|.+..+|.+||. .|+..|+|..+
T Consensus       197 D~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~vm  261 (350)
T KOG4285|consen  197 DTWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVM  261 (350)
T ss_pred             cceEEEeccCcc-chhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccceE
Confidence            456778888876 567888999999999776433      222589999999999999999 58888888543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=92.50  E-value=0.054  Score=54.50  Aligned_cols=81  Identities=20%  Similarity=0.313  Sum_probs=62.6

Q ss_pred             CccEEEEcCCCCCCC-HHHH--HHHHhccCCeEEEEEEeeCCCC---CcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           28 LTTSLYVGDLDFNVT-DSQL--YDLFSQVGQVLSVRVCRDLSTR---RSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        28 ~~~sL~V~nLp~~vt-e~~L--~~~Fs~~G~V~~i~v~~d~~t~---~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ...-+||-+|+..+. |..|  .+.|.+||.|..|.+.++..+-   -...-+||.|...+||.+|++..++....|+.+
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            345678889988764 4445  4589999999999999876311   122448999999999999999999999999987


Q ss_pred             EeecccC
Q 006282          102 RIMYSHR  108 (652)
Q Consensus       102 ~i~~s~~  108 (652)
                      ++.+...
T Consensus       156 ka~~gtt  162 (327)
T KOG2068|consen  156 KASLGTT  162 (327)
T ss_pred             HHhhCCC
Confidence            7765443

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=92.35  E-value=3.1  Score=41.34  Aligned_cols=157  Identities=15%  Similarity=0.220  Sum_probs=102.0

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeC-------CCCCcccEEEEEeCCHHHHHHHH----hh
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDL-------STRRSLGYGYVNYANPADAARAL----DV   90 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~-------~t~~s~g~AfV~F~~~e~A~~Al----~~   90 (652)
                      .|.+...+++|...|+..+++--.+...|-.||+|.+|.++.+.       ...+......+-|-+.+.+....    +.
T Consensus         8 kGdD~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQr   87 (309)
T PF10567_consen    8 KGDDEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQR   87 (309)
T ss_pred             CCCccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHH
Confidence            56788999999999999999999999999999999999999876       11233356889999988764432    22


Q ss_pred             cC--CcccCCceeEeecccC---------C-c--------------ccccCCCcceeecCCCccccHHHHHh----hhcc
Q 006282           91 LN--FTPLNNKSIRIMYSHR---------D-P--------------SIRKSGTGNIFIKNLDKSIDHKALHD----TFSS  140 (652)
Q Consensus        91 ln--~~~i~G~~i~i~~s~~---------~-~--------------~~~~~~~~~lfV~nLp~~~t~~~L~~----~Fs~  140 (652)
                      |+  ...++...+++.|..-         + .              -..+..++.|.|.= ...++.+++.+    ++..
T Consensus        88 LsEfK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF-~~~~~~~dl~~~kL~fL~~  166 (309)
T PF10567_consen   88 LSEFKTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEF-KDPVDKDDLIEKKLPFLKN  166 (309)
T ss_pred             HHHHHHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEe-cCccchhHHHHHhhhhhcc
Confidence            22  1345666676655331         0 0              01122333344432 23343333332    2222


Q ss_pred             CC----CeeEEEEeeC---CCCCcccEEEEEEcCHHHHHHHHHHhc
Q 006282          141 FG----NILSCKIATD---GSGQSKGFGFVQFENKESAQNAIDKLN  179 (652)
Q Consensus       141 fG----~I~~~~v~~~---~~g~skG~afV~F~t~e~A~~Ai~~ln  179 (652)
                      -+    -+.++.++..   .....+.||.++|-+...|.+.+..+.
T Consensus       167 ~~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  167 SNNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             CCCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            23    2567777654   244567899999999999999988764

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.95  E-value=0.73  Score=48.21  Aligned_cols=77  Identities=19%  Similarity=0.274  Sum_probs=64.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC---ceeEee
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVG-QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN---KSIRIM  104 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G-~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G---~~i~i~  104 (652)
                      ++.|.|--+|..+|-.||..|+..+- .|.+|+++||....+  -...|.|.+.+||....+++|+..|..   -.+++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnr--ymvLIkFr~q~da~~Fy~efNGk~Fn~le~e~Chll  151 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNR--YMVLIKFRDQADADTFYEEFNGKQFNSLEPEVCHLL  151 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCce--EEEEEEeccchhHHHHHHHcCCCcCCCCCccceeEE
Confidence            88999999999999999999987654 799999999876544  479999999999999999999987744   455555


Q ss_pred             ccc
Q 006282          105 YSH  107 (652)
Q Consensus       105 ~s~  107 (652)
                      |..
T Consensus       152 ~V~  154 (493)
T KOG0804|consen  152 YVD  154 (493)
T ss_pred             EEE
Confidence            543

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=91.71  E-value=0.11  Score=54.40  Aligned_cols=73  Identities=21%  Similarity=0.232  Sum_probs=59.7

Q ss_pred             ceeeecCCCCCC-CHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSI-DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~-te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +.|-+.-.+... +-++|..+|..||+|..|.|-..     .--|.|+|.+..+|-+|.. .++..|+++.|+|.|.+..
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            345555555555 55799999999999999988654     3369999999999988887 8999999999999998864

>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=91.38  E-value=1.1  Score=38.42  Aligned_cols=65  Identities=20%  Similarity=0.192  Sum_probs=49.6

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcC-CeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG-~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      +.+-..|+.++.++|..+.+.+- .|..++|++|... .+=-+++.|.+.++|..-...+||+.++.
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            33444555666677777777764 5778899988542 46678999999999999999999999874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=91.17  E-value=0.11  Score=52.38  Aligned_cols=80  Identities=23%  Similarity=0.396  Sum_probs=61.5

Q ss_pred             ceeeecCCCCCCCHHHHH---HHhhhcCCeeEEEEecCCC--CC--CccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          312 LNLYIKNLGDSIDDEKLK---ELFSEFGTITSCKVMRDPS--GI--SKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~---~~F~~fG~I~~v~i~~~~~--g~--s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      .-+||-+|+..+.++.+.   +.|..||.|.+|.+..+..  ..  ...-++|+|...++|..||...+|...+|+.|..
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            447888888877655543   5788999999999888752  11  1223799999999999999999999999988777


Q ss_pred             EecccHH
Q 006282          385 AVAQRKE  391 (652)
Q Consensus       385 ~~~~~~~  391 (652)
                      .+...+-
T Consensus       158 ~~gttky  164 (327)
T KOG2068|consen  158 SLGTTKY  164 (327)
T ss_pred             hhCCCcc
Confidence            7666543

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=91.12  E-value=0.57  Score=37.01  Aligned_cols=60  Identities=23%  Similarity=0.318  Sum_probs=38.5

Q ss_pred             CCCCCHHHHHHHhhhcC-----CeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          320 GDSIDDEKLKELFSEFG-----TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       320 p~~~te~~L~~~F~~fG-----~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      -+.++..+|..++..-+     .|-.++|..+       |.||+-.. +.|..++..|++..+.|+++.|+.|
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            35678888999887764     4556777766       89999976 7899999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.59  E-value=0.89  Score=48.72  Aligned_cols=81  Identities=16%  Similarity=0.304  Sum_probs=58.3

Q ss_pred             HHHHhhcCCcccCCceeEeecccCCcccccCCCcceeecCCCccccHHHHHhhhcc--CCCeeEEEEeeCCCCCcccEEE
Q 006282           85 ARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSS--FGNILSCKIATDGSGQSKGFGF  162 (652)
Q Consensus        85 ~~Al~~ln~~~i~G~~i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~--fG~I~~~~v~~~~~g~skG~af  162 (652)
                      ..+|.+.-+..++.+-.+|...+        +...|.++.|+.++-.++++.+|+.  .-.+.+|.+..+.      -.|
T Consensus       151 ~Evlresp~VqvDekgekVrp~~--------kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWy  216 (684)
T KOG2591|consen  151 VEVLRESPNVQVDEKGEKVRPNH--------KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWY  216 (684)
T ss_pred             HHHHhcCCCceeccCccccccCc--------ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceE
Confidence            44444444445555544444332        2345788999999999999999987  4478899987642      259


Q ss_pred             EEEcCHHHHHHHHHHhc
Q 006282          163 VQFENKESAQNAIDKLN  179 (652)
Q Consensus       163 V~F~t~e~A~~Ai~~ln  179 (652)
                      |+|+++.||..|.+.|.
T Consensus       217 ITfesd~DAQqAykylr  233 (684)
T KOG2591|consen  217 ITFESDTDAQQAYKYLR  233 (684)
T ss_pred             EEeecchhHHHHHHHHH
Confidence            99999999999998763

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.56  E-value=0.6  Score=50.00  Aligned_cols=69  Identities=17%  Similarity=0.357  Sum_probs=54.3

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhh--cCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcC--cEecCeeEEEE
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSE--FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYVA  385 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~--fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng--~~~~g~~l~v~  385 (652)
                      .|.|.++-|+..+-.|+++.+|..  +-.+++|.+-.+.      -=||+|++..||+.|.+.|..  +.|-||+|..+
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            467889999999999999999975  5678888876653      269999999999999987743  35566665443

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=90.22  E-value=0.021  Score=62.03  Aligned_cols=120  Identities=21%  Similarity=0.209  Sum_probs=79.1

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ....++||+|+...+..+-++.+...+|.|.++....        |||+.|..+.....|+..++...++|..+.+..-.
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d~  109 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVDE  109 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhccchh
Confidence            3446799999999999999999999999998876543        99999999999999999999999988888776632


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhh
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFS  333 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~  333 (652)
                      ..-.......................+-++|+|++...++......|.
T Consensus       110 q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~  157 (668)
T KOG2253|consen  110 QTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQ  157 (668)
T ss_pred             hhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHh
Confidence            211111000000000011111111133477777777666655555554

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=89.81  E-value=1.4  Score=33.84  Aligned_cols=55  Identities=16%  Similarity=0.409  Sum_probs=44.3

Q ss_pred             CCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          322 SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       322 ~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      .++-++++..+..|+ -.  +|..|.+|     =||.|.+.++|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~--~I~~d~tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WD--RIRDDRTG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cc--eEEecCCE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            578899999999994 33  34455444     589999999999999999999998877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=89.51  E-value=0.66  Score=45.94  Aligned_cols=63  Identities=17%  Similarity=0.185  Sum_probs=50.1

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP  381 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~  381 (652)
                      .-|-|-+++..- ..-|..+|++||+|.+.....  +   -.|-.|.|.+.-+|.+||. .||++|+|..
T Consensus       198 ~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~~--n---gNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  198 TWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTPS--N---GNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             ceEEEeccCccc-hhHHHHHHHhhCeeeeeecCC--C---CceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            457777887653 456788999999999876542  2   3499999999999999998 8999998754

>KOG2893 consensus Zn finger protein [General function prediction only]

Probab=88.57  E-value=24  Score=33.92  Aligned_cols=49  Identities=14%  Similarity=0.172  Sum_probs=22.7

Q ss_pred             CCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHH
Q 006282          320 GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL  369 (652)
Q Consensus       320 p~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~  369 (652)
                      ..++++|.|.-.-.+. .--.|.|...+-=...|.++-|+.-..+...+|
T Consensus        17 nrefddekiliqhqka-khfkchichkkl~sgpglsihcmqvhketid~i   65 (341)
T KOG2893|consen   17 NREFDDEKILIQHQKA-KHFKCHICHKKLFSGPGLSIHCMQVHKETIDKI   65 (341)
T ss_pred             ccccchhhhhhhhhhh-ccceeeeehhhhccCCCceeehhhhhhhhhhcc
Confidence            3455566554333322 223455544431122556666666555544443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=87.35  E-value=0.41  Score=53.69  Aligned_cols=72  Identities=28%  Similarity=0.407  Sum_probs=62.8

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec--CeeEEEEecccH
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVAVAQRK  390 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~--g~~l~v~~~~~~  390 (652)
                      .++.|..-..+-.-|-.+|+.||.|.+.+..++     -..|.|.|.+.+.|..|+++++|+.+-  |-+.+|.+++.-
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            567778888899999999999999999998887     337999999999999999999999764  788888888754

>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=87.22  E-value=0.82  Score=42.91  Aligned_cols=70  Identities=16%  Similarity=0.241  Sum_probs=46.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhh-cCCee---EEEEecCC--C-CCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSE-FGTIT---SCKVMRDP--S-GISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~-fG~I~---~v~i~~~~--~-g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      .++.|.|++||+.+|++++.+.+++ ++.-.   .+.-....  . -..-.-|+|.|.+.++.......++|..|.+
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            3558999999999999999998887 66662   33211111  1 1123469999999999999999999988753

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.

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.12  E-value=3.4  Score=44.77  Aligned_cols=122  Identities=15%  Similarity=0.248  Sum_probs=77.1

Q ss_pred             CCCccEEEEcCCCCC-CCHHHHHHHHhcc----CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           26 QFLTTSLYVGDLDFN-VTDSQLYDLFSQV----GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~-vte~~L~~~Fs~~----G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ...+.+|-|=||.|+ +.-.+|+-+|+.|    |.|.+|.||..-.                    -.+.|....+.|.+
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeF--------------------GkeRM~eEeV~GP~  230 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEF--------------------GKERMKEEEVHGPP  230 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhh--------------------hHHHhhhhcccCCh
Confidence            567899999999998 7999999999977    6999999987521                    23445556677876


Q ss_pred             eEeecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcC
Q 006282          101 IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNG  180 (652)
Q Consensus       101 i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng  180 (652)
                      +.+.-.........          .+....+.-.+..++.|+ +...+         --||.|+|.+.+.|....+.+.|
T Consensus       231 ~el~~~~e~~~~s~----------sD~ee~~~~~~~kLR~Yq-~~rLk---------YYyAVvecDsi~tA~~vYe~CDG  290 (650)
T KOG2318|consen  231 KELFKPVEEYKESE----------SDDEEEEDVDREKLRQYQ-LNRLK---------YYYAVVECDSIETAKAVYEECDG  290 (650)
T ss_pred             hhhccccccCcccc----------cchhhhhhHHHHHHHHHH-hhhhe---------eEEEEEEecCchHHHHHHHhcCc
Confidence            65542221110000          011111111223333332 11111         12799999999999999999999


Q ss_pred             ceecCee
Q 006282          181 MLINDKQ  187 (652)
Q Consensus       181 ~~l~g~~  187 (652)
                      ..+....
T Consensus       291 ~EfEsS~  297 (650)
T KOG2318|consen  291 IEFESSA  297 (650)
T ss_pred             ceecccc
Confidence            8876543

>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=85.91  E-value=2.4  Score=33.44  Aligned_cols=58  Identities=14%  Similarity=0.276  Sum_probs=36.4

Q ss_pred             CCCCHHHHHHHHhccC-----CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           39 FNVTDSQLYDLFSQVG-----QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        39 ~~vte~~L~~~Fs~~G-----~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++..+|..++...+     .|-.|+|..+        |+||+-... .|+++++.|++..++|+.++|..
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~   73 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVER   73 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEE
Confidence            3578888888887653     5778888764        889988654 78899999999999999999874

; PDB: 2G0C_A 3MOJ_B.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=85.88  E-value=1.9  Score=35.11  Aligned_cols=79  Identities=18%  Similarity=0.243  Sum_probs=49.1

Q ss_pred             EEEEEcCHHHHHHHHHHhc-CceecCeeeeec--ccccch-hhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCee
Q 006282          161 GFVQFENKESAQNAIDKLN-GMLINDKQVFVG--HFLRKQ-ERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT  236 (652)
Q Consensus       161 afV~F~t~e~A~~Ai~~ln-g~~l~g~~~~v~--~~~~~~-~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~  236 (652)
                      |+|+|..++.|.+.++.-. ...+++..+.|.  +..... .+-........++|.|+|||...++++|++..       
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L-------   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL-------   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE-------
Confidence            6899999999999986532 233455554443  222211 11111123566789999999999999998764       


Q ss_pred             EEEEeeCCCC
Q 006282          237 SAVVMRDGDG  246 (652)
Q Consensus       237 ~~~i~~~~~g  246 (652)
                      .+.+.+..+|
T Consensus        74 eIhFqK~snG   83 (88)
T PF07292_consen   74 EIHFQKPSNG   83 (88)
T ss_pred             EEEEecCCCC
Confidence            4455555443

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=84.34  E-value=3.6  Score=31.59  Aligned_cols=55  Identities=15%  Similarity=0.363  Sum_probs=42.6

Q ss_pred             cccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeee
Q 006282          128 SIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV  190 (652)
Q Consensus       128 ~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v  190 (652)
                      .++-++++..++.|+-.   +|..|.+|    | ||.|.+..+|+++....++..+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~tG----f-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDRTG----F-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecCCE----E-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            35788999999998533   44455444    4 99999999999999999998887766544

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=81.79  E-value=4.4  Score=42.68  Aligned_cols=68  Identities=19%  Similarity=0.297  Sum_probs=58.2

Q ss_pred             CcceeecCCCccccHHHHHhhhccCC-CeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecC
Q 006282          117 TGNIFIKNLDKSIDHKALHDTFSSFG-NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIND  185 (652)
Q Consensus       117 ~~~lfV~nLp~~~t~~~L~~~Fs~fG-~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g  185 (652)
                      ...|+|-.+|..++..||..++..+- .|..+++++|..+ ++-..++.|.+.++|....+.+||..++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            67799999999999999999988765 6899999996443 44467899999999999999999988753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	652
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-64
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-22
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-18
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		7e-64
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-22
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-19
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		3e-32
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-13
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		8e-31
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-14
2dyd_A	85	Solution Structure Of The Pabc Domain From Triticum		8e-29
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		7e-27
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-23
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-16
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-16
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		9e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		7e-23
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		7e-17
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		8e-23
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-15
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-23
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-15
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-19
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-16
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-14
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		9e-19
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		9e-16
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		6e-14
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		1e-16
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		7e-16
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		7e-10
1nmr_A	85	Solution Structure Of C-Terminal Domain From Trypan		2e-15
1g9l_A	144	Solution Structure Of The Pabc Domain Of Human Poly		2e-15
1jgn_A	98	Solution Structure Of The C-Terminal Pabc Domain Of		2e-15
3kur_A	79	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		3e-15
3kus_A	88	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		3e-15
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-15
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-11
3pth_A	82	The Pabc1 Mlle Domain Bound To The Variant Pam2 Mot		4e-15
2rqg_B	83	Structure Of Gspt1ERF3A-Pabc Length = 83		4e-15
2x04_A	80	Crystal Structure Of The Pabc-Tnrc6c Complex Length		8e-15
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		1e-13
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		6e-10
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		5e-13
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-05
4ive_A	98	Crystal Structure Of A Polyadenylate-binding Protei		3e-12
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-11
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		3e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-11
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-09
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		3e-11
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-09
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		3e-09
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-11
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-11
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		5e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-11
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-09
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-11
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-07
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		7e-11
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		8e-11
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		1e-08
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-10
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-10
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-10
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		8e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-10
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		3e-08
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-10
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		5e-10
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		6e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		7e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-05
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		8e-09
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		8e-09
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		3e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		9e-09
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-06
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-08
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-08
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		6e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-06
2khc_A	118	Bruno Rrm3+ Length = 118		6e-08
2khc_A	118	Bruno Rrm3+ Length = 118		4e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-07
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		8e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		9e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		8e-07
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		1e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-07
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		2e-07
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		3e-07
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		3e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-07
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		3e-07
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		5e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		1e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		1e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		9e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-06
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		1e-06
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		7e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		3e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-06
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		3e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		3e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		3e-06
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		1e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		3e-06
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		1e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		4e-06
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		1e-05
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		4e-06
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		2e-05
2ghp_A	292	Crystal Structure Of The N-Terminal 3 Rna Binding D		4e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		4e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		1e-05
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		4e-06
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		5e-06
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		5e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		5e-06
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		5e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		6e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		1e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		6e-06
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		8e-06
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		1e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		8e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		8e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		5e-05
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		8e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		9e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		6e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		1e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		8e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		1e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		5e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		4e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-05
3ntw_A	65	Structure Of The Mlle Domain Of Edd In Complex With		2e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		3e-05
1i2t_A	61	X-Ray Structure Of The Human Hyperplastic Discs Pro		3e-05
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		3e-05
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		3e-04
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		4e-05
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		4e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-05
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		4e-05
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		6e-05
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		4e-05
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		1e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-05
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		5e-05
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		7e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		7e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		8e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		8e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		9e-05
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		9e-05
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		7e-04
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-04
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		2e-04
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-04
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		2e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		1e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		1e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		1e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		2e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		2e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-04
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		2e-04
2f9d_A	125	2.5 Angstrom Resolution Structure Of The Spliceosom		3e-04
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		4e-04
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		4e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		4e-04
2dk2_A	97	Solution Structure Of Rrm Domain In Heterogeneous N		4e-04
2fho_B	87	Nmr Solution Structure Of The Human Spliceosomal Pr		5e-04
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		6e-04
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		6e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		6e-04
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		7e-04
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		7e-04
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		9e-04
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		9e-04

>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 =  241 bits (616), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 112/179 (62%), Positives = 142/179 (79%), Gaps = 1/179 (0%)
Query: 23  SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
           S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PA
Sbjct: 4   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63
Query: 83  DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
           DA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123
Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
           NILSCK+  D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F  ++ERE 
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 181

>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 =  102 bits (254), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 60/187 (32%), Positives = 104/187 (55%), Gaps = 6/187 (3%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 167
           +PS       ++++ +L   +    L++ FS  G ILS ++  D  + +S G+ +V F+ 
Sbjct: 2   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 227
              A+ A+D +N  +I  K V +       +R+    K+   N+F+KNLD+S  ++ L  
Sbjct: 62  PADAERALDTMNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 117
Query: 228 IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 287
            F  +G I S  V+ D +G SK +GFV+FE  + A +A+E +NG   +DR+ +VG+ + +
Sbjct: 118 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176
Query: 288 SEREQEL 294
            ERE EL
Sbjct: 177 KEREAEL 183

>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 = 90.5 bits (223), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 62/192 (32%), Positives = 99/192 (51%), Gaps = 18/192 (9%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           +N      +   +  +Q+     +   G                N++IKNL  SID++ L
Sbjct: 72  MNFDVIKGKPVRIMWSQRDPSLRKSGVG----------------NIFIKNLDKSIDNKAL 115
Query: 329 KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
            + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++  + ++V   +
Sbjct: 116 YDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 174
Query: 389 RKEERRARLQAQ 400
            ++ER A L A+
Sbjct: 175 SRKEREAELGAR 186

>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 =  241 bits (616), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 115/188 (61%), Positives = 146/188 (77%), Gaps = 2/188 (1%)
Query: 14  GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
           GP G +   S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY
Sbjct: 1   GPLG-SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59
Query: 74  GYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKA 133
            YVN+  PADA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KA
Sbjct: 60  AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKA 119
Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHF 193
           L+DTFS+FGNILSCK+  D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178
Query: 194 LRKQERET 201
             ++ERE 
Sbjct: 179 KSRKEREA 186

>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 =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 110/204 (53%), Gaps = 6/204 (2%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 167
           +PS       ++++ +L   +    L++ FS  G ILS ++  D  + +S G+ +V F+ 
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 227
              A+ A+D +N  +I  K V +       +R+    K+   N+F+KNLD+S  ++ L  
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 228 IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 287
            F  +G I S  V+ D +G SK +GFV+FE  + A +A+E +NG   +DR+ +VG+ + +
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Query: 288 SEREQELKGQFEQAMKETVDKFQG 311
            ERE EL  + ++     V  + G
Sbjct: 182 KEREAELGARAKEFYPYDVPDYAG 205

>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 = 92.8 bits (229), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/200 (35%), Positives = 108/200 (54%), Gaps = 22/200 (11%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 269 LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
           +N   FD  +   GK  +   S+R+  L+       K  V      N++IKNL  SID++
Sbjct: 77  MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 118
Query: 327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 386
            L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++  + ++V  
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 387 AQRKEERRARLQAQFSQMRP 406
            + ++ER A L A+  +  P
Sbjct: 178 FKSRKEREAELGARAKEFYP 197

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score =  136 bits (343), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 64/92 (69%), Positives = 81/92 (88%), Gaps = 1/92 (1%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENK 168
           DPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+  D +G SKG+GFV FE +
Sbjct: 3   DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 169 ESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           E+A+ AI+K+NGML+ND++VFVG F  ++ERE
Sbjct: 62  EAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 93

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/83 (46%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 13  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
           NG ++  + ++V   + ++ER A
Sbjct: 72  NGMLLNDRKVFVGRFKSRKEREA 94

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score =  132 bits (331), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 65/108 (60%), Positives = 86/108 (79%), Gaps = 3/108 (2%)
Query: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           G+GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+  D +G SKG+GFV FE +E+A+ AI
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 176 DKLNGMLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTT 221
           +K+NGML+ND++VFVG F  ++ERE    A   +F NV++KN    +T
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 77.8 bits (190), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 42/95 (44%), Positives = 61/95 (64%), Gaps = 1/95 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPV 407
           NG ++  + ++V   + ++ER A L A+  +   V
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNV 100

>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum Aevestium Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score =  125 bits (314), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 63/79 (79%), Positives = 70/79 (88%)
Query: 554 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 613
           PI AL++ALAN+ PE QR +LGE+LYPLV+QLE D AAKVTGMLLEMDQTEVLHLLESP+
Sbjct: 6   PIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPD 65
Query: 614 ALKAKVAEAMEVLRSVAQQ 632
           ALKAKVAEAMEVLRS  Q 
Sbjct: 66  ALKAKVAEAMEVLRSAQQH 84

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score =  119 bits (297), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 55/90 (61%), Positives = 75/90 (83%), Gaps = 1/90 (1%)
Query: 306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 365
           + ++Q +NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS+PEEA
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEA 68
Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEERRA 395
           ++A+ EMNG+++ +KPLYVA+AQRKEER++
Sbjct: 69  TKAVTEMNGRIVATKPLYVALAQRKEERQS 98

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/152 (36%), Positives = 90/152 (59%), Gaps = 3/152 (1%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +   LF  +G++ S ++ RD  T +SLGYG+VNY +P DA +A++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            LN   L  K+I++ Y+   PS       N+++  L K++  K L   FS +G I++ +I
Sbjct: 63  TLNGLRLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNG 180
             D  +G S+G GF++F+ +  A+ AI  LNG
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 84.0 bits (206), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/157 (31%), Positives = 90/157 (57%), Gaps = 8/157 (5%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++  +     F S G I SCK+  D  +GQS G+GFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG-TIT 236
           LNG+ +  K + V +      R + A   +  N++V  L ++ T ++L+++F +YG  IT
Sbjct: 64  LNGLRLQTKTIKVSY-----ARPSSA-SIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 237 SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 273
           S +++    G S+  GF+ F+   +A +A++ LNG+K
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 83.6 bits (205), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 50/169 (29%), Positives = 87/169 (51%), Gaps = 20/169 (11%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 267
            N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEK 327
            LNG +   +   V  A+  S                     +  NLY+  L  ++  ++
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMTQKE 104
Query: 328 LKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK 375
           L++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  +NG+
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 55/152 (36%), Positives = 90/152 (59%), Gaps = 3/152 (1%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +   LF  +G + S ++ RD  T +SLGYG+VNY++P DA +A++
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            LN   L  K+I++ Y+   PS       N+++  L K++  K +   FS +G I++ +I
Sbjct: 65  TLNGLKLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
             D  +G S+G GF++F+ +  A+ AI  LNG
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 54/178 (30%), Positives = 92/178 (51%), Gaps = 24/178 (13%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T ++ K +FG  G I S  ++RD   G+S  +GFVN+ + +DA KA+  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG K   +   V  A+  S                     +  NLY+  L  ++  +++
Sbjct: 66  LNGLKLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMSQKEM 107
Query: 329 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 385
           ++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  +NG+    KPL  A
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPLGAA 161

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  ++ K LF   G I SCK++RD  +G S G GFV +S P +A +A+  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 66  LNGLKLQTKTIKVSYAR 82

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score =  105 bits (262), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 56/152 (36%), Positives = 88/152 (57%), Gaps = 3/152 (1%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +L  LFS +G+V S ++ RD     SLGYG+VNY    DA RA++
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            LN   L +K+I++ Y+   PS       N++I  L +++  K + D FS FG I++ ++
Sbjct: 63  TLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
             D  +G S+G  F++F+ +  A+ AI   NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T ++L+ +F   G + SA ++RD   G S  +GFVN+  A DA +A+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG +   +   V  A+  SE            +K+        NLYI  L  ++  + +
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 329 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 374
           +++FS FG I + +V+ D  +G+S+G  F+ F    EA  A+   NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV + T ++A RA+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 372 MNGKMIVSKPLYVAVAQRKEE 392
           +NG  + SK + V+ A+   E
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE 84

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score =  105 bits (262), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 56/152 (36%), Positives = 88/152 (57%), Gaps = 3/152 (1%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +L  LFS +G+V S ++ RD     SLGYG+VNY    DA RA++
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            LN   L +K+I++ Y+   PS       N++I  L +++  K + D FS FG I++ ++
Sbjct: 63  TLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
             D  +G S+G  F++F+ +  A+ AI   NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T ++L+ +F   G + SA ++RD   G S  +GFVN+  A DA +A+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG +   +   V  A+  SE            +K+        NLYI  L  ++  + +
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 329 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 374
           +++FS FG I + +V+ D  +G+S+G  F+ F    EA  A+   NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV + T ++A RA+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 372 MNGKMIVSKPLYVAVAQRKEE 392
           +NG  + SK + V+ A+   E
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE 84

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 92.0 bits (227), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/154 (32%), Positives = 85/154 (55%), Gaps = 3/154 (1%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  ++TD +LY LF  +G + + R+ RD  T  S GY +V++ +  D+ RA+ 
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
           VLN   + NK +++ Y+   P        N+++ NL ++I    L   F  +G+I+   I
Sbjct: 64  VLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNGML 182
             D  +G+ +G  FV++  +E AQ AI  LN ++
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 83.6 bits (205), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 48/154 (31%), Positives = 83/154 (53%), Gaps = 8/154 (5%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L + +  + L+  F + G I +C+I  D  +G S G+ FV F ++  +Q AI  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 237
           LNG+ + +K++ V +     E        K  N++V NL  + TD+ L  IFG+YG+I  
Sbjct: 65  LNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 238 AVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
             ++RD   G+ +   FV +   ++A +A+ ALN
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 78.2 bits (191), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/182 (29%), Positives = 93/182 (51%), Gaps = 22/182 (12%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG    ++   V  A+   E           ++K+T       NLY+ NL  +I D++L
Sbjct: 65  LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 106
Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 385
             +F ++G+I    ++RD  +G  +G  FV ++  EEA  A++ +N  +    S+PL V 
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166
Query: 386 VA 387
           +A
Sbjct: 167 LA 168

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F++  ++ RA+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K L V+ A+
Sbjct: 65  LNGITVRNKRLKVSYAR 81

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 92.0 bits (227), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/154 (32%), Positives = 84/154 (54%), Gaps = 3/154 (1%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  + TD +LY LF  +G + + R+ RD  T  S GY +V++ +  D+ RA+ 
Sbjct: 15  TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
           VLN   + NK +++ Y+   P        N+++ NL ++I    L   F  +G+I+   I
Sbjct: 75  VLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNGML 182
             D  +G+ +G  FV++  +E AQ AI  LN ++
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 82.0 bits (201), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 53/164 (32%), Positives = 87/164 (53%), Gaps = 11/164 (6%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 167
           DP  R S T N+ +  L +    + L+  F + G I +C+I  D  +G S G+ FV F +
Sbjct: 9   DP--RASNT-NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTS 65
Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 227
           +  +Q AI  LNG+ + +K++ V +     E        K  N++V NL  + TD+ L  
Sbjct: 66  EXDSQRAIKVLNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDT 119
Query: 228 IFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
           IFG+YG+I    ++RD   G+ +   FV +   ++A +A+ ALN
Sbjct: 120 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 76.3 bits (186), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L +  TD +L  +F   G I +  + RD   G S  + FV+F +  D+ +A++ 
Sbjct: 16  NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG    ++   V  A+   E           ++K+T       NLY+ NL  +I D++L
Sbjct: 76  LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 117
Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 385
             +F ++G+I    ++RD  +G  +G  FV ++  EEA  A++ +N  +    S+PL V 
Sbjct: 118 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 177
Query: 386 VAQ 388
           +A+
Sbjct: 178 LAE 180

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 85.1 bits (209), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 96/180 (53%), Gaps = 17/180 (9%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NLD++ T++ LK+ F   G I +  +M D + K+  + FV +  + DA  A++ LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 271 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 330
           GK+ ++    +  A             F+     + D F   NL++ +L  ++DDE L+ 
Sbjct: 63  GKQIENNIVKINWA-------------FQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 331 LFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 389
            F +F +  S  VM D  +G S+G GFV+F++ ++A  A+  M G+ +  +PL +  A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 = 82.4 bits (202), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 92/172 (53%), Gaps = 7/172 (4%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++ ++   +    +   F+ FG I S  ++ D  + + KGF FV++E  E+AQ A++++
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKTK-----FNNVFVKNLDESTTDEDLKKIFGEYG 233
           N +++  + + VG      + + +  +       FN ++V ++ +  +D+D+K +F  +G
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 234 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
            I SA + RD   GK K +GF+ +E A  +  AV ++N      +   VGKA
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

>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 = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 255
           Q +  +AI ++   V+V ++     ++ +++ F  +G I S  +  D    K K F FV 
Sbjct: 20  QRQGALAIMSR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 314
           +E  + A  A+E +N      R   VG+            GQ +  + +  ++ +  N +
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 128
Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
           Y+ ++   + D+ +K +F  FG I S  + RDP +G  KG GF+ +   + +  A++ MN
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188

>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma Cruzi Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 42/69 (60%), Positives = 52/69 (75%)
Query: 558 LSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKA 617
           LST LAN +PEQQ+ +LGE LY  +  +   AAAKVTGMLLEMD  E+L+LL++P  L A
Sbjct: 11  LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDA 70
Query: 618 KVAEAMEVL 626
           KV EA+EVL
Sbjct: 71  KVQEALEVL 79

>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A) Binding Protein Length = 144

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 554 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 613
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 52  PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 109
Query: 614 ALKAKVAEAMEVLRS 628
           +L++KV EA+ VL++
Sbjct: 110 SLRSKVDEAVAVLQA 124

>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human Poly(A)-Binding Protein In Complex With The Peptide From Paip2 Length = 98

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 554 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 613
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 614 ALKAKVAEAMEVLRS 628
           +L++KV EA+ VL++
Sbjct: 64  SLRSKVDEAVAVLQA 78

>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein Length = 79

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 554 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 613
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 614 ALKAKVAEAMEVLRS 628
           +L++KV EA+ VL++
Sbjct: 64  SLRSKVDEAVAVLQA 78

>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein In Complex With The Binding Region Of Paip2 Length = 88

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 554 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 613
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 614 ALKAKVAEAMEVLRS 628
           +L++KV EA+ VL++
Sbjct: 64  SLRSKVDEAVAVLQA 78

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 45/172 (26%), Positives = 91/172 (52%), Gaps = 7/172 (4%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++ ++   +    +   F+ FG I S  ++ D  + + KGF FV++E  E+AQ A++++
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYG 233
           N +++  + + VG      + + +  +       FN ++V ++ +  +D+D+K +F  +G
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 234 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
            I S  + RD   GK K +GF+ +E A  +  AV ++N      +   VGKA
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 255
           Q +  +AI  +   V+V ++     ++ +++ F  +G I S  +  D    K K F FV 
Sbjct: 5   QRQRALAIMCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 61
Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 314
           +E  + A  A+E +N      R   VG+            GQ +  + +  ++ +  N +
Sbjct: 62  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 113
Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
           Y+ ++   + D+ +K +F  FG I SC + RDP +G  KG GF+ +   + +  A++ MN
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173

>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of Larp4b Length = 82

Iteration: 1
 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 554 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 613
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 5   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 62
Query: 614 ALKAKVAEAMEVLRS 628
           +L++KV EA+ VL++
Sbjct: 63  SLRSKVDEAVAVLQA 77

>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc Length = 83

Iteration: 1
 Score = 79.7 bits (195), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 554 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 613
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 4   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 61
Query: 614 ALKAKVAEAMEVLRS 628
           +L++KV EA+ VL++
Sbjct: 62  SLRSKVDEAVAVLQA 76

>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex Length = 80

Iteration: 1
 Score = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/76 (48%), Positives = 61/76 (80%), Gaps = 1/76 (1%)
Query: 554 PITALSTA-LANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESP 612
           P+ +L+ + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESP
Sbjct: 2   PLGSLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 61
Query: 613 EALKAKVAEAMEVLRS 628
           E+L++KV EA+ VL++
Sbjct: 62  ESLRSKVDEAVAVLQA 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 = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/172 (26%), Positives = 87/172 (50%), Gaps = 7/172 (4%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++ ++   +    +   F+ FG I S   + D  + + KGF FV++E  E+AQ A+++ 
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYG 233
           N + +  + + VG      + + +  +       FN ++V ++ +  +D+D+K +F  +G
Sbjct: 75  NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 234 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
            I S  + RD   GK K +GF+ +E A  +  AV + N      +   VGKA
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186

>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 = 62.8 bits (151), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 14/180 (7%)
Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 255
           Q +  +AI  +   V+V ++     ++ +++ F  +G I S     D    K K F FV 
Sbjct: 4   QRQRALAIXCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVE 60
Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 314
           +E  + A  A+E  N      R   VG+            GQ +  + +  ++ +  N +
Sbjct: 61  YEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 112
Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
           Y+ ++   + D+ +K +F  FG I SC + RDP +G  KG GF+ +   + +  A++  N
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 73.2 bits (178), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 45/162 (27%), Positives = 87/162 (53%), Gaps = 28/162 (17%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFE---NADDAAKAV 266
           +F+  L+  TT+++L++ FG+YGT+T   +M+D   G+S+ FGF++FE   + D+  K  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 267 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
             L+GK  D +     +A  + E+++  K                  +++  +G  +  +
Sbjct: 66  HILDGKVIDPK-----RAIPRDEQDKTGK------------------IFVGGIGPDVRPK 102
Query: 327 KLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 367
           + +E FS++GTI   ++M D  +G S+G GFV + + +   R
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP---EEA 365
           +   ++I  L     ++ L+E F ++GT+T  K+M+DP +G S+G GF++F  P   +E 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 366 SRALAEMNGKMIVSK 380
            +    ++GK+I  K
Sbjct: 62  VKTQHILDGKVIDPK 76

>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3 (pabpc3) From Homo Sapiens At 2.30 A Resolution Length = 98

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 58/83 (69%)
Query: 556 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEAL 615
           T  ++ LA+A P++Q+  LGE L+PL++      A K+TG LLE+D +E+L+ LESPE+L
Sbjct: 6   TLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPESL 65
Query: 616 KAKVAEAMEVLRSVAQQQANNPA 638
           ++KV EA+ VL++   ++A   A
Sbjct: 66  RSKVDEAVAVLQAHQAKEATQKA 88

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 55/181 (30%), Positives = 82/181 (45%), Gaps = 15/181 (8%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A   +
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 65
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
           N  P +    R++   R  S   S           IF+  + +  +   L D F  +G I
Sbjct: 66  NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 124
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQN-AIDKLNGMLINDKQVFVGHFLRKQERETV 202
              +I TD GSG+ +GF FV F++ +S     I K +   +N     V   L KQE  + 
Sbjct: 125 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASA 182
Query: 203 A 203
           +
Sbjct: 183 S 183

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 65  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 111
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A   +
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 70
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
           N  P +    R++   R  S   S           IF+  + +  +   L D F  +G I
Sbjct: 71  NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 129
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
              +I TD GSG+ +GF FV F++ +S    +
Sbjct: 130 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 176
           +FI  L      ++L   F  +G +  C +  D  + +S+GFGFV +   E    A++  
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 177 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 234
             K++G ++  K+      + +++ +          +FV  + E T +  L+  F +YG 
Sbjct: 74  PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 235 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 266
           I    +M D G GK + F FV F++ D   K V
Sbjct: 129 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 10  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 70  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 116
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 117 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A   +
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
           N  P +    R++   R  S   S           IF+  + +  +   L D F  +G I
Sbjct: 73  NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
              +I TD GSG+ +GF FV F++ +S    +
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 176
           +FI  L      ++L   F  +G +  C +  D  + +S+GFGFV +   E    A++  
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 177 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 234
             K++G ++  K+      + +++ +          +FV  + E T +  L+  F +YG 
Sbjct: 76  PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 235 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 266
           I    +M D G GK + F FV F++ D   K V
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 72  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A   +
Sbjct: 15  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 71
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
           N  P +    R++   R  S   S           IF+  + +  +   L D F  +G I
Sbjct: 72  NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 130
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
              +I TD GSG+ +GF FV F++ +S    +
Sbjct: 131 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 11  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 71  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 117
Query: 326 EKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAF 359
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 118 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A   +
Sbjct: 17  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 73
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
           N  P +    R++   R  S   S           IF+  + +  +   L D F  +G I
Sbjct: 74  NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 132
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
              +I TD GSG+ +GF FV F++ +S    +
Sbjct: 133 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 13  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 73  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 119
Query: 326 EKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAF 359
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 120 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 66.6 bits (161), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A   +
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
           N  P +    R++   R  S   S           IF+  + +  +   L D F  +G I
Sbjct: 73  NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
              +I TD GSG+ +GF FV F++ +S    +
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 72  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 326 EKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAF 359
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 66.2 bits (160), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 36/150 (24%), Positives = 75/150 (50%), Gaps = 14/150 (9%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           + L+VG+L  ++T+ ++  LF + G+   V + +D       G+G++       A  A  
Sbjct: 23  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            L+  PL  K +R+ ++          + ++ ++NL + + ++ L + FS FG +    +
Sbjct: 77  ELDNMPLRGKQLRVRFA--------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 150 ATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
             D  G+  G G V+F  K +A+ A+D+ +
Sbjct: 129 IVDDRGRPSGKGIVEFSGKPAARKALDRCS 158

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 40/156 (25%), Positives = 68/156 (43%), Gaps = 17/156 (10%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            +F+ NL   I  + +   F  +G      I  D     KGFGF++ E +  A+ A  +L
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 78
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 238
           + M +  KQ+             V       ++ V+NL +  ++E L++ F  +G +  A
Sbjct: 79  DNMPLRGKQL------------RVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERA 126
Query: 239 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF 274
           VV+ D  G+    G V F     A KA++  +   F
Sbjct: 127 VVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSF 162

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/164 (26%), Positives = 70/164 (42%), Gaps = 29/164 (17%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
           T+ + +FV NL    T+E+++K+F +YG      + +D     K FGF+  E    A  A
Sbjct: 20  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 74
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
              L+                   R ++L+ +F              +L ++NL   + +
Sbjct: 75  KVELDNMPL---------------RGKQLRVRF---------ACHSASLTVRNLPQYVSN 110
Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           E L+E FS FG +    V+ D  G   G G V FS    A +AL
Sbjct: 111 ELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 49/188 (26%), Positives = 83/188 (44%), Gaps = 30/188 (15%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 267
           +FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A  
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 322
           AL+  K                    L G     Q + A  E  +  +   L+I  +   
Sbjct: 78  ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 118
Query: 323 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---S 379
             +  ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+    +   S
Sbjct: 119 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 178
Query: 380 KPLYVAVA 387
            P+ V  A
Sbjct: 179 SPMVVKFA 186

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 55/87 (63%), Gaps = 2/87 (2%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNIL-SCKIATD-GSGQSKGFGFVQFENKESAQ 172
           SG+  IFI NLD  ID K L+DTFS+FG IL + KI  D  +G SKG+ F+ F + +++ 
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQER 199
            AI+ +NG  + ++ + V +  +K  +
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSK 89

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 53/82 (64%), Gaps = 2/82 (2%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTIT-SCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           ++I NL   ID++ L + FS FG I  + K+MRDP +G SKG  F+ F++ + +  A+  
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
           MNG+ + ++P+ V+ A +K+ +
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSK 89

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/188 (26%), Positives = 83/188 (44%), Gaps = 30/188 (15%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 267
           +FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 322
           AL+  K                    L G     Q + A  E  +  +   L+I  +   
Sbjct: 66  ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 106
Query: 323 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---S 379
             +  ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+    +   S
Sbjct: 107 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 166
Query: 380 KPLYVAVA 387
            P+ V  A
Sbjct: 167 SPMVVKFA 174

>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 = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 48/78 (61%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +L  LFS +G+V S ++ RD     SLGYG+VNY    DA RA++
Sbjct: 5   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 90  VLNFTPLNNKSIRIMYSH 107
            LN   L +K+I++ Y+ 
Sbjct: 65  TLNGLRLQSKTIKVSYAR 82

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV + T ++A RA+  
Sbjct: 6   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + SK + V+ A+
Sbjct: 66  LNGLRLQSKTIKVSYAR 82

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
           +FV  L   T ++ L+++F +YG I+  VV++D +  +S+ FGFV FEN DDA  A+ A+
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 270 NGKKFDDREWYVGKAQKKSE 289
           NGK  D R+  V +A K S+
Sbjct: 75  NGKSVDGRQIRVDQAGKSSD 94

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           L++  L    +++ L+++FS++G I+   V++D  +  S+G GFV F   ++A  A+  M
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
           NGK +  + + V  A +  + R+
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNRS 97

>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 = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 48/80 (60%)
Query: 27  FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
           F  T+L V  L  N T  +L  LFS +G+V S ++ RD     SLGYG+VNY    DA R
Sbjct: 17  FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 87  ALDVLNFTPLNNKSIRIMYS 106
           A++ LN   L +K+I++ Y+
Sbjct: 77  AINTLNGLRLQSKTIKVSYA 96

>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 = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 367
           FQG NL +  L  +   ++L+ LFS  G + S K++RD  +G S G GFV + T ++A R
Sbjct: 17  FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 368 ALAEMNGKMIVSKPLYVAVAQ 388
           A+  +NG  + SK + V+ A+
Sbjct: 77  AINTLNGLRLQSKTIKVSYAR 97

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 52/85 (61%), Gaps = 1/85 (1%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +   LF  +G + S ++ RD  T +SLGYG+VNY++P DA +A++
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 90  VLNFTPLNNKSIRIMYSH-RDPSIR 113
            LN   L  K+I++ Y+     SIR
Sbjct: 65  TLNGLKLQTKTIKVSYARPSSASIR 89

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  ++ K LF   G I SCK++RD  +G S G GFV +S P +A +A+  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 66  LNGLKLQTKTIKVSYAR 82

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 46/164 (28%), Positives = 69/164 (42%), Gaps = 29/164 (17%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
           T+   +FV NL    T+ED K++F  YG  +   + RD     + FGF+  E+   A  A
Sbjct: 20  TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIA 74
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
              L+G     R   +  A                          G  L +KNL   + +
Sbjct: 75  KAELDGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSN 110
Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           E L++ FS+FG +    V+ D  G + G GFV F+    A +AL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           Q   L++ NL   I +E  K LF  +G  +   + RD     +G GF+   +   A  A 
Sbjct: 21  QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAK 75
Query: 370 AEMNGKMIVSKPLYVAVA 387
           AE++G ++ S+PL +  A
Sbjct: 76  AELDGTILKSRPLRIRFA 93

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 59.7 bits (143), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/166 (26%), Positives = 73/166 (43%), Gaps = 27/166 (16%)
Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVEA 268
           FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A  A
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDSI 323
           L+  K                    L G     Q + A  E  +  +   L+I  +    
Sbjct: 67  LHNXKV-------------------LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKC 107
Query: 324 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
            +  ++  FS FG I  C+++R P G+S+G  FV F+T   A  A+
Sbjct: 108 TENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 59.3 bits (142), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 47/78 (60%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +F+  L+  T ++ LK +FG++G I+  ++++D   KS+ F F+ FEN  DA  A + +N
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 271 GKKFDDREWYVGKAQKKS 288
           GK    +   V +A+K S
Sbjct: 70  GKSLHGKAIKVEQAKKPS 87

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L+I  L    +++ LK +F + G I+   +++D +  S+G  F+ F  P +A  A  +MN
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 374 GKMIVSKPLYVAVAQR 389
           GK +  K + V  A++
Sbjct: 70  GKSLHGKAIKVEQAKK 85

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 58.9 bits (141), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G GF    + E+    +   
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 373 NGKMIVSKP 381
           NGK I + P
Sbjct: 87  NGKFIKTPP 95

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 58.9 bits (141), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 28/77 (36%), Positives = 47/77 (61%)
Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  ++TD +LY LF  +G + + R+ RD  T  S GY +V++ +  D+ RA+ 
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 90  VLNFTPLNNKSIRIMYS 106
           VLN   + NK +++ Y+
Sbjct: 64  VLNGITVRNKRLKVSYA 80

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F++  ++ RA+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K L V+ A+
Sbjct: 65  LNGITVRNKRLKVSYAR 81

>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 = 58.9 bits (141), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 31/100 (31%), Positives = 56/100 (56%), Gaps = 3/100 (3%)
Query: 19  AAGASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           ++G+SG +  T++   ++VGDL   +T   +   F+  G++   RV +D++T +S GYG+
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61
Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKS 115
           V++ N  DA  A+  +    L  + IR  ++ R P   KS
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101

>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 = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           ++F+ +L   I  + +   F+ FG I   ++  D  +G+SKG+GFV F NK  A+NAI +
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 178 LNGMLINDKQVFVGHFLRK 196
           + G  +  +Q+      RK
Sbjct: 77  MGGQWLGGRQIRTNWATRK 95

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 269 LNGKKFDDRE 278
           + G+    R+
Sbjct: 77  MGGQWLGGRQ 86

>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 = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 4/89 (4%)
Query: 303 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 361
           K+T + F   ++++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F  
Sbjct: 10  KDTSNHF---HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 362 PEEASRALAEMNGKMIVSKPLYVAVAQRK 390
             +A  A+ +M G+ +  + +    A RK
Sbjct: 67  KWDAENAIQQMGGQWLGGRQIRTNWATRK 95

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
            NL++ +L  ++DDE L+  F +F +  S  VM D  +G S+G GFV+F++ ++A  A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 371 EMNGKMIVSKPLYVAVAQRKEE 392
            M G+ +  +PL +  A + E 
Sbjct: 62  SMQGQDLNGRPLRINWAAKLEH 83

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 54/95 (56%), Gaps = 3/95 (3%)
Query: 19  AAGASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           ++G+SG +  T++   ++VGDL   +T   +   F+  G++   RV +D++T +S GYG+
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGF 61
Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP 110
           V++ N  DA  A+  +    L  + IR  ++ R P
Sbjct: 62  VSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKP 96

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A+  
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 269 LNGKKFDDREWYVGKAQKK 287
           + G+    R+     A +K
Sbjct: 77  MGGQWLGGRQIRTNWATRK 95

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 48/89 (53%), Gaps = 4/89 (4%)
Query: 303 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 361
           K+T + F    +++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F  
Sbjct: 10  KDTSNHFH---VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 362 PEEASRALAEMNGKMIVSKPLYVAVAQRK 390
             +A  A+  M G+ +  + +    A RK
Sbjct: 67  KLDAENAIVHMGGQWLGGRQIRTNWATRK 95

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 56.2 bits (134), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 268
           N+F+ +L +  TD DL   F  +G + SA V  D     SKCFGFV+F+N D A  A++A
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 269 LNG 271
           +NG
Sbjct: 102 MNG 104

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +G NL+I +L     D  L   F  FG + S KV  D  + +SK  GFV+F  P+ A  A
Sbjct: 39  EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 369 LAEMNGKMIVSKPLYV 384
           +  MNG  + +K L V
Sbjct: 99  IKAMNGFQVGTKRLKV 114

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 44/72 (61%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYVG L FN+T+  L  +F   G++ S+++  D  T RS GYG++ +++   A +AL+ L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 92  NFTPLNNKSIRI 103
           N   L  + +++
Sbjct: 89  NGFELAGRPMKV 100

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
           + LY+ +L  +I ++ L+ +F  FG I S ++M D  +G SKG GF+ FS  E A +AL 
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 371 EMNGKMIVSKPLYVA-VAQRKE 391
           ++NG  +  +P+ V  V +R +
Sbjct: 87  QLNGFELAGRPMKVGHVTERTD 108

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 55.8 bits (133), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 48/80 (60%), Gaps = 4/80 (5%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKV--MRDPSGI--SKGSGFVAFSTPEEASRAL 369
           L+IKNL  S  +E LK +FS+ G I SC +   ++ +G+  S G GFV +  PE+A +AL
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 370 AEMNGKMIVSKPLYVAVAQR 389
            ++ G  +    L V +++R
Sbjct: 68  KQLQGHTVDGHKLEVRISER 87

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 55.5 bits (132), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG    ++ LYVG L FN+T+  L  +F   G++ ++ + +D  T RS GYG++ +++
Sbjct: 1   GSSG----SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSD 56
Query: 81  PADAARALDVLNFTPLNNKSIRI 103
              A RAL+ LN   L  + +R+
Sbjct: 57  SECARRALEQLNGFELAGRPMRV 79

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 52.4 bits (124), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           LY+ +L  +I ++ L+ +F  FG I +  +M+D  +G SKG GF+ FS  E A RAL ++
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 373 NGKMIVSKPLYVA 385
           NG  +  +P+ V 
Sbjct: 68  NGFELAGRPMRVG 80

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++  LG    DE ++++F  FGTI  C V+R P G SKG  FV F T  EA  A+  +
Sbjct: 14  KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 373 NGKMIV---SKPLYVAVAQRKEE 392
           +    +   S  L V  A  ++E
Sbjct: 74  HSSRTLPGASSSLVVKFADTEKE 96

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           S++VG++ +  T+ QL D+FS+VG V+S R+  D  T +  GYG+  Y +   A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 91  LNFTPLNNKSIRI 103
           LN    + +++R+
Sbjct: 70  LNGREFSGRALRV 82

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 1/91 (1%)
Query: 203 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADD 261
           A+     +VFV N+    T+E LK IF E G + S  ++ D + GK K +GF  +++ + 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 262 AAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
           A  A+  LNG++F  R   V  A  +  +E+
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 41/73 (56%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + VFV NLD     + LK++F   G +  A ++ D DGKS+  G V FE + +A +A+  
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 269 LNGKKFDDREWYV 281
            NG+   DR  +V
Sbjct: 76  FNGQLLFDRPMHV 88

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 46/79 (58%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G  +++ NL   +  +KLKE+FS  G +    ++ D  G S+G G V F    EA +A++
Sbjct: 15  GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 371 EMNGKMIVSKPLYVAVAQR 389
             NG+++  +P++V + +R
Sbjct: 75  MFNGQLLFDRPMHVKMDER 93

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           ++YVG LD  V++  L++LF Q G V++  + +D  T +  GYG+V + +  DA  A+ +
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 91  LNFTPLNNKSIRI 103
           ++   L  K IR+
Sbjct: 77  MDMIKLYGKPIRV 89

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           NL +  +  ++D+ +L++LF  +G I S K++ D  +  S+G GFV F +   A +A+A 
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
           +NG  I++K L VA+A    +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/90 (32%), Positives = 51/90 (56%)
Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           + +LYVG+L F  T+ Q+Y+LFS+ G +  + +  D   + + G+ +V Y + ADA  A+
Sbjct: 39  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
             +N T L+++ IR  +       R+ G G
Sbjct: 99  RYINGTRLDDRIIRTDWDAGFKEGRQYGRG 128

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 6/125 (4%)
Query: 192 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC- 250
           HF    E +   +K K   ++V NL   TT+E + ++F + G I   ++  D   K+ C 
Sbjct: 24  HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 251 FGFVNFENADDAAKAVEALNGKKFDDR----EWYVGKAQKKSEREQELKGQFEQAMKETV 306
           F FV + +  DA  A+  +NG + DDR    +W  G  + +        GQ     ++  
Sbjct: 83  FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDY 142
Query: 307 DKFQG 311
           D  +G
Sbjct: 143 DAGRG 147

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/76 (36%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG+  IF++NL      K L D F+  G++L   I  + +G+SKG G V+FE+ E A+ A
Sbjct: 3   SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 61
Query: 175 IDKLNGMLINDKQVFV 190
              +NGM ++ +++ V
Sbjct: 62  CRMMNGMKLSGREIDV 77

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID-- 176
           +FI  L      K L D FS FG ++ C +  D  +G+S+GFGFV F+  ES    +D  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 177 --KLNGMLINDKQ 187
             KLNG +I+ K+
Sbjct: 62  EHKLNGKVIDPKR 74

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 371
           ++I  L      + LK+ FS+FG +  C +  DP +G S+G GFV F   E   + + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 372 ---MNGKMIVSK 380
              +NGK+I  K
Sbjct: 62  EHKLNGKVIDPK 73

>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 = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +G NL+I +L     D+ L ++F  FG + S KV  D  + +SK  GFV++  P  A  A
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRA 395
           +  MNG  I  K L V + + K + ++
Sbjct: 84  IQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           + +LYVG+L F  T+ Q+Y+LFS+ G +  + +  D   + + G+ +V Y + ADA  A+
Sbjct: 18  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAM 76
Query: 89  DVLNFTPLNNKSIR 102
             +N T L+++ IR
Sbjct: 77  RYINGTRLDDRIIR 90

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 192 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 251
           HF    E +   +K K   ++V NL   TT+E + ++F + G I   ++  D    +  F
Sbjct: 3   HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 252 GFVNFENADDAAKAVEALNGKKFDDR----EWYVG 282
            FV + +  DA  A+  +NG + DDR    +W  G
Sbjct: 62  CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 96

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R
Sbjct: 24  TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 82

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 265
           K  N++V NL  + TD+ L  IFG+YG+I    ++RD   G+ +   FV +   ++A +A
Sbjct: 12  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 266 VEALN 270
           + ALN
Sbjct: 72  ISALN 76

>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 = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 50/85 (58%), Gaps = 3/85 (3%)
Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
           +  +  NLY+ NL  +I D++L  +F ++G+I    ++RD  +G  +G  FV ++  EEA
Sbjct: 9   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 366 SRALAEMNGKMIV--SKPLYVAVAQ 388
             A++ +N  +    S+PL V +A+
Sbjct: 69  QEAISALNNVIPEGGSQPLSVRLAE 93

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/187 (24%), Positives = 85/187 (45%), Gaps = 18/187 (9%)
Query: 211 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 264
           ++V N+    T+E +   F      G +T A    V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ------AMKETVDKFQGLNLYIKN 318
           A+ A +G  F  +   +    ++    Q L G  E        +  TV       L+I  
Sbjct: 67  AM-AFDGIIFQGQSLKI----RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121
Query: 319 LGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMI 377
           L + ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Query: 378 VSKPLYV 384
             K L V
Sbjct: 182 GDKKLLV 188

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           N+++  L K++  K +   FS +G I++ +I  D  +G S+G GF++F+ +  A+ AI  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 178 LNG 180
           LNG
Sbjct: 63  LNG 65

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 5/74 (6%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
           NLY+  L  ++  +++++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 372 MNGKMIVSKPLYVA 385
           +NG+    KPL  A
Sbjct: 63  LNGQ----KPLGAA 72

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 271
           V  L   TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 272 KKFDDREWYV 281
            + D R   V
Sbjct: 111 MELDGRRIRV 120

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R
Sbjct: 27  TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG   IF++NL      K L D F+  G++L   I  + +G+SKG G V+FE+ E A+ A
Sbjct: 6   SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 64
Query: 175 IDKLNGMLINDKQVFV 190
              +NGM ++ +++ V
Sbjct: 65  CRMMNGMKLSGREIDV 80

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 32  LYVGDLDFNVTDSQLYDLFS---QVG--------QVLSVRVCRDLSTRRSLGYGYVNYAN 80
           LYVG++ F +T+  + D F+   ++G         VL+V++ +D    ++  +      +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVD 64
Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSS 140
               A A D + F     +S++I   H    +   G   +FI  L   ++   + +  +S
Sbjct: 65  ETTQAMAFDGIIF---QGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 119
Query: 141 FGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           FG + +  +  D  +G SKG+ F ++ +      AI  LNGM + DK++ V
Sbjct: 120 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 211 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 264
           ++V N+    T+E +   F      G +T A    V+     + K F F+ F + D+  +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 324
           A+ A +G  F  +   +    ++    Q L G  +              L+I  L + ++
Sbjct: 69  AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 109
Query: 325 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 383
           D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K L 
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 384 V 384
           V
Sbjct: 170 V 170

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/234 (20%), Positives = 100/234 (42%), Gaps = 20/234 (8%)
Query: 40  NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK 99
           +VT+ +++DL S       ++ C      +  G  +V   N   A  A++  + + L  +
Sbjct: 31  DVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRER 83
Query: 100 SIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSK 158
            + +     D          + + NL  S+  +   +    FG++  C  + ++ +GQSK
Sbjct: 84  ELSVQLQPTD--------ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK 135
Query: 159 GFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDE 218
           G+GF ++  K+SA  A   L G  +  + ++V H+    +     + ++   + V  L  
Sbjct: 136 GYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSRC--LCVDRLPP 192
Query: 219 STTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
              D D L +      + T   +    DG+ K F  + +E A+ A +A +  +G
Sbjct: 193 GFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADG 246

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/176 (23%), Positives = 74/176 (42%), Gaps = 31/176 (17%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+ A 
Sbjct: 22  KILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAF 75
Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
           +  +                RE+EL  Q +       D      L + NL  S+  ++ +
Sbjct: 76  HQSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFE 111
Query: 330 ELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
           EL   FG++  C  V  + +G SKG GF  +   + A+RA +++ GK +  + LYV
Sbjct: 112 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/234 (20%), Positives = 100/234 (42%), Gaps = 20/234 (8%)
Query: 40  NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK 99
           +VT+ +++DL S       ++ C      +  G  +V   N   A  A++  + + L  +
Sbjct: 33  DVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRER 85
Query: 100 SIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSK 158
            + +     D          + + NL  S+  +   +    FG++  C  + ++ +GQSK
Sbjct: 86  ELSVQLQPTD--------ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK 137
Query: 159 GFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDE 218
           G+GF ++  K+SA  A   L G  +  + ++V H+    +     + ++   + V  L  
Sbjct: 138 GYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSRC--LCVDRLPP 194
Query: 219 STTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
              D D L +      + T   +    DG+ K F  + +E A+ A +A +  +G
Sbjct: 195 GFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADG 248

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/176 (23%), Positives = 74/176 (42%), Gaps = 31/176 (17%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+ A 
Sbjct: 24  KILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAF 77
Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
           +  +                RE+EL  Q +       D      L + NL  S+  ++ +
Sbjct: 78  HQSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFE 113
Query: 330 ELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
           EL   FG++  C  V  + +G SKG GF  +   + A+RA +++ GK +  + LYV
Sbjct: 114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 49/234 (20%), Positives = 100/234 (42%), Gaps = 20/234 (8%)
Query: 40  NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK 99
           +VT+ +++DL S       ++ C      +  G  +V   N   A  A++  + + L  +
Sbjct: 33  DVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRER 85
Query: 100 SIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSK 158
            + +     D          + + NL  S+  +   +    FG++  C  + ++ +GQSK
Sbjct: 86  ELSVQLQPTD--------ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK 137
Query: 159 GFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDE 218
           G+GF ++  K+SA  A   L G  +  + ++V H+    +     + ++   + V  L  
Sbjct: 138 GYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSRC--LCVDRLPP 194
Query: 219 STTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
              D D L +      + T   +    DG+ K F  + +E A+ A +A +  +G
Sbjct: 195 GFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADG 248

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/176 (23%), Positives = 74/176 (42%), Gaps = 31/176 (17%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+ A 
Sbjct: 24  KILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAF 77
Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
           +  +                RE+EL  Q +       D      L + NL  S+  ++ +
Sbjct: 78  HQSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFE 113
Query: 330 ELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
           EL   FG++  C  V  + +G SKG GF  +   + A+RA +++ GK +  + LYV
Sbjct: 114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 38/67 (56%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++  N
Sbjct: 31  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 271 GKKFDDR 277
           G   D R
Sbjct: 91  GVPLDGR 97

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ + N
Sbjct: 31  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 374 GKMIVSKPLYV 384
           G  +  +P+ +
Sbjct: 91  GVPLDGRPMNI 101

>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains Of The Yeast Splicing Factor Prp24 Length = 292

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 64/269 (23%), Positives = 116/269 (43%), Gaps = 21/269 (7%)
Query: 25  NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
           N+ LTT L V +L  +   +++Y  F   G ++ V V   L  +++  +  + +A    A
Sbjct: 38  NRELTTVL-VKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGA 94
Query: 85  ARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
             A+   +     N+   I+ SH            ++  N   S   + + D       +
Sbjct: 95  LAAITKTHKVVGQNE---IIVSHLTEC-------TLWXTNFPPSYTQRNIRDLLQDINVV 144
Query: 145 -LSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVF--VGHFLRKQERET 201
            LS ++ +     S+ F ++   +KE A+  ++KLNG+ I    +   V + L K +R T
Sbjct: 145 ALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR-T 203
Query: 202 VAIKTKFNNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKS--KCFGFVNFEN 258
            +   +   + ++NL     DE+ L++ F  +G+I    +       S   C  F  FEN
Sbjct: 204 DSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFEN 263
Query: 259 ADDAAKAVEALNGKKFDDREWYVGKAQKK 287
            D A +A++  N     +RE  V  A KK
Sbjct: 264 KDSAERALQX-NRSLLGNREISVSLADKK 291

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 32  LYVGDLDFNVTDSQLYDLFS---QVG--------QVLSVRVCRDLSTRRSLGYGYVNYAN 80
           LYVG++ F +T+  + D F+   ++G         VL+V++ +D    ++  +      +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVD 62
Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSS 140
               A A D + F     +S++I   H    +   G   +FI  L   ++   + +  +S
Sbjct: 63  ETTQAMAFDGIIF---QGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 117
Query: 141 FGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           FG + +  +  D  +G SKG+ F ++ +      AI  LNGM + DK++ V
Sbjct: 118 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 211 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 264
           ++V N+    T+E +   F      G +T A    V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 324
           A+ A +G  F  +   +    ++    Q L G  +              L+I  L + ++
Sbjct: 67  AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 107
Query: 325 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 383
           D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K L 
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 384 V 384
           V
Sbjct: 168 V 168

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++ NL   + +E L ELF + G +T   + +D  G  K  GFV F  PE  S A+A +N
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 374 GKMIVSKPLYVA 385
           G  +  +P+ V+
Sbjct: 79  GIRLYGRPINVS 90

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 54/90 (60%), Gaps = 11/90 (12%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L+++NL +++ +E L++ FS+FG +   K ++D +       F+ F   + A +A+ EMN
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYA-------FIHFDERDGAVKAMEEMN 66
Query: 374 GKMIVSKPLYVAVA----QRKEERRARLQA 399
           GK +  + + +  A    Q+++ER+A+ QA
Sbjct: 67  GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 48/85 (56%), Gaps = 6/85 (7%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSC---KVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +L++ +L   +DD  L E F +     SC   KV+ D +G+SKG GFV F+   E  RAL
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVK--VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 370 AEMNGKM-IVSKPLYVAVAQRKEER 393
            E  G + + SKP+ ++VA  K  R
Sbjct: 69  TECQGAVGLGSKPVRLSVAIPKASR 93

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDRE 278
           TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R 
Sbjct: 27  TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 279 WYV 281
             V
Sbjct: 87  IRV 89

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++  L     +E +  LF  FG I  C V+R P G SKG  FV FS+  EA  A+  ++
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 374 GKMIV---SKPLYVAVAQRKEE 392
           G   +   S  L V  A   +E
Sbjct: 78  GSQTMPGASSSLVVKFADTDKE 99

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           K++   + V N+     D DL+++FG++G I    ++ +  G SK FGFV FEN+ DA +
Sbjct: 26  KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 84
Query: 265 AVEALNGKKFDDREWYVGKAQKK 287
           A E L+G   + R+  V  A  +
Sbjct: 85  AREKLHGTVVEGRKIEVNNATAR 107

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 305 TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE 364
           T +K Q   L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F    +
Sbjct: 23  TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 365 ASRALAEMNGKMIVSKPLYV 384
           A RA  +++G ++  + + V
Sbjct: 82  ADRAREKLHGTVVEGRKIEV 101

>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 = 49.3 bits (116), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 267
           + V+V NL  S T+ DL +IF +YG +    +M+D D  KSK   F+ F + D A     
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 268 ALNGKKFDDR 277
           A+N K+   R
Sbjct: 77  AINNKQLFGR 86

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 37/67 (55%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA +  N
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 271 GKKFDDR 277
           G   D R
Sbjct: 92  GVPLDGR 98

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 36/68 (52%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A  + N
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 374 GKMIVSKP 381
           G  +  +P
Sbjct: 92  GVPLDGRP 99

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 43/168 (25%), Positives = 73/168 (43%), Gaps = 21/168 (12%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+FV NL+ + +  +LK    +        V+    G ++ FG+V+FE+A+D  KA+E  
Sbjct: 9   NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALELT 68
Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
             K F +         K S++E++ +                  L  KNL   +  ++LK
Sbjct: 69  GLKVFGNEIKLEKPKGKDSKKERDAR-----------------TLLAKNLPYKVTQDELK 111
Query: 330 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 377
           E+F +   I     +    G SKG  ++ F T  +A +   E  G  I
Sbjct: 112 EVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 21  GASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN 77
           G+SG+  + T+   LYVG L   V D  L+  F   G +  +++  D  T +  G+ +V 
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 78  YANPADAARALDVLNFTPLNNKSIRI 103
           +    DAA A+D +N + L  ++IR+
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRV 86

>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: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID +
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 179 N 179
           N
Sbjct: 75  N 75

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 26/84 (30%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 167
           + S  +   G  F+  L      K L D F+ FG ++ C I  D  +G+S+GFGF+ F++
Sbjct: 3   NASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
Query: 168 KESAQNAID----KLNGMLINDKQ 187
             S +  +D    +L+G +I+ K+
Sbjct: 63  AASVEKVLDQKEHRLDGRVIDPKK 86

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
           V N+     D DL+++FG++G I    ++ +  G SK FGFV FEN+ DA +A E L+G 
Sbjct: 20  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 273 KFDDREWYVGKAQKK 287
             + R+  V  A  +
Sbjct: 79  VVEGRKIEVNNATAR 93

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F    +A RA  +++
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 374 GKMIVSKPLYV 384
           G ++  + + V
Sbjct: 77  GTVVEGRKIEV 87

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
           +FV+NL  ++++EDL+K+F  YG ++      D    K K F FV F   + A KA   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
           +G+ F  R  +V  +  K E  Q
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQ 93

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+++NL  +  +E L++LFS +G ++      D  +   KG  FV F  PE A +A AE+
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 373 NGKMIVSKPLYVAVAQRKEE 392
           +G++   + L+V  +  K+E
Sbjct: 71  DGQVFQGRMLHVLPSTIKKE 90

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/88 (28%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  +D  +D   +   F+ +G++   KI TD +G SKG+GFV F N    Q  ++  +
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTK 207
            +  + K++ +G  +RKQ   T  ++ +
Sbjct: 70  QINFHGKKLKLGPAIRKQNLSTYHVQPR 97

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K VE+
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 269 ---LNGKKF 274
               +GKK 
Sbjct: 70  QINFHGKKL 78

>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 = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           ++YVG+L ++ T  Q+ +LFSQ G+V +V++  D  T++  G+G+V     +  + A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61
Query: 91  LNFTPLNNKSIRIMYSHRDPSI 112
           L+ T    ++IR+  ++   S+
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSL 83

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNG 271
           V NL E T + DL+++F  +G+I+   + +D   G+SK F F++F   +DAA+A+  ++G
Sbjct: 20  VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 272 KKFD 275
             +D
Sbjct: 80  FGYD 83

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNG 374
           + NL +   +  L+ELF  FG+I+   + +D + G SKG  F++F   E+A+RA+A ++G
Sbjct: 20  VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++  L     ++ ++ LF  FG I  C ++R P G SKG  FV +S+  EA  A+  ++
Sbjct: 18  LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 374 GKMIV---SKPLYVAVAQRKEE 392
           G   +   S  L V  A   +E
Sbjct: 78  GSQTMPGASSSLVVKFADTDKE 99

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 194 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFG 252
           L +++RE    K +F  +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FG
Sbjct: 17  LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 253 FVNFENADDAAKAVEA 268
           FV F +  +   A+ A
Sbjct: 73  FVTFSSMAEVDAAMAA 88

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
           +K Q   L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS+  E 
Sbjct: 23  EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 366 SRALA----EMNGKMIVSK 380
             A+A     ++G+++  K
Sbjct: 83  DAAMAARPHSIDGRVVEPK 101

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 271
           V NL   T+ + L+++F +YG +    + RD   K S+ F FV F +  DA  A++A++G
Sbjct: 52  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 272 KKFDDREWYVGKAQ 285
              D RE  V  A+
Sbjct: 112 AVLDGRELRVQMAR 125

>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2 Peptide From Paip1 Length = 65

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 570 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 626
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++
Sbjct: 6   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELI 62

>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 = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID +
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 179 N 179
           N
Sbjct: 126 N 126

>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein: An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding Protein Length = 61

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 570 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 626
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELI 57

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/138 (25%), Positives = 58/138 (42%), Gaps = 14/138 (10%)
Query: 31  SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
           ++Y+ +L+  +   +L    Y +FSQ GQ+L + V R L  R   G  +V +   + A  
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 87  ALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS 146
           AL  +   P  +K +RI Y+  D  I     G    ++  +        +T        +
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQET-------PA 120
Query: 147 CKIATDGSGQSKGFGFVQ 164
            K A  G G +   G VQ
Sbjct: 121 TKKAVQGGGATPVVGAVQ 138

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 313 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
            +YI NL + I  ++LK+    +FS+FG I    V R  S   +G  FV F     A+ A
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
           L  M G     KP+ +  A+   +  A+++  F
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 15 PNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYG 74
          P G   G+SG +     +++G L +  T   L + F Q G+V    V RD  T+RS G+G
Sbjct: 16 PRGSHMGSSGCK-----MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
Query: 75 YVNYANPADAARAL 88
          +V + + A   + L
Sbjct: 71 FVTFMDQAGVDKVL 84

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           G  ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + L
Sbjct: 25  GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 370 A----EMNGKMIVSKPLYVAVAQRK 390
           A    E++ K I  K  +   AQ K
Sbjct: 85  AQSRHELDSKTIDPKVAFPRRAQPK 109

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  +D  +D   +   F+ +G++   KI TD +G SKG+GFV F N    Q  ++  +
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 180 GMLINDKQVFVGHFLRKQ 197
            +  + K++ +G  +RKQ
Sbjct: 70  QINFHGKKLKLGPAIRKQ 87

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K VE+
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 269 ---LNGKKF 274
               +GKK 
Sbjct: 70  QINFHGKKL 78

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 45/79 (56%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VGDL   +T + +   F+  G++   RV +D++T +S GYG+V++ N  DA  A+  +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 92  NFTPLNNKSIRIMYSHRDP 110
               L  + IR  ++ R P
Sbjct: 69  GGQWLGGRQIRTNWATRKP 87

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           ++F+ +L   I   A+   F+ FG I   ++  D  +G+SKG+GFV F NK  A+NAI +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 178 LNGMLINDKQVFVGHFLRK 196
           + G  +  +Q+      RK
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++   
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 271 GKKFDDR 277
           G   D R
Sbjct: 151 GVPLDGR 157

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G  L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ 
Sbjct: 88  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 371 EMNGKMIVSKPLYV 384
           +  G  +  +P+ +
Sbjct: 148 QYKGVPLDGRPMDI 161

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+  +D  +D   +   F+ +G++   KI TD +G SKG+GFV F N    Q  ++  +
Sbjct: 13  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 70
Query: 180 GMLINDKQVFVGHFLRKQ 197
            +  + K++ +G  +RKQ
Sbjct: 71  QINFHGKKLKLGPAIRKQ 88

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K VE+
Sbjct: 11  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 269 ---LNGKKF 274
               +GKK 
Sbjct: 71  QINFHGKKL 79

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FVK L E TT+E LK+ F   G++ + +V     G SK FGFV+F + +DA  A EA+ 
Sbjct: 18  LFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 271 GKKFD 275
             + D
Sbjct: 76  DGEID 80

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/86 (29%), Positives = 48/86 (55%), Gaps = 3/86 (3%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LY+ +L + +T  ++YD+F + G +  +RV     TR   G  YV Y +  DA  A+D L
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAVDHL 67
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGT 117
           +   ++N+ + ++Y + + + +K  T
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDT 93

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID +
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 179 N 179
           N
Sbjct: 65  N 65

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 179 N 179
           N
Sbjct: 68  N 68

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 179 N 179
           N
Sbjct: 70  N 70

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 271
           V NL   T+ + L+++F +YG +    + RD   K S+ F FV F +  DA  A++A++G
Sbjct: 75  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 272 KKFDDREWYVGKAQ 285
              D RE  V  A+
Sbjct: 135 AVLDGRELRVQMAR 148

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31  SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
           ++Y+ +L+  +   +L    Y +FSQ GQ+L + V R L  R   G  +V +   + A  
Sbjct: 10  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 87  ALDVLNFTPLNNKSIRIMYSHRDPSI 112
           AL  +   P  +K +RI Y+  D  I
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDSDI 92

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 313 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
            +YI NL + I  ++LK+    +FS+FG I    V R  S   +G  FV F     A+ A
Sbjct: 10  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
           L  M G     KP+ +  A+   +  A+++  F
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 37/68 (54%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 270 NGKKFDDR 277
            G   D R
Sbjct: 97  KGVPLDGR 104

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G  L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ 
Sbjct: 35  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 371 EMNGKMIVSKPLYV 384
           +  G  +  +P+ +
Sbjct: 95  QYKGVPLDGRPMDI 108

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 37/68 (54%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 270 NGKKFDDR 277
            G   D R
Sbjct: 97  KGVPLDGR 104

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           G  L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ 
Sbjct: 35  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 371 EMNGKMIVSKPLYV 384
           +  G  +  +P+ +
Sbjct: 95  QYKGVPLDGRPMDI 108

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+V NL  +    +L++ FG YG + S  V R+  G    F FV FE+  DAA AV  L+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 271 GK 272
           G+
Sbjct: 132 GR 133

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
           + ++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 268 AL 269
           AL
Sbjct: 66  AL 67

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP-------ADA 84
          L+VG LD++ T   L   FSQ G+V+   + +D +T +S G+G+V + +P       A  
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 85 ARALDVLNFTP 95
             LD  N  P
Sbjct: 79 PHTLDGRNIDP 89

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 265
           +   +FV  LD STT E L+  F +YG +   V+M+D    +S+ FGFV F++ +     
Sbjct: 15  EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 266 VEA----LNGKKFDDR 277
           + +    L+G+  D +
Sbjct: 75  LASRPHTLDGRNIDPK 90

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V+V NL  +    +L++ FG YG + S  V R+  G    F FV FE+  DAA AV  L+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 271 GK 272
           G+
Sbjct: 132 GR 133

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +Y+G + ++ T+ Q+ DL S VG V+++++  D  T RS GY ++ + +   +A A+  L
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 92  NFTPLNNKSIRIMYS 106
           N   L ++ ++  YS
Sbjct: 67  NGYQLGSRFLKCGYS 81

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +Y+G + ++ T+ Q+ DL S VG V+++++  D  T RS GY ++ + +   +A A+  L
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 92  NFTPLNNKSIRIMYS 106
           N   L ++ ++  YS
Sbjct: 65  NGYQLGSRFLKCGYS 79

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 264
           T F  +FV  L   TTD  L+K F  +G I  AVV+ D   GKS+ +GFV   +   A +
Sbjct: 15  TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 265 AVE----ALNGKKFDDREWYVG 282
           A +     ++G+K +    Y+G
Sbjct: 75  ACKDPNPIIDGRKANVNLAYLG 96

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +Y+G + ++ T+ Q+ DL S VG V+++++  D  T RS GY ++ + +   +A A+  L
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 92  NFTPLNNKSIRIMYS 106
           N   L ++ ++  YS
Sbjct: 66  NGYQLGSRFLKCGYS 80

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31  SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
           ++Y+ +L+  +   +L    Y +FSQ GQ+L + V R L  R   G  +V +   + A  
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 87  ALDVLNFTPLNNKSIRIMYSHRDPSI 112
           AL  +   P  +K +RI Y+  D  I
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDI 93

>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal Protein P14 Bound To Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LY+ +L + +T  ++YD+F + G +  +RV     TR   G  YV Y +  DA  A D L
Sbjct: 21  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 77
Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGT 117
           +   + N+ + ++Y + + + +K  T
Sbjct: 78  SGFNVCNRYLVVLYYNANRAFQKMDT 103

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV+       + +L +IFG +G +    ++         F FV FE A+ AAKA+E ++
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 86
Query: 271 GKKFDDREWYVGKAQKKSER 290
           GK F ++   V  ++  ++R
Sbjct: 87  GKSFANQPLEVVYSKLPAKR 106

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 77/168 (45%), Gaps = 21/168 (12%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  KA+E L
Sbjct: 15  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
            G K    E  + K           KG+  + ++          L  KNL  +I +++LK
Sbjct: 74  TGLKVFGNEIKLEKP----------KGRDSKKVR------AARTLLAKNLSFNITEDELK 117
Query: 330 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 377
           E+F +   I     +    G SKG  ++ F +  +A + L E  G  I
Sbjct: 118 EVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
           L+I  L + ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 373 NGKMIVSKPLYV 384
           NG  +  K L V
Sbjct: 64  NGMQLGDKKLLV 75

>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleoprotein R (Hnrnp R) Length = 97

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 204 IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 263
           +  K   +FV+NL  + T+E L+K F E+G +     ++D       + FV+FE+   A 
Sbjct: 11  VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAV 63
Query: 264 KAVEALNGK 272
           KA++ +NGK
Sbjct: 64  KAMDEMNGK 72

>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein Complex P14-Sf3b155 Length = 87

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LY+ +L + +T  ++YD+F + G +  +RV     TR   G  YV Y +  DA  A D L
Sbjct: 15  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 71
Query: 92  NFTPLNNKSIRIMY 105
           +   + N+ + ++Y
Sbjct: 72  SGFNVCNRYLVVLY 85

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 6/93 (6%)
Query: 313 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
            +YI NL + I  ++LK+    +FS FG I    V R  S   +G  FV F     A+ A
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
           L  M G     KP+ +  A+   +  A+++  F
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 39/72 (54%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +FI  L  S   + L +   + G +   ++ T+ +G+ KG  +V++EN+  A  A+ K++
Sbjct: 20  LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 180 GMLINDKQVFVG 191
           GM I +  + V 
Sbjct: 80  GMTIKENIIKVA 91

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEALNG 271
           V NL   T+ + L+++F +YG +    + R+   K+ + F FV F +  DA  A  A++G
Sbjct: 18  VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 272 KKFDDREWYV 281
            + D RE  V
Sbjct: 78  AELDGRELRV 87

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V N+  + T+++L+  F EYG +    +++D       + FV+ E A+DA +A+  L+
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 271 GKKFDDREWYV 281
             +F  +  +V
Sbjct: 66  NTEFQGKRMHV 76

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI--ATDGSGQSKGFGFVQFENKES 170
           +K  T  I ++N+    + + + + FS+FG + + ++     G+G  +GFGFV F  K+ 
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 171 AQNAIDKL 178
           A+ A + L
Sbjct: 71  AKKAFNAL 78

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 267
           +FV  L  +TT ED+K  F ++G +  A++M D    + + FGFV FE+ D   K  E
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 371 --EMNGKMIVSK 380
             E++ K I  K
Sbjct: 63  RHELDSKTIDPK 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	652
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-129
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-83
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-53
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-47
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-124
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-96
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-61
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-60
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-84
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-63
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-52
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-25
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-81
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-72
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-62
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-79
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-63
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-50
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-25
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-77
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-75
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-60
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-74
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-68
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-55
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-27
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-61
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-51
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-73
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-58
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-28
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-49
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-45
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-59
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-48
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-48
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-51
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-38
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-35
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-24
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-49
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-32
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-30
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-17
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-46
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-36
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-29
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-20
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-44
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-34
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-31
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-22
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-43
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-30
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-18
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-43
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-34
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-26
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-19
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-43
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	6e-31
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-24
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-43
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-31
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-27
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-42
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-38
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-30
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-18
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-42
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-41
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-38
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-18
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-42
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-27
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-23
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	9e-18
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-40
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-28
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-27
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-21
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-40
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-29
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-23
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-40
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-38
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-33
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-40
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-27
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-22
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-17
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-39
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-30
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-27
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-22
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-38
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-31
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-20
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-38
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-34
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-25
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-38
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-22
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-21
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-37
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-28
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-38
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-36
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-30
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-36
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-30
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-29
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-20
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-35
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-31
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-26
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-21
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-35
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-28
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-23
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-35
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-22
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-21
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-17
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-35
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-33
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-34
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-30
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-29
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-33
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	9e-32
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-22
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-18
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	7e-33
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-32
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-23
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-21
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-20
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-31
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-25
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-24
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-19
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-31
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-31
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-23
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-23
2div_A	99	TRNA selenocysteine associated protein; structural	3e-31
2div_A	99	TRNA selenocysteine associated protein; structural	2e-18
2div_A	99	TRNA selenocysteine associated protein; structural	1e-17
2div_A	99	TRNA selenocysteine associated protein; structural	1e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-29
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-27
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-18
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-17
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-29
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-25
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-19
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	8e-17
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	3e-29
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-29
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-28
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-24
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-22
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-28
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-24
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-22
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-18
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	1e-28
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	2e-28
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-28
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-22
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-19
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-17
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-28
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-27
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-20
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-19
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-27
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-21
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-19
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-27
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-23
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-19
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-27
1x4e_A	85	RNA binding motif, single-stranded interacting pro	9e-25
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-23
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-19
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-27
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-24
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-23
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-21
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-27
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-25
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-18
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-26
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-25
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-25
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-19
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-26
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-24
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-16
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-26
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-21
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-19
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-26
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-19
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	1e-25
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-25
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-22
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-20
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-18
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-25
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-22
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-19
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-25
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-21
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-19
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-25
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-20
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	9e-18
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-17
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-25
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-20
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-20
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-25
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-22
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-18
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-18
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	9e-25
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	9e-23
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-22
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-24
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-20
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-18
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-24
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-20
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-24
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-20
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-19
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-19
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-24
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-23
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-18
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-18
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-24
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-20
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-24
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-18
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-20
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-19
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-18
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-23
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-20
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-23
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-20
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-19
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	7e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-18
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-23
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-19
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-18
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-17
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-23
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	9e-18
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	7e-23
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-23
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-20
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-23
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-22
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-20
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-22
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-15
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-22
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-17
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-22
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-16
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-22
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-20
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-16
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-16
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-22
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-16
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	7e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-22
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-20
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-17
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-22
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-19
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-17
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-22
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-21
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-19
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-22
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	7e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-16
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-21
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-18
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-21
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-17
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-21
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-16
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-21
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-15
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-21
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-20
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-18
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-21
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-19
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-21
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-19
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-17
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-21
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-17
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-20
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-15
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-15
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-20
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-19
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-14
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-20
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-14
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-20
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-15
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-20
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-14
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-20
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-17
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-16
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-16
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-20
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-17
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-20
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-20
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-15
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-19
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-17
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-15
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-13
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-19
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-19
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-12
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-19
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-10
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-09
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-17
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-16
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-19
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-15
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-19
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-15
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	8e-19
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-13
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	4e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-18
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-16
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-14
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-18
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-13
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	6e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-18
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-15
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-13
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-18
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-16
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-18
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-14
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	9e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-18
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-18
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-18
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-17
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-18
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-14
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-09
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-17
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	7e-17
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-12
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-16
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-14
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-14
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-17
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-15
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-11
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	7e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-17
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-15
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-17
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	6e-13
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-17
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-16
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	6e-17
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-15
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-17
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-13
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-12
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-17
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-16
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-15
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-17
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-15
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-14
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-13
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-16
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-13
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-08
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-16
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-16
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-12
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-16
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-12
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-11
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-16
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-16
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-11
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-15
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-14
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-11
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-15
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-15
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-15
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	8e-15
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-14
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-14
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-08
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-12
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	8e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	6e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-13
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-12
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-13
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	9e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	6e-12
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-13
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-12
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-10
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	7e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	7e-12
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-11
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	8e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-11
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	6e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	9e-07
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-10
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-09
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	8e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-08
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-08
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	9e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	5e-08
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	6e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	7e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	5e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	7e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	7e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-06
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-07
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	6e-07
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	3e-04
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	1e-06
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	7e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	8e-04
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	2e-06
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	2e-06
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	3e-06
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	5e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	6e-06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	1e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	5e-04
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-05
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	8e-04

>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 =  380 bits (979), Expect = e-129
 Identities = 61/328 (18%), Positives = 126/328 (38%), Gaps = 44/328 (13%)

Query: 70  SLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPS---IRKSGTGNIFIKNLD 126
           S+ YG+       D+ R LD                + +  +    R      + +KNL 
Sbjct: 1   SMEYGHHA---RPDSKRPLD-------EGSPAAAGLTSKKANEALTRNRELTTVLVKNLP 50

Query: 127 KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDK 186
           KS +   ++  F   G I+   +A     ++  F  ++F   + A  AI K + ++    
Sbjct: 51  KSYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITKTHKVV-GQN 108

Query: 187 QVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGD 245
           ++ V H                  +++ N   S T  +++ +  +   +  ++ +     
Sbjct: 109 EIIVSHL-------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF 155

Query: 246 GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKET 305
             S+ F +++  + +DA   VE LNG K +        +    + ++             
Sbjct: 156 NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR-----------TD 204

Query: 306 VDKFQGLNLYIKNLGDSIDDEK-LKELFSEFGTITSCKVMRD--PSGISKGSGFVAFSTP 362
               +G  + I+NL   + DE  L+E F  FG+I    +         +    F+ F   
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK 264

Query: 363 EEASRALAEMNGKMIVSKPLYVAVAQRK 390
           + A RAL +MN  ++ ++ + V++A +K
Sbjct: 265 DSAERAL-QMNRSLLGNREISVSLADKK 291

>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 =  264 bits (676), Expect = 1e-83
 Identities = 54/264 (20%), Positives = 111/264 (42%), Gaps = 20/264 (7%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T++ V +L  +   +++Y  F   G ++ V V      +++  +  + +A    A  A+ 
Sbjct: 42  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAIT 99

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI-LSCK 148
             +   +    I + +              +++ N   S   + + D       + LS +
Sbjct: 100 KTHKV-VGQNEIIVSHLTEC---------TLWMTNFPPSYTQRNIRDLLQDINVVALSIR 149

Query: 149 IATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG--HFLRKQERETVAIKT 206
           + +     S+ F ++   +KE A+  ++KLNG+ I    +     + L K +R   A   
Sbjct: 150 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSA-TL 208

Query: 207 KFNNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAA 263
           +   + ++NL     DE+ L++ F  +G+I    +         + C  F+ FEN D A 
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 268

Query: 264 KAVEALNGKKFDDREWYVGKAQKK 287
           +A++ +N     +RE  V  A KK
Sbjct: 269 RALQ-MNRSLLGNREISVSLADKK 291

>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 =  184 bits (470), Expect = 1e-53
 Identities = 39/248 (15%), Positives = 78/248 (31%), Gaps = 40/248 (16%)

Query: 157 SKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNL 216
           S  +G     +   ++  +D+ +                K+  E +    +   V VKNL
Sbjct: 1   SMEYGHHARPD---SKRPLDEGSPAAAGLTS--------KKANEALTRNRELTTVLVKNL 49

Query: 217 DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD 276
            +S     + K F   G I    V      K+  F  + F   D A  A+   +      
Sbjct: 50  PKSYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITKTHKV-VGQ 107

Query: 277 REWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG 336
            E  V    +                           L++ N   S     +++L  +  
Sbjct: 108 NEIIVSHLTEC-------------------------TLWMTNFPPSYTQRNIRDLLQDIN 142

Query: 337 TIT-SCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRA 395
            +  S ++       S+   ++  ++ E+A   + ++NG  I    L   V+    E+  
Sbjct: 143 VVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS-NPLEKSK 201

Query: 396 RLQAQFSQ 403
           R  +   +
Sbjct: 202 RTDSATLE 209

>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 =  166 bits (422), Expect = 7e-47
 Identities = 36/180 (20%), Positives = 76/180 (42%), Gaps = 9/180 (5%)

Query: 25  NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
           +     +L++ +   + T   + DL   +  V        L    S  + Y++  +  DA
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 85  ARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG-----NIFIKNLDKSI-DHKALHDTF 138
              ++ LN   +   ++    S+     +++ +       I I+NL   + D   L ++F
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232

Query: 139 SSFGNILSCKIATD--GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRK 196
             FG+I    I         +    F+ FENK+SA+ A+ ++N  L+ ++++ V    +K
Sbjct: 233 EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291

>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 =  369 bits (950), Expect = e-124
 Identities = 64/312 (20%), Positives = 115/312 (36%), Gaps = 37/312 (11%)

Query: 96  LNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSG 155
           L+ + IR    H +   R      I I+ L   + ++ +HD  S +  +  C +      
Sbjct: 3   LDPEEIRKRLEHTERQFRNRR--KILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----D 54

Query: 156 QSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKN 215
           + KG  FV   N E A+ AI+  +   + ++++ V             ++     + V N
Sbjct: 55  KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV------------QLQPTDALLCVAN 102

Query: 216 LDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKF 274
           L  S T +  +++   +G++    ++     G+SK +GF  +   D AA+A   L GK  
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162

Query: 275 DDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD-EKLKELFS 333
             R  YV            L  +                L +  L    +D + L    S
Sbjct: 163 GPRTLYVHWTDAGQLTPALLHSR---------------CLCVDRLPPGFNDVDALCRALS 207

Query: 334 EFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 393
              + T C++     G  KG   + + T E A  A  + +G  +    L V+        
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

Query: 394 RARLQAQFSQMR 405
           R+ L A  +   
Sbjct: 268 RSMLAALIAAQA 279

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  297 bits (762), Expect = 2e-96
 Identities = 52/273 (19%), Positives = 97/273 (35%), Gaps = 20/273 (7%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             + +  L  +VT+ +++DL S    +    V       +  G  +V   N   A  A++
Sbjct: 23  RKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAIN 75

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
             + + L  + + +     D          + + NL  S+  +   +    FG++  C +
Sbjct: 76  AFHQSRLRERELSVQLQPTDA--------LLCVANLPPSLTQQQFEELVRPFGSLERCFL 127

Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKF 208
                +GQSKG+GF ++  K+SA  A   L G  +  + ++V      Q           
Sbjct: 128 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPA---LLHS 184

Query: 209 NNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
             + V  L     D D L +      + T   +    DG+ K F  + +E A+ A +A +
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQ 244

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 300
             +G         V            L      
Sbjct: 245 QADGLSLGGSHLRVSFCAPGPPGRSMLAALIAA 277

>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 =  296 bits (761), Expect = 2e-97
 Identities = 117/224 (52%), Positives = 153/224 (68%), Gaps = 12/224 (5%)

Query: 14  GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
           GP G +   S   +   SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY
Sbjct: 1   GPLG-SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59

Query: 74  GYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKA 133
            YVN+  PADA RALD +NF  +  K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KA
Sbjct: 60  AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKA 119

Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHF 193
           L+DTFS+FGNILSCK+  D    SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F
Sbjct: 120 LYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178

Query: 194 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 237
             ++ERE   +  +    +  +         +    G  G I +
Sbjct: 179 KSRKEREA-ELGARAKEFYPYD---------VPDYAGSSGRIVT 212

>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 =  203 bits (518), Expect = 1e-61
 Identities = 61/209 (29%), Positives = 110/209 (52%), Gaps = 6/209 (2%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
              +PS       ++++ +L   +    L++ FS  G ILS ++  D  + +S G+ +V 
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63

Query: 165 FENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDED 224
           F+    A+ A+D +N  +I  K V +       +R+    K+   N+F+KNLD+S  ++ 
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIM----WSQRDPSLRKSGVGNIFIKNLDKSIDNKA 119

Query: 225 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
           L   F  +G I S  V+ D +  SK +GFV+FE  + A +A+E +NG   +DR+ +VG+ 
Sbjct: 120 LYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178

Query: 285 QKKSEREQELKGQFEQAMKETVDKFQGLN 313
           + + ERE EL  + ++     V  + G +
Sbjct: 179 KSRKEREAELGARAKEFYPYDVPDYAGSS 207

>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 =  199 bits (509), Expect = 2e-60
 Identities = 63/201 (31%), Positives = 103/201 (51%), Gaps = 18/201 (8%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           +N      +   +  +Q+                  ++ K    N++IKNL  SID++ L
Sbjct: 77  MNFDVIKGKPVRIMWSQRDP----------------SLRKSGVGNIFIKNLDKSIDNKAL 120

Query: 329 KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
            + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++  + ++V   +
Sbjct: 121 YDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 179

Query: 389 RKEERRARLQAQFSQMRPVAM 409
            ++ER A L A+  +  P  +
Sbjct: 180 SRKEREAELGARAKEFYPYDV 200

>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 = 95.8 bits (239), Expect = 1e-22
 Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 1/89 (1%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
             +   +LY+ +L   + +  L E FS  G I S +V RD  +  S G  +V F  P +A
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70

Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEERR 394
            RAL  MN  +I  KP+ +  +QR    R
Sbjct: 71  ERALDTMNFDVIKGKPVRIMWSQRDPSLR 99

>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 =  260 bits (667), Expect = 3e-84
 Identities = 47/162 (29%), Positives = 87/162 (53%), Gaps = 2/162 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
            LYVG+LD  +T+  L   F   G + ++++  D    +++ Y +V Y    DA  AL  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQT 60

Query: 91  LNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA 150
           LN   + N  ++I ++ +        T N+F+ +L+ ++D + L + F  F + LS  + 
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 120

Query: 151 TDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG 191
            D  +G S+G+GFV F +++ AQNA+D + G  +N + + + 
Sbjct: 121 WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162

>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 =  205 bits (524), Expect = 4e-63
 Identities = 50/180 (27%), Positives = 94/180 (52%), Gaps = 17/180 (9%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NLD++ T++ LK+ F   G I +  +M D + K+  + FV +  + DA  A++ LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 271 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 330
           GK+ ++    +  A +  +   +                   NL++ +L  ++DDE L+ 
Sbjct: 63  GKQIENNIVKINWAFQSQQSSSD----------------DTFNLFVGDLNVNVDDETLRN 106

Query: 331 LFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 389
            F +F +  S  VM D  +G S+G GFV+F++ ++A  A+  M G+ +  +PL +  A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 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 =  176 bits (449), Expect = 3e-52
 Identities = 48/168 (28%), Positives = 83/168 (49%), Gaps = 5/168 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++ NLDK+I    L   F   G I + KI  D + ++  + FV++     A  A+  LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 239
           G  I +  V +    + Q+           N+FV +L+ +  DE L+  F ++ +  S  
Sbjct: 63  GKQIENNIVKINWAFQSQQSS----SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 240 VMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK 286
           VM D   G S+ +GFV+F + DDA  A++++ G+  + R   +  A K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 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 =  100 bits (252), Expect = 5e-25
 Identities = 23/81 (28%), Positives = 42/81 (51%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+ NL  +I ++ LK+ F   G I + K+M D +  +    FV +    +A+ AL  +N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 374 GKMIVSKPLYVAVAQRKEERR 394
           GK I +  + +  A + ++  
Sbjct: 63  GKQIENNIVKINWAFQSQQSS 83

>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 = 93.7 bits (234), Expect = 2e-22
 Identities = 28/78 (35%), Positives = 44/78 (56%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L+VGDL+ NV D  L + F      LS  V  D+ T  S GYG+V++ +  DA  A+D 
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 91  LNFTPLNNKSIRIMYSHR 108
           +    LN + +RI ++ +
Sbjct: 149 MQGQDLNGRPLRINWAAK 166

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  255 bits (653), Expect = 2e-81
 Identities = 48/196 (24%), Positives = 97/196 (49%), Gaps = 11/196 (5%)

Query: 108 RDPSIRKSG----TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGF 162
           R  + ++ G       +++ ++   +    +   F+ FG I S  ++ D  + + KGF F
Sbjct: 15  RGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAF 74

Query: 163 VQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLD 217
           V++E  E+AQ A++++N +++  + + VG      + + +  +       FN ++V ++ 
Sbjct: 75  VEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVH 134

Query: 218 ESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDD 276
           +  +D+D+K +F  +G I SA + RD   GK K +GF+ +E A  +  AV ++N      
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 194

Query: 277 REWYVGKAQKKSEREQ 292
           +   VGKA        
Sbjct: 195 QYLRVGKAVTPPMPLL 210

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  232 bits (593), Expect = 1e-72
 Identities = 47/213 (22%), Positives = 90/213 (42%), Gaps = 14/213 (6%)

Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 239
             +   +Q+  G   ++Q           + V+V ++     ++ +++ F  +G I S  
Sbjct: 5   ASMTGGQQMGRGSAAQRQGALA-----IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSID 59

Query: 240 VMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 298
           +  D    K K F FV +E  + A  A+E +N      R   VG+     + +  +    
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 119

Query: 299 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFV 357
           E+A            +Y+ ++   + D+ +K +F  FG I S  + RDP +G  KG GF+
Sbjct: 120 EEARAFN-------RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172

Query: 358 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 390
            +   + +  A++ MN   +  + L V  A   
Sbjct: 173 EYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  204 bits (520), Expect = 7e-62
 Identities = 43/193 (22%), Positives = 89/193 (46%), Gaps = 10/193 (5%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           AA   G   + + +YVG + + + +  +   F+  G + S+ +  D  T +  G+ +V Y
Sbjct: 18  AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 77

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYSH----RDPSIRK-----SGTGNIFIKNLDKSI 129
             P  A  AL+ +N   L  ++I++          P I +          I++ ++ + +
Sbjct: 78  EVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDL 137

Query: 130 DHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV 188
               +   F +FG I S  +A D  +G+ KG+GF+++E  +S+Q+A+  +N   +  + +
Sbjct: 138 SDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197

Query: 189 FVGHFLRKQERET 201
            VG  +       
Sbjct: 198 RVGKAVTPPMPLL 210

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  109 bits (275), Expect = 2e-27
 Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 1/107 (0%)

Query: 301 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
           A +          +Y+ ++   + ++ +++ F+ FG I S  +  D  +   KG  FV +
Sbjct: 18  AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 77

Query: 360 STPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 406
             PE A  AL +MN  M+  + + V       + +  +     + R 
Sbjct: 78  EVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 97.0 bits (242), Expect = 5e-23
 Identities = 20/109 (18%), Positives = 46/109 (42%)

Query: 3   QIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC 62
            I+V   + +     +    +        +YV  +  +++D  +  +F   G++ S  + 
Sbjct: 99  NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLA 158

Query: 63  RDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPS 111
           RD +T +  GYG++ Y     +  A+  +N   L  + +R+  +   P 
Sbjct: 159 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM 207

>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 =  248 bits (636), Expect = 2e-79
 Identities = 57/164 (34%), Positives = 94/164 (57%), Gaps = 5/164 (3%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +   LF  +G++ S ++ RD  T +SLGYG+VNY +P DA +A++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            LN   L  K+I++ Y+   PS       N+++  L K++  K L   FS +G I++ +I
Sbjct: 63  TLNGLRLQTKTIKVSYA--RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120

Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLIN--DKQVFV 190
             D  +G S+G GF++F+ +  A+ AI  LNG   +   + + V
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164

>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 =  207 bits (528), Expect = 1e-63
 Identities = 53/182 (29%), Positives = 93/182 (51%), Gaps = 22/182 (12%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG +   +   V  A+  S   +                    NLY+  L  ++  ++L
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIR------------------DANLYVSGLPKTMTQKEL 105

Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA 385
           ++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  +NG+     ++P+ V 
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

Query: 386 VA 387
            A
Sbjct: 166 FA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  170 bits (434), Expect = 5e-50
 Identities = 49/170 (28%), Positives = 89/170 (52%), Gaps = 10/170 (5%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++  +     F S G I SCK+  D  +GQS G+GFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 237
           LNG+ +  K + V +          A      N++V  L ++ T ++L+++F +YG I +
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRDA------NLYVSGLPKTMTQKELEQLFSQYGRIIT 117

Query: 238 AVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFD--DREWYVGKA 284
           + ++ D   G S+  GF+ F+   +A +A++ LNG+K         V  A
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  102 bits (256), Expect = 2e-25
 Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
           +NG  + +K + V+ A+     
Sbjct: 64  LNGLRLQTKTIKVSYARPSSAS 85

>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 = 81.1 bits (201), Expect = 4e-18
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 2/88 (2%)

Query: 20  AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
           A  S       +LYV  L   +T  +L  LFSQ G++++ R+  D  T  S G G++ + 
Sbjct: 79  ARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 138

Query: 80  NPADAARALDVLNFTPLN--NKSIRIMY 105
              +A  A+  LN    +   + I + +
Sbjct: 139 KRIEAEEAIKGLNGQKPSGATEPITVKF 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 =  246 bits (631), Expect = 2e-77
 Identities = 54/250 (21%), Positives = 93/250 (37%), Gaps = 37/250 (14%)

Query: 186 KQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD 245
             + +  FL+  E+      T+   +FV NL    T+ED K++F  YG  +   + RD  
Sbjct: 4   FTIDIKSFLKPGEKT----YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-- 57

Query: 246 GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKET 305
              + FGF+  E+   A  A   L+G     R   +  A                     
Sbjct: 58  ---RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT-------------------- 94

Query: 306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 365
                G  L +KNL   + +E L++ FS+FG +    V+ D  G + G GFV F+    A
Sbjct: 95  ----HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA 150

Query: 366 SRALAEMNGKMIV----SKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYP 421
            +AL        +     +P+ V   ++ ++     +    + +        PPR     
Sbjct: 151 RKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPG 210

Query: 422 PGPSGLGQQF 431
                   ++
Sbjct: 211 TFEFEYASRW 220

>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 =  242 bits (619), Expect = 1e-75
 Identities = 55/278 (19%), Positives = 109/278 (39%), Gaps = 46/278 (16%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             L+VG+L  ++T+     LF + G+   V + RD       G+G++   +   A  A  
Sbjct: 23  CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKA 76

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            L+ T L ++ +RI ++             + +KNL   + ++ L   FS FG +    +
Sbjct: 77  ELDGTILKSRPLRIRFATHGA--------ALTVKNLSPVVSNELLEQAFSQFGPVEKAVV 128

Query: 150 ATDGSGQSKGFGFVQFENKESAQNAIDKLNG----MLINDKQVFVGHFLRKQERETVAIK 205
             D  G++ G GFV+F  K  A+ A+++       +    + V V    +  + + +  K
Sbjct: 129 VVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEK 188

Query: 206 T-KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
             +    + K  ++          F + GT       R                     K
Sbjct: 189 LMQKTQQYHKEREQPP-------RFAQPGTFEFEYASR--------------------WK 221

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 302
           A++ +  ++ +  +  + +A++K E E E      Q M
Sbjct: 222 ALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLM 259

>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 =  200 bits (511), Expect = 5e-60
 Identities = 48/256 (18%), Positives = 95/256 (37%), Gaps = 40/256 (15%)

Query: 98  NKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQS 157
             +I I    +      +    +F+ NL   I  +     F  +G      I  D     
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57

Query: 158 KGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLD 217
           +GFGF++ E++  A+ A  +L+G ++  + + +    R               + VKNL 
Sbjct: 58  RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI----RFATHGA--------ALTVKNLS 105

Query: 218 ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF--- 274
              ++E L++ F ++G +  AVV+ D  G++   GFV F     A KA+E      F   
Sbjct: 106 PVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLT 165

Query: 275 -DDREWYVGKAQKKSEREQELKGQFEQAMK-------------------ETVDKFQGLNL 314
              R   V   ++  + +   +   ++  +                   E   +++ L+ 
Sbjct: 166 TTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDE 225

Query: 315 YIKNLGDSIDDEKLKE 330
             K   + +D    + 
Sbjct: 226 MEKQQREQVDRNIREA 241

>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 = 72.4 bits (178), Expect = 2e-14
 Identities = 25/118 (21%), Positives = 43/118 (36%), Gaps = 3/118 (2%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +L V +L   V++  L   FSQ G V    V  D    R+ G G+V +A    A +AL
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL 154

Query: 89  DVLN-FTPLNNKSIRIMY-SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
           +       L   + R +     +    + G     ++   +    +     F+  G  
Sbjct: 155 ERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTF 212

>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 =  234 bits (599), Expect = 5e-74
 Identities = 41/182 (22%), Positives = 79/182 (43%), Gaps = 9/182 (4%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           SH       +   N+FI NL+ +     L    S         +    +G ++ FG+V F
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDL 225
           E+ E  + A+ +L G+ +   ++ +     +  ++          +  KNL  + T+++L
Sbjct: 62  ESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKK----VRAARTLLAKNLSFNITEDEL 116

Query: 226 KKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ 285
           K++F +   I     +   DGKSK   ++ F++  DA K +E   G + D R   +    
Sbjct: 117 KEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172

Query: 286 KK 287
           +K
Sbjct: 173 EK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  219 bits (561), Expect = 2e-68
 Identities = 46/186 (24%), Positives = 80/186 (43%), Gaps = 21/186 (11%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
            T   N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  K
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 324
           A+E L G K    E  + K + +  ++                      L  KNL  +I 
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGRDSKKVR----------------AARTLLAKNLSFNIT 112

Query: 325 DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
           +++LKE+F +   I     +    G SKG  ++ F +  +A + L E  G  I  + + +
Sbjct: 113 EDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

Query: 385 AVAQRK 390
                K
Sbjct: 169 YYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  184 bits (470), Expect = 3e-55
 Identities = 34/167 (20%), Positives = 74/167 (44%), Gaps = 6/167 (3%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            +L++G+L+ N + ++L    S++     + V     T  +  +GYV++ +  D  +AL+
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE 72

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
            L    +    I++       S +      +  KNL  +I    L + F     I     
Sbjct: 73  -LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL--- 128

Query: 150 ATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRK 196
                G+SKG  +++F+++  A+  +++  G  I+ + V + +   K
Sbjct: 129 -VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  108 bits (271), Expect = 2e-27
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 304 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 363
           E  +     NL+I NL  +    +LK   SE        V+   +G ++  G+V F + E
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65

Query: 364 EASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           +  +AL E+ G  +    + +   + ++ ++ R
Sbjct: 66  DLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVR 97

>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 = 80.0 bits (198), Expect = 1e-17
 Identities = 17/80 (21%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +L   +L FN+T+ +L ++F    ++  V         +S G  Y+ + + ADA + L
Sbjct: 99  ARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNL 153

Query: 89  DVLNFTPLNNKSIRIMYSHR 108
           +      ++ +S+ + Y+  
Sbjct: 154 EEKQGAEIDGRSVSLYYTGE 173

>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 =  232 bits (594), Expect = 3e-73
 Identities = 45/184 (24%), Positives = 81/184 (44%), Gaps = 20/184 (10%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAV 266
            +FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 267 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
            AL+  K      +  + +                  E  +  +   L+I  +     + 
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADS--------------EKNNAVEDRKLFIGMISKKCTEN 110

Query: 327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---SKPLY 383
            ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+    +   S P+ 
Sbjct: 111 DIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170

Query: 384 VAVA 387
           V  A
Sbjct: 171 VKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  201 bits (513), Expect = 2e-61
 Identities = 35/164 (21%), Positives = 69/164 (42%), Gaps = 7/164 (4%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD---GSGQSKGFGFVQFENKESA 171
           S    +F+  + ++   K L + F  +G +    +  D      QSKG  FV F  +++A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 172 QNAIDKLNGMLINDKQVFVGHF-LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFG 230
             A + L+ M +               E+       +   +F+  + +  T+ D++ +F 
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSEKNN---AVEDRKLFIGMISKKCTENDIRVMFS 117

Query: 231 EYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF 274
            +G I    ++R  DG S+   FV F     A  A++A++  + 
Sbjct: 118 SFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQT 161

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  173 bits (441), Expect = 6e-51
 Identities = 42/169 (24%), Positives = 69/169 (40%), Gaps = 9/169 (5%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLST--RRSLGYGYVNYANPADAARA 87
             ++VG +    ++  L +LF Q G V  + V RD S    +S G  +V +     A  A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 88  LDVLNFTPLNNKS---IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
            + L+   +       I++  +  + +        +FI  + K      +   FSSFG I
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122

Query: 145 LSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNG---MLINDKQVFV 190
             C+I     G S+G  FV F  +  AQ AI  ++    M      + V
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171

>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 (252), Expect = 7e-25
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPEEASRAL 369
            +++  +  +  ++ L+ELF ++G +    V+RD S     SKG  FV F T + A  A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRAR 396
             ++   ++    +    +  +  +  
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNN 91

>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 =  232 bits (593), Expect = 3e-73
 Identities = 51/164 (31%), Positives = 88/164 (53%), Gaps = 5/164 (3%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  ++TD +LY LF  +G + + R+ RD  T  S GY +V++ +  D+ RA+ 
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
           VLN   + NK +++ Y+   P        N+++ NL ++I    L   F  +G+I+   I
Sbjct: 64  VLNGITVRNKRLKVSYA--RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121

Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLIN--DKQVFV 190
             D  +G+ +G  FV++  +E AQ AI  LN ++     + + V
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  226 bits (578), Expect = 5e-71
 Identities = 52/182 (28%), Positives = 90/182 (49%), Gaps = 22/182 (12%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
           LNG    ++   V  A+   E  ++                   NLY+ NL  +I D++L
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDDQL 106

Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA 385
             +F ++G+I    ++RD  +G  +G  FV ++  EEA  A++ +N  +    S+PL V 
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166

Query: 386 VA 387
           +A
Sbjct: 167 LA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  193 bits (492), Expect = 2e-58
 Identities = 50/174 (28%), Positives = 88/174 (50%), Gaps = 10/174 (5%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
           +   N+ +  L + +  + L+  F + G I +C+I  D  +G S G+ FV F ++  +Q 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG 233
           AI  LNG+ + +K++ V +     E        K  N++V NL  + TD+ L  IFG+YG
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGESI------KDTNLYVTNLPRTITDDQLDTIFGKYG 114

Query: 234 TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFD--DREWYVGKA 284
           +I    ++RD   G+ +   FV +   ++A +A+ ALN    +   +   V  A
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  110 bits (278), Expect = 2e-28
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F++  ++ RA+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 372 MNGKMIVSKPLYVAVAQRKEERR 394
           +NG  + +K L V+ A+   E  
Sbjct: 65  LNGITVRNKRLKVSYARPGGESI 87

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 81.5 bits (202), Expect = 3e-18
 Identities = 23/75 (30%), Positives = 35/75 (46%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
            T+LYV +L   +TD QL  +F + G ++   + RD  T R  G  +V Y    +A  A+
Sbjct: 89  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148

Query: 89  DVLNFTPLNNKSIRI 103
             LN       S  +
Sbjct: 149 SALNNVIPEGGSQPL 163

>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 =  204 bits (522), Expect = 2e-62
 Identities = 41/191 (21%), Positives = 81/191 (42%), Gaps = 10/191 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSA------VVMRDGDGKSKCFGFVNFENADDAAK 264
           ++V N+    T+E +   F     +          V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 265 AVEALNGKKFDDREWYVGKAQKKSERE--QELKGQFEQAMKETVDKFQGLNLYIKNLGDS 322
           A+ A +G  F  +   + +           E    +   +  TV       L+I  L + 
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 323 IDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP 381
           ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K 
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 382 LYVAVAQRKEE 392
           L V  A    +
Sbjct: 186 LLVQRASVGAK 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 =  169 bits (430), Expect = 3e-49
 Identities = 31/191 (16%), Positives = 79/191 (41%), Gaps = 22/191 (11%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG------SGQSKGFGFVQFENKESAQN 173
           +++ N+   I  +A+ D F++   +     A           Q K F F++F + +    
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQERETVA--------------IKTKFNNVFVKNLDES 219
           A+   +G++   + + +      Q    ++              +    + +F+  L   
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDRE 278
             D+ +K++   +G + +  +++D   G SK + F  + + +   +A+  LNG +  D++
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 279 WYVGKAQKKSE 289
             V +A   ++
Sbjct: 186 LLVQRASVGAK 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 =  159 bits (404), Expect = 2e-45
 Identities = 33/186 (17%), Positives = 75/186 (40%), Gaps = 25/186 (13%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSV-----RVCRDLSTRRSLGYGYVNYANPADAA 85
            LYVG++ F +T+  + D F+   ++  +          +   +   + ++ + +  +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 86  RALDVLNFTPLNNKSIRIMYSH------------------RDPSIRKSGTGNIFIKNLDK 127
           +A+   +      +S++I   H                     ++       +FI  L  
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 128 SIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDK 186
            ++   + +  +SFG + +  +  D  +G SKG+ F ++ +      AI  LNGM + DK
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184

Query: 187 QVFVGH 192
           ++ V  
Sbjct: 185 KLLVQR 190

>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 = 80.1 bits (198), Expect = 2e-17
 Identities = 19/108 (17%), Positives = 39/108 (36%), Gaps = 8/108 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCK------VMRDPSGISKGSGFVAFSTPEEASR 367
           LY+ N+   I +E + + F+    +          V+       K   F+ F + +E ++
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 368 ALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPP 415
           A+A  +G +   + L +      +          S   P  +   VP 
Sbjct: 67  AMA-FDGIIFQGQSLKIRRPHDYQPLPGM-SENPSVYVPGVVSTVVPD 112

>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 =  195 bits (498), Expect = 3e-59
 Identities = 34/168 (20%), Positives = 74/168 (44%), Gaps = 9/168 (5%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSV-----RVCRDLSTRRSLGYGYVNYANPADAA 85
            LYVG++ F +T+  + D F+   ++  +          +   +   + ++ + +  +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 86  RALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNIL 145
           +A+   +      +S++I   H        G   +FI  L   ++   + +  +SFG + 
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQP--LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLK 122

Query: 146 SCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGH 192
           +  +  D  +G SKG+ F ++ +      AI  LNGM + DK++ V  
Sbjct: 123 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  167 bits (424), Expect = 1e-48
 Identities = 39/184 (21%), Positives = 76/184 (41%), Gaps = 26/184 (14%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSA------VVMRDGDGKSKCFGFVNFENADDAAK 264
           ++V N+    T+E +   F     +          V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 324
           A+ A +G  F  +   + +           K                  L+I  L + ++
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHK------------------LFIGGLPNYLN 107

Query: 325 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 383
           D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K L 
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167

Query: 384 VAVA 387
           V  A
Sbjct: 168 VQRA 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 =  164 bits (418), Expect = 9e-48
 Identities = 31/172 (18%), Positives = 74/172 (43%), Gaps = 14/172 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG------SGQSKGFGFVQFENKESAQN 173
           +++ N+   I  +A+ D F++   +     A           Q K F F++F + +    
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG 233
           A+   +G++   + + +      Q           + +F+  L     D+ +K++   +G
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLP------GAHKLFIGGLPNYLNDDQVKELLTSFG 119

Query: 234 TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
            + +  +++D   G SK + F  + + +   +A+  LNG +  D++  V +A
Sbjct: 120 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 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 = 72.3 bits (178), Expect = 5e-15
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 7/87 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCK------VMRDPSGISKGSGFVAFSTPEEASR 367
           LY+ N+   I +E + + F+    +          V+       K   F+ F + +E ++
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 368 ALAEMNGKMIVSKPLYVAVAQRKEERR 394
           A+A  +G +   + L +      +   
Sbjct: 67  AMA-FDGIIFQGQSLKIRRPHDYQPLP 92

>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 =  171 bits (436), Expect = 4e-51
 Identities = 64/111 (57%), Positives = 84/111 (75%), Gaps = 3/111 (2%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
            G+GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+  D    SKG+GFV FE +E+A+ A
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERA 61

Query: 175 IDKLNGMLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDE 223
           I+K+NGML+ND++VFVG F  ++ERE    A   +F NV++KN    +T  
Sbjct: 62  IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score =  135 bits (343), Expect = 5e-38
 Identities = 41/118 (34%), Positives = 65/118 (55%), Gaps = 11/118 (9%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
            N+F+KNLD+S  ++ L   F  +G I S  V+ D +  SK +GFV+FE  + A +A+E 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEK 64

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
           +NG   +DR+ +VG+ + + ERE EL  + ++            N+YIKN G      
Sbjct: 65  MNGMLLNDRKVFVGRFKSRKEREAELGARAKEFT----------NVYIKNFGPGSTRA 112

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score =  127 bits (321), Expect = 5e-35
 Identities = 42/98 (42%), Positives = 62/98 (63%), Gaps = 1/98 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65

Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMG 410
           NG ++  + ++V   + ++ER A L A+  +   V + 
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIK 103

>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 = 96.5 bits (241), Expect = 4e-24
 Identities = 28/105 (26%), Positives = 50/105 (47%), Gaps = 8/105 (7%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++ +LD ++ +  LYD FS  G +LS +V  D     S GYG+V++     A RA++ +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 92  NFTPLNNKSIRIMY------SHRDPSIRKSGTGNIFIKNLDKSID 130
           N   LN++ + +           +   R     N++IKN      
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110

>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 =  167 bits (424), Expect = 2e-49
 Identities = 32/109 (29%), Positives = 51/109 (46%)

Query: 288 SEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP 347
           S     LK    QA      +    NLYI NL  S+D+++L+ +   FG + S +++RD 
Sbjct: 2   SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61

Query: 348 SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           SG S+G GF    + E+    +   NGK I + P   A  +    + + 
Sbjct: 62  SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSG 110

>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 =  119 bits (301), Expect = 3e-32
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 196 KQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVN 255
           +  ++    +    N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF  
Sbjct: 16  QMAKQQ---EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFAR 72

Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSER 290
            E+ +     +   NGK            +    +
Sbjct: 73  MESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 =  113 bits (285), Expect = 4e-30
 Identities = 25/106 (23%), Positives = 44/106 (41%), Gaps = 4/106 (3%)

Query: 94  TPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG 153
           + L    ++     +    ++    N++I NL  S+D + L +    FG ++S +I  D 
Sbjct: 6   SGLKASGVQA----QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61

Query: 154 SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           SG S+G GF + E+ E  +  I   NG  I               +
Sbjct: 62  SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 = 76.1 bits (188), Expect = 6e-17
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+LY+ +L  ++ + +L ++    GQV+S R+ RD S+  S G G+    +       + 
Sbjct: 26  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIG 84

Query: 90  VLNFTPLNNKSIRI 103
             N   +       
Sbjct: 85  HFNGKFIKTPPGVS 98

>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 =  158 bits (403), Expect = 1e-46
 Identities = 55/97 (56%), Positives = 77/97 (79%), Gaps = 1/97 (1%)

Query: 301 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 360
           +  + + ++Q +NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS
Sbjct: 5   SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFS 63

Query: 361 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARL 397
           +PEEA++A+ EMNG+++ +KPLYVA+AQRKEER++  
Sbjct: 64  SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  131 bits (331), Expect = 1e-36
 Identities = 43/104 (41%), Positives = 61/104 (58%), Gaps = 4/104 (3%)

Query: 191 GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC 250
           G      +R T   + +  N++VKNLD+   DE L+K F  +GTITSA VM +  G+SK 
Sbjct: 1   GSSGSSGDRIT---RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKG 56

Query: 251 FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQEL 294
           FGFV F + ++A KAV  +NG+    +  YV  AQ+K ER+   
Sbjct: 57  FGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  110 bits (278), Expect = 3e-29
 Identities = 36/89 (40%), Positives = 54/89 (60%), Gaps = 1/89 (1%)

Query: 112 IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESA 171
           I +    N+++KNLD  ID + L   FS FG I S K+  +  G+SKGFGFV F + E A
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEA 68

Query: 172 QNAIDKLNGMLINDKQVFVGHFLRKQERE 200
             A+ ++NG ++  K ++V    RK+ER+
Sbjct: 69  TKAVTEMNGRIVATKPLYVALAQRKEERQ 97

>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 = 86.1 bits (214), Expect = 1e-20
 Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 3/88 (3%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYV +LD  + D +L   FS  G + S +V  +    RS G+G+V +++P +A +A+  +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           N   +  K + +  + R    R+SG  +
Sbjct: 76  NGRIVATKPLYVALAQRKEE-RQSGPSS 102

>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 =  158 bits (401), Expect = 3e-44
 Identities = 48/278 (17%), Positives = 95/278 (34%), Gaps = 13/278 (4%)

Query: 119 NIFIKNLDKSID----HKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
            I+I NL++ I      K+L+  FS FG IL   ++     + +G  FV F+   SA NA
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 68

Query: 175 IDKLNGMLINDKQVFVGHFLRKQER--ETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEY 232
           +  + G    DK + + +     +   +      + +    K   +S      KK     
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 233 GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
           G       ++                     +                 G+    +   Q
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 293 ELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISK 352
           +L        +   +      L++ NL +  ++  L  LF++F      +++     I  
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI-- 246

Query: 353 GSGFVAFSTPEEASRALAEMNG-KMIVSKPLYVAVAQR 389
              FV F    +A  A   + G K+  +  + ++ A++
Sbjct: 247 --AFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>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 =  130 bits (328), Expect = 3e-34
 Identities = 38/205 (18%), Positives = 62/205 (30%), Gaps = 7/205 (3%)

Query: 313 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
            +YI NL + I  ++LK+    +FS+FG I    V R      +G  FV F     A+ A
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNA 68

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGP-SVPPRMPMYPPGPSGL 427
           L  M G     KP+ +  A+   +  A+++  F +               P       G 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 428 GQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGA 487
           G   + G     +          + +           P   +P          PG     
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 488 GPVQQTQQPLPIMPHQMPPRGHAYR 512
             +     P   +    P       
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLT 213

>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 =  121 bits (304), Expect = 7e-31
 Identities = 53/278 (19%), Positives = 89/278 (32%), Gaps = 30/278 (10%)

Query: 32  LYVGDLDFNVTD----SQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
           +Y+ +L+  +        LY +FSQ GQ+L + V R L  R   G  +V +   + A  A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATNA 68

Query: 88  LDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG------NIFIKNLDKSIDHKALHDTFSSF 141
           L  +   P  +K +RI Y+  D  I     G          K   KS +  A        
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 142 GNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG---------- 191
           G                                       +I    +  G          
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 192 --HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK 249
                +    + ++     + +F+ NL E T +  L  +F ++       ++        
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD--- 245

Query: 250 CFGFVNFENADDAAKAVEALNGKKF-DDREWYVGKAQK 286
              FV F+N   A  A +AL G K   +    +  A+K
Sbjct: 246 -IAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>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 = 97.6 bits (242), Expect = 1e-22
 Identities = 26/104 (25%), Positives = 51/104 (49%), Gaps = 6/104 (5%)

Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           + +++ NL+E    ++LKK    IF ++G I   +V R    K +   FV F+    A  
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATN 67

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDK 308
           A+ ++ G  F D+   +  A+  S+   ++KG F +  ++   +
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKR 111

>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 =  152 bits (385), Expect = 1e-43
 Identities = 28/146 (19%), Positives = 58/146 (39%), Gaps = 13/146 (8%)

Query: 262 AAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGD 321
                + +  +    RE   G+  ++      +   +E              +Y+KNL  
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNC-------RIYVKNLAK 55

Query: 322 SIDDEKLKELFSEFGTITS--CKVMRD----PSGISKGSGFVAFSTPEEASRALAEMNGK 375
            + ++ LK +F  +   +S   ++M D      G  KG  F+     + A++AL E NG 
Sbjct: 56  HVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGY 115

Query: 376 MIVSKPLYVAVAQRKEERRARLQAQF 401
           ++  KP+ V  A+    ++   + + 
Sbjct: 116 VLFGKPMVVQFARSARPKQDPKEGKR 141

>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 =  115 bits (290), Expect = 2e-30
 Identities = 29/140 (20%), Positives = 58/140 (41%), Gaps = 11/140 (7%)

Query: 171 AQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIK-----TKFNNVFVKNLDESTTDEDL 225
             +  D++    I+ +++  G   R++       +          ++VKNL +   ++DL
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62

Query: 226 KKIFGEYGTITSAV------VMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREW 279
           K IFG Y   +S        +    +G+ K   F+   N   AAKA++  NG     +  
Sbjct: 63  KYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM 122

Query: 280 YVGKAQKKSEREQELKGQFE 299
            V  A+    ++   +G+ +
Sbjct: 123 VVQFARSARPKQDPKEGKRK 142

>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 = 80.6 bits (199), Expect = 4e-18
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCK------IATDGSGQSKGFGFVQFENKESAQ 172
            I++KNL K +  K L   F  + +  S        I     G+ KG  F+   N+++A 
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQER 199
            A+ + NG ++  K + V      + +
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSARPK 133

>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 = 68.3 bits (167), Expect = 8e-14
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 5/93 (5%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLS-----VRVCRDLSTRRSLGYGYVNYANPADAAR 86
           +YV +L  +V +  L  +F +     S     +   R +   R  G  ++   N   AA+
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107

Query: 87  ALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           AL   N   L  K + + ++      +    G 
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSARPKQDPKEGK 140

>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 =  150 bits (381), Expect = 2e-43
 Identities = 30/103 (29%), Positives = 53/103 (51%), Gaps = 4/103 (3%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
            G  +++ NL   +  +KLKE+FS  G +    ++ D  G S+G G V F    EA +A+
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 412
           +  NG+++  +P++V + +R   +      +    RP   GPS
Sbjct: 74  SMFNGQLLFDRPMHVKMDERALPKGDFFPPE----RPQQSGPS 112

>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 =  126 bits (318), Expect = 1e-34
 Identities = 28/94 (29%), Positives = 46/94 (48%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + VFV NLD     + LK++F   G +  A ++ D DGKS+  G V FE + +A +A+  
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 302
            NG+   DR  +V   ++   +      +  Q  
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGDFFPPERPQQS 109

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score =  103 bits (260), Expect = 1e-26
 Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 2/98 (2%)

Query: 106 SHRDPSIRKSGTG--NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFV 163
           S       ++G     +F+ NLD  +  K L + FS  G ++   I  D  G+S+G G V
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTV 61

Query: 164 QFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
            FE    A  AI   NG L+ D+ + V    R   +  
Sbjct: 62  TFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGD 99

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 82.0 bits (203), Expect = 6e-19
 Identities = 21/90 (23%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 14  GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
           G +G +      + L ++++V +LD+ V   +L ++FS  G V+   +  D    +S G 
Sbjct: 1   GSSGSSGALQAGR-LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGI 58

Query: 74  GYVNYANPADAARALDVLNFTPLNNKSIRI 103
           G V +    +A +A+ + N   L ++ + +
Sbjct: 59  GTVTFEQSIEAVQAISMFNGQLLFDRPMHV 88

>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 =  150 bits (382), Expect = 2e-43
 Identities = 27/119 (22%), Positives = 49/119 (41%)

Query: 282 GKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC 341
           G  Q   + ++     F+           G  L + NL   + D  ++ELF+EFGT+   
Sbjct: 6   GGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 65

Query: 342 KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQ 400
            V  D SG S G+  V F    +A +A+ +  G  +  +P+ + +   + +        
Sbjct: 66  AVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 =  116 bits (292), Expect = 6e-31
 Identities = 26/89 (29%), Positives = 41/89 (46%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++ 
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQ 297
             G   D R   +     + + E      
Sbjct: 96  YKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 = 96.3 bits (240), Expect = 7e-24
 Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 1/98 (1%)

Query: 104 MYSHRDPSIRKSGTG-NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGF 162
           ++           TG  + + NLD  +    + + F+ FG +    +  D SG+S G   
Sbjct: 21  LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD 80

Query: 163 VQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           V FE +  A  A+ +  G+ ++ + + +     + + E
Sbjct: 81  VHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLE 118

>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 = 85.9 bits (213), Expect = 3e-20
 Identities = 30/102 (29%), Positives = 48/102 (47%), Gaps = 6/102 (5%)

Query: 7   QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS 66
           QH    SG  G     +G +     L V +LDF V+D+ + +LF++ G +    V  D  
Sbjct: 18  QHDLFDSGCGGGEGVETGAK-----LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-R 71

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR 108
           + RSLG   V++   ADA +A+      PL+ + + I     
Sbjct: 72  SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS 113

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score =  149 bits (379), Expect = 4e-43
 Identities = 33/107 (30%), Positives = 52/107 (48%), Gaps = 1/107 (0%)

Query: 294 LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISK 352
           L  Q   A     +  +G NL+I +L     D+ L ++F  FG + S KV  D  + +SK
Sbjct: 8   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

Query: 353 GSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQA 399
             GFV++  P  A  A+  MNG  I  K L V + + K + ++   +
Sbjct: 68  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 =  116 bits (292), Expect = 5e-31
 Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
            N+F+ +L +   D+DL ++F  +G + SA V  D     SKCFGFV+++N   A  A++
Sbjct: 26  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQEL 294
           ++NG +   +   V   + K++ +   
Sbjct: 86  SMNGFQIGMKRLKVQLKRSKNDSKSGP 112

>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 =  104 bits (262), Expect = 6e-27
 Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFE 166
                      N+FI +L +    + L   F  FGN++S K+  D  +  SK FGFV ++
Sbjct: 16  AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 75

Query: 167 NKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           N  SAQ AI  +NG  I  K++ V     K + +
Sbjct: 76  NPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 109

>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 = 86.6 bits (215), Expect = 1e-20
 Identities = 24/91 (26%), Positives = 42/91 (46%)

Query: 12  MSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSL 71
           ++  +  AAG+        +L++  L     D  L  +F   G V+S +V  D  T  S 
Sbjct: 8   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIR 102
            +G+V+Y NP  A  A+  +N   +  K ++
Sbjct: 68  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK 98

>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 =  151 bits (382), Expect = 2e-42
 Identities = 39/200 (19%), Positives = 77/200 (38%), Gaps = 26/200 (13%)

Query: 210 NVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
            + V NL+ E  T + L  +FG YG +    ++ +     K    V   + + A  A+  
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 60

Query: 269 LNGKKFDDREWYVGKA-------QKKSEREQELKGQFEQAMKETVDKFQGLN-------- 313
           LNG K   +   +  +        ++ + +Q L   +  +      K    N        
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 314 --LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
             L++ N+  S+ +E LK LFS  G +             +    +   + EEA +AL +
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQALID 177

Query: 372 MNGKMIV-SKPLYVAVAQRK 390
           ++   +  +  L V+ ++  
Sbjct: 178 LHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score =  139 bits (351), Expect = 4e-38
 Identities = 32/191 (16%), Positives = 70/191 (36%), Gaps = 37/191 (19%)

Query: 116 GTGNIFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           G   + + NL+ + +  ++L   F  +G++   KI  +     K    VQ  +   AQ A
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLA 57

Query: 175 IDKLNGMLINDKQVFVGHF------LRKQERETVAIKTKF-------------------- 208
           +  LNG  ++ K + +         L ++ +E   +   +                    
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 209 ---NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
                + + N+  S ++EDLK +F   G +           K +    +   + ++A +A
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQA 174

Query: 266 VEALNGKKFDD 276
           +  L+     +
Sbjct: 175 LIDLHNHDLGE 185

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score =  115 bits (290), Expect = 8e-30
 Identities = 38/201 (18%), Positives = 64/201 (31%), Gaps = 47/201 (23%)

Query: 29  TTSLYVGDLD-FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
            + L V +L+   VT   L+ LF   G V  V++  +           V  A+   A  A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57

Query: 88  LDVLNFTPLNNKSIRIMYSHRDPSIRKSG------------------------------- 116
           +  LN   L+ K IRI  S                                         
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 117 --TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
             +  + + N+  S+  + L   FSS G ++          + +    +Q  + E A  A
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQA 174

Query: 175 IDKLNGMLINDKQVFVGHFLR 195
           +  L+   + +      H LR
Sbjct: 175 LIDLHNHDLGE-----NHHLR 190

>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 = 83.4 bits (206), Expect = 2e-18
 Identities = 17/116 (14%), Positives = 44/116 (37%), Gaps = 5/116 (4%)

Query: 313 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
            L + NL  + +  + L  LF  +G +   K++ +     K +  V  +   +A  A++ 
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 60

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGL 427
           +NG  +  KP+ + +++ +  +  R   +   +        +             +
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116

>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 = 55.7 bits (134), Expect = 4e-09
 Identities = 16/93 (17%), Positives = 37/93 (39%), Gaps = 5/93 (5%)

Query: 15  PNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYG 74
               +         + +L++ ++  +V++  L  LFS  G V+          ++     
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMA 161

Query: 75  YVNYANPADAARALDVLNFTPL-NNKSIRIMYS 106
            +   +  +A +AL  L+   L  N  +R+ +S
Sbjct: 162 LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>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 =  149 bits (379), Expect = 3e-42
 Identities = 42/173 (24%), Positives = 83/173 (47%), Gaps = 11/173 (6%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
           +  +FI  L+       L + F  +G +   KI  D  +G+S+GFGF+ FE   S    +
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62

Query: 176 DKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTI 235
              +  +++ K +     + + E++          +FV  +      ++ ++ F ++GTI
Sbjct: 63  KTQH--ILDGKVIDPKRAIPRDEQDKT------GKIFVGGIGPDVRPKEFEEFFSQWGTI 114

Query: 236 TSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 287
             A +M D D G+S+ FGFV +++AD   +  +      F DR+  + +A+ +
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  145 bits (368), Expect = 8e-41
 Identities = 42/182 (23%), Positives = 90/182 (49%), Gaps = 23/182 (12%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L+  TT+++L++ FG+YGT+T   +M+D   G+S+ FGF++FE      + V+  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
           +    D +     +A  + E+++  K                  +++  +G  +  ++ +
Sbjct: 66  H--ILDGKVIDPKRAIPRDEQDKTGK------------------IFVGGIGPDVRPKEFE 105

Query: 330 ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
           E FS++GTI   ++M D  +G S+G GFV + + +   R   +        + + +  A+
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAE 164

Query: 389 RK 390
            +
Sbjct: 165 PR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  137 bits (347), Expect = 7e-38
 Identities = 38/168 (22%), Positives = 85/168 (50%), Gaps = 8/168 (4%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++G L+++ T+  L + F + G V  +++ +D +T RS G+G++++  P+     +   
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 92  NFTPLNNKSIRIMYSH-RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA 150
           +   L+ K I    +  RD   +   TG IF+  +   +  K   + FS +G I+  ++ 
Sbjct: 66  HI--LDGKVIDPKRAIPRDEQDK---TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120

Query: 151 TD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQ 197
            D  +GQS+GFGFV +++ ++      +   +   D+++ +     + 
Sbjct: 121 LDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAEPRH 167

>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 = 82.6 bits (205), Expect = 1e-18
 Identities = 24/92 (26%), Positives = 50/92 (54%), Gaps = 7/92 (7%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +   ++I  L     ++ L+E F ++GT+T  K+M+DP +G S+G GF++F  P      
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 369 LAEM---NGKMIVSKPLYVAVAQRKEERRARL 397
           +      +GK+I  K    A+ + ++++  ++
Sbjct: 62  VKTQHILDGKVIDPKR---AIPRDEQDKTGKI 90

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 66.0 bits (162), Expect = 8e-13
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 1/84 (1%)

Query: 20  AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
           A     Q  T  ++VG +  +V   +  + FSQ G ++  ++  D  T +S G+G+V Y 
Sbjct: 78  AIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137

Query: 80  NPADAARALDVLNFTPLNNKSIRI 103
           +     R      F    ++ I I
Sbjct: 138 SADAVDRVC-QNKFIDFKDRKIEI 160

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  149 bits (378), Expect = 4e-42
 Identities = 27/126 (21%), Positives = 50/126 (39%)

Query: 275 DDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSE 334
             R      ++ K   ++     F+           G  L + NL   + D  ++ELF+E
Sbjct: 52  GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAE 111

Query: 335 FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 394
           FGT+    V  D SG S G+  V F    +A +A+ +  G  +  +P+ + +   + +  
Sbjct: 112 FGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLE 171

Query: 395 ARLQAQ 400
                 
Sbjct: 172 HHHHHH 177

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  108 bits (271), Expect = 1e-27
 Identities = 28/106 (26%), Positives = 43/106 (40%)

Query: 192 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 251
           H L                + V NLD   +D D++++F E+GT+  A V  D  G+S   
Sbjct: 72  HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT 131

Query: 252 GFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQ 297
             V+FE   DA KA++   G   D R   +     + + E      
Sbjct: 132 ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 95.3 bits (237), Expect = 7e-23
 Identities = 25/135 (18%), Positives = 51/135 (37%), Gaps = 7/135 (5%)

Query: 66  STRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNL 125
             R ++  G  N   P    + L      P   +              ++G   + + NL
Sbjct: 44  RNRPAIARGGRNRPAPYSRPKPL------PDKWQHDLFDSGCGGGEGVETGA-KLLVSNL 96

Query: 126 DKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIND 185
           D  +    + + F+ FG +    +  D SG+S G   V FE +  A  A+ +  G+ ++ 
Sbjct: 97  DFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG 156

Query: 186 KQVFVGHFLRKQERE 200
           + + +     + + E
Sbjct: 157 RPMDIQLVASQIDLE 171

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 80.7 bits (199), Expect = 9e-18
 Identities = 30/104 (28%), Positives = 48/104 (46%), Gaps = 6/104 (5%)

Query: 7   QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS 66
           QH    SG  G     +G +     L V +LDF V+D+ + +LF++ G +    V  D  
Sbjct: 71  QHDLFDSGCGGGEGVETGAK-----LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-R 124

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP 110
           + RSLG   V++   ADA +A+      PL+ + + I       
Sbjct: 125 SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  141 bits (357), Expect = 5e-40
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 1/98 (1%)

Query: 292 QELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGI 350
             L      A  + ++  +G NL+I +L     D  L   F  FG + S KV  D  + +
Sbjct: 21  VALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSL 80

Query: 351 SKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
           SK  GFV+F  P+ A  A+  MNG  + +K L V + +
Sbjct: 81  SKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  107 bits (268), Expect = 8e-28
 Identities = 35/115 (30%), Positives = 57/115 (49%), Gaps = 4/115 (3%)

Query: 78  YANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG-NIFIKNLDKSIDHKALHD 136
              P   + +   L+ +PL + ++    +       +   G N+FI +L +      L  
Sbjct: 2   AGLPQFGSASA--LSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLAS 59

Query: 137 TFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           TF  FGN++S K+  D  +  SK FGFV F+N +SAQ AI  +NG  +  K++ V
Sbjct: 60  TFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  106 bits (267), Expect = 1e-27
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N+F+ +L +  TD DL   F  +G + SA V  D     SKCFGFV+F+N D A  A++A
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101

Query: 269 LNGKKFDDREWYVGKAQ 285
           +NG +   +   V   +
Sbjct: 102 MNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 89.0 bits (221), Expect = 2e-21
 Identities = 25/96 (26%), Positives = 41/96 (42%)

Query: 7   QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS 66
                +S     AAG         +L++  L    TD+ L   F   G V+S +V  D  
Sbjct: 18  LASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ 77

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR 102
           T  S  +G+V++ NP  A  A+  +N   +  K ++
Sbjct: 78  TSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK 113

>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 =  140 bits (356), Expect = 5e-40
 Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 5/105 (4%)

Query: 289 EREQELKGQ-----FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKV 343
            R ++L  +     F+           G  L + NL   + D  ++ELF+EFGT+    V
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 344 MRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
             D SG S G+  V F    +A +A+ + NG  +  +P+ + +  
Sbjct: 62  HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score =  111 bits (280), Expect = 2e-29
 Identities = 29/94 (30%), Positives = 42/94 (44%)

Query: 192 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 251
           H L        A       + V NLD   +D D++++F E+GT+  A V  D  G+S   
Sbjct: 13  HDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGT 72

Query: 252 GFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ 285
             V+FE   DA KA++  NG   D R   +    
Sbjct: 73  ADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 95.0 bits (237), Expect = 1e-23
 Identities = 21/85 (24%), Positives = 38/85 (44%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           S           G + + NLD  +    + + F+ FG +    +  D SG+S G   V F
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHF 77

Query: 166 ENKESAQNAIDKLNGMLINDKQVFV 190
           E K  A  A+ + NG+ ++ + + +
Sbjct: 78  ERKADALKAMKQYNGVPLDGRPMNI 102

>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 = 86.6 bits (215), Expect = 1e-20
 Identities = 32/97 (32%), Positives = 50/97 (51%), Gaps = 6/97 (6%)

Query: 7   QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS 66
           QH    SG  G A   +G +     L V +LDF V+D+ + +LF++ G +    V  D  
Sbjct: 12  QHDLFDSGFGGGAGVETGGK-----LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-R 65

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI 103
           + RSLG   V++   ADA +A+   N  PL+ + + I
Sbjct: 66  SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 102

>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 =  143 bits (364), Expect = 7e-40
 Identities = 47/195 (24%), Positives = 87/195 (44%), Gaps = 16/195 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L   TTDE L+  F ++GT+T  VVMRD +  +S+ FGFV +   ++   A+ A 
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74

Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
              K D R     +A  + + ++            TV K     +++  + +  ++  L+
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQR-------PGAHLTVKK-----IFVGGIKEDTEEHHLR 122

Query: 330 ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
           + F ++G I   ++M D  SG  +G  FV F   +   + +       +      V  A 
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKAL 181

Query: 389 RKEERRARLQAQFSQ 403
            K+E  +   +Q  +
Sbjct: 182 SKQEMASASSSQRGR 196

>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 =  138 bits (350), Expect = 6e-38
 Identities = 44/197 (22%), Positives = 76/197 (38%), Gaps = 4/197 (2%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
           S  +          +FI  L      ++L   F  +G +  C +  D  + +S+GFGFV 
Sbjct: 2   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61

Query: 165 FENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDED 224
           +   E    A++      ++ + V     + +++ +          +FV  + E T +  
Sbjct: 62  YATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120

Query: 225 LKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 283
           L+  F +YG I    +M D   GK + F FV F++ D   K V        +     V K
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRK 179

Query: 284 AQKKSEREQELKGQFEQ 300
           A  K E       Q  +
Sbjct: 180 ALSKQEMASASSSQRGR 196

>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 =  124 bits (313), Expect = 6e-33
 Identities = 48/173 (27%), Positives = 79/173 (45%), Gaps = 7/173 (4%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A++  
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGTGN----IFIKNLDKSIDHKALHDTFSSFGNILSC 147
               ++ + +    +      ++ G       IF+  + +  +   L D F  +G I   
Sbjct: 76  PHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134

Query: 148 KIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           +I TD GSG+ +GF FV F++ +S    + +     +N     V   L KQE 
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM 186

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  140 bits (355), Expect = 8e-40
 Identities = 32/102 (31%), Positives = 53/102 (51%), Gaps = 2/102 (1%)

Query: 304 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTP 362
            +       +L++ +L   +DD  L E F + + +    KV+ D +G+SKG GFV F+  
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 363 EEASRALAEMNGKMIV-SKPLYVAVAQRKEERRARLQAQFSQ 403
            E  RAL E  G + + SKP+ ++VA  K  R   +++  S 
Sbjct: 62  LEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  105 bits (264), Expect = 2e-27
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGE-YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           ++FV +L     D  L + F + Y +     V+ D  G SK +GFV F +  +  +A+  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 269 LNGKKF-DDREWYVGKAQKKSEREQELKGQ 297
             G      +   +  A  K+ R + ++  
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVESG 100

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 89.6 bits (223), Expect = 8e-22
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSS-FGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
           ++F+ +L   +D   L++ F   + +    K+  D +G SKG+GFV+F ++   + A+ +
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 178 LNG-MLINDKQVFVGHFLRKQER 199
             G + +  K V +   + K  R
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASR 93

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 76.5 bits (189), Expect = 3e-17
 Identities = 31/99 (31%), Positives = 46/99 (46%), Gaps = 3/99 (3%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQV-GQVLSVRVCRDLSTRRSLGYGYVNYA 79
           G+SG+     SL+VGDL  +V D  LY+ F +V       +V  D  T  S GYG+V + 
Sbjct: 1   GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFT 59

Query: 80  NPADAARALDVLN-FTPLNNKSIRIMYSHRDPSIRKSGT 117
           +  +  RAL        L +K +R+  +    S  K   
Sbjct: 60  DELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVE 98

>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 =  138 bits (350), Expect = 3e-39
 Identities = 35/89 (39%), Positives = 55/89 (61%), Gaps = 2/89 (2%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDG-SGQSKGFGFVQFENKESAQ 172
           SG+  IFI NLD  ID K L+DTFS+FG IL   KI  D  +G SKG+ F+ F + +++ 
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQERET 201
            AI+ +NG  + ++ + V +  +K  + +
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSKGS 91

>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 =  113 bits (286), Expect = 2e-30
 Identities = 30/88 (34%), Positives = 53/88 (60%), Gaps = 2/88 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDP-SGISKGSGFVAFSTPEEASRALA 370
            ++I NL   ID++ L + FS FG I    K+MRDP +G SKG  F+ F++ + +  A+ 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 371 EMNGKMIVSKPLYVAVAQRKEERRARLQ 398
            MNG+ + ++P+ V+ A +K+ + +   
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score =  104 bits (262), Expect = 4e-27
 Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 2/84 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
            +F+ NLD    ++ L   F  +G I     +MRD D G SK + F+NF + D +  A+E
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 268 ALNGKKFDDREWYVGKAQKKSERE 291
           A+NG+   +R   V  A KK  + 
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKG 90

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 90.3 bits (225), Expect = 4e-22
 Identities = 30/100 (30%), Positives = 56/100 (56%), Gaps = 6/100 (6%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSV-RVCRDLSTRRSLGYGYVNYA 79
           G+SG+    + +++G+LD  + +  LYD FS  G +L   ++ RD  T  S GY ++N+A
Sbjct: 1   GSSGS----SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFA 56

Query: 80  NPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           +   +  A++ +N   L N+ I + Y+ +  S + SG  +
Sbjct: 57  SFDASDAAIEAMNGQYLCNRPITVSYAFKKDS-KGSGPSS 95

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  137 bits (347), Expect = 1e-38
 Identities = 23/114 (20%), Positives = 47/114 (41%), Gaps = 7/114 (6%)

Query: 281 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 340
           +G +         L  +          +     L+++     + + +L E+F  FG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 341 CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 394
            K++        G  FV F   E A++A+ E++GK   ++PL V  ++   +R 
Sbjct: 61  VKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  117 bits (296), Expect = 1e-31
 Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNF 256
                   +     +FV+       + +L +IFG +G +    ++         F FV F
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEF 72

Query: 257 ENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
           E A+ AAKA+E ++GK F ++   V  ++  ++R +
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 86.2 bits (214), Expect = 1e-20
 Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFEN 167
                 +     +F++     +    L++ F  FG +   KI         GF FV+FE 
Sbjct: 22  HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEE 74

Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
            ESA  AI++++G    ++ + V +     +R
Sbjct: 75  AESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 75.0 bits (185), Expect = 1e-16
 Identities = 18/113 (15%), Positives = 44/113 (38%), Gaps = 8/113 (7%)

Query: 2   AQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRV 61
           +     H + +             +   T L+V     +V +S+L ++F   G +  V++
Sbjct: 4   SHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

Query: 62  CRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRK 114
                     G+ +V +     AA+A++ ++     N+ + ++YS       +
Sbjct: 64  LN--------GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108

>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 =  137 bits (347), Expect = 2e-38
 Identities = 27/96 (28%), Positives = 50/96 (52%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 266
               +F+  L+  T ++ LK +FG++G I+  ++++D   KS+ F F+ FEN  DA  A 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 267 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 302
           + +NGK    +   V +A+K S +    +     + 
Sbjct: 66  KDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSR 101

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score =  125 bits (316), Expect = 2e-34
 Identities = 26/112 (23%), Positives = 51/112 (45%)

Query: 306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 365
           V+      L+I  L    +++ LK +F + G I+   +++D +  S+G  F+ F  P +A
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRM 417
             A  +MNGK +  K + V  A++   +    +   +  R  +   S+    
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHH 113

>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 = 98.9 bits (247), Expect = 7e-25
 Identities = 24/89 (26%), Positives = 41/89 (46%)

Query: 112 IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESA 171
           +     G +FI  L++  + K L   F   G I    +  D + +S+GF F+ FEN   A
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 172 QNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           +NA   +NG  ++ K + V    +   + 
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>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 = 78.9 bits (195), Expect = 7e-18
 Identities = 24/89 (26%), Positives = 46/89 (51%), Gaps = 2/89 (2%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             L++G L+    +  L  +F + G +  V + +D  T +S G+ ++ + NPADA  A  
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAK 66

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
            +N   L+ K+I++  + + PS +  G  
Sbjct: 67  DMNGKSLHGKAIKVEQA-KKPSFQSGGRR 94

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  135 bits (343), Expect = 4e-38
 Identities = 28/101 (27%), Positives = 53/101 (52%), Gaps = 3/101 (2%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G   +     +LYVG+L  +VT+  +  LFSQ+G   S ++  + ++     Y +V +
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEF 62

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
               DAA AL  +N   +  K +++ ++   PS +KSG  +
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWA-TTPSSQKSGPSS 102

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 90.8 bits (226), Expect = 3e-22
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            ++V NL    T+  + ++F + G   S  ++ +       + FV F    DAA A+ A+
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAM 75

Query: 270 NGKKFDDREWYVGKAQKKSERE 291
           NG+K   +E  V  A   S ++
Sbjct: 76  NGRKILGKEVKVNWATTPSSQK 97

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 86.9 bits (216), Expect = 7e-21
 Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
           D  Q   LY+ NL   + +  + +LFS+ G   SCK++ + +  +    FV F    +A+
Sbjct: 11  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA 69

Query: 367 RALAEMNGKMIVSKPLYVAVAQRKEERR 394
            ALA MNG+ I+ K + V  A     ++
Sbjct: 70  AALAAMNGRKILGKEVKVNWATTPSSQK 97

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 73.1 bits (180), Expect = 6e-16
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
                     +++ NL + +    +   FS  G   SCK+ T+ +  +  + FV+F    
Sbjct: 8   MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHR 66

Query: 170 SAQNAIDKLNGMLINDKQV 188
            A  A+  +NG  I  K+V
Sbjct: 67  DAAAALAAMNGRKILGKEV 85

>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 =  140 bits (353), Expect = 4e-38
 Identities = 35/199 (17%), Positives = 72/199 (36%), Gaps = 37/199 (18%)

Query: 108 RDPSIRKSGTGNIFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFE 166
             P +  +G   + + NL+ + +  ++L   F  +G++   KI  +     K    VQ  
Sbjct: 25  AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMA 80

Query: 167 NKESAQNAIDKLNGMLINDKQVFVGHFLRK-----QERETVAIKTKF------------- 208
           +   AQ A+  LNG  ++ K + +     +     +E +     TK              
Sbjct: 81  DGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPG 140

Query: 209 -----------NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFE 257
                        + + N+  S ++EDLK +F   G +         D K      +   
Sbjct: 141 SKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK---MALIQMG 197

Query: 258 NADDAAKAVEALNGKKFDD 276
           + ++A +A+  L+     +
Sbjct: 198 SVEEAVQALIDLHNHDLGE 216

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score =  137 bits (345), Expect = 5e-37
 Identities = 36/201 (17%), Positives = 76/201 (37%), Gaps = 26/201 (12%)

Query: 209 NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           + + V NL+ E  T + L  +FG YG +    ++       K    V   + + A  A+ 
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQLAMS 90

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ----------------- 310
            LNG K   +   +  ++ ++ +      + +   K+  +                    
Sbjct: 91  HLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 150

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
              L++ N+  S+ +E LK LFS  G +             +    +   + EEA +AL 
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQALI 207

Query: 371 EMNGKMIV-SKPLYVAVAQRK 390
           +++   +  +  L V+ ++  
Sbjct: 208 DLHNHDLGENHHLRVSFSKST 228

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score =  113 bits (283), Expect = 1e-28
 Identities = 40/217 (18%), Positives = 65/217 (29%), Gaps = 47/217 (21%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLD-FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSL 71
               G  A         + L V +L+   VT   L+ LF   G V  V++          
Sbjct: 18  GSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI-----LFNKK 72

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG--------------- 116
               V  A+   A  A+  LN   L+ K IRI  S                         
Sbjct: 73  ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132

Query: 117 ------------------TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSK 158
                             +  + + N+  S+  + L   FSS G ++          + +
Sbjct: 133 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDR 189

Query: 159 GFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLR 195
               +Q  + E A  A+  L+   + +      H LR
Sbjct: 190 KMALIQMGSVEEAVQALIDLHNHDLGE-----NHHLR 221

>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 = 79.3 bits (195), Expect = 8e-17
 Identities = 22/107 (20%), Positives = 46/107 (42%), Gaps = 6/107 (5%)

Query: 313 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
            L + NL  + +  + L  LF  +G +   K++ +     K +  V  +   +A  A++ 
Sbjct: 36  VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 91

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 418
           +NG  +  KP+ + +++ +  +  R + Q  Q      G S   R  
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQLPR-EGQEDQGLTKDYGNSPLHRFK 137

>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 =  139 bits (350), Expect = 5e-38
 Identities = 28/204 (13%), Positives = 59/204 (28%), Gaps = 29/204 (14%)

Query: 209 NNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
             + V  LD+S  + D +  +F  YG +     M+           V   +     +A+ 
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAIT 60

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKF------------------ 309
            LN      ++  V  +++ +    +  G  + +                          
Sbjct: 61  HLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

Query: 310 -QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 367
                L+  N    + +E   E+  E G      V           SG + + +  +A  
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 368 ALAEMNGKMI----VSKPLYVAVA 387
            L  +N   +       P  + + 
Sbjct: 181 TLGFLNHYQMKNPNGPYPYTLKLC 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 =  133 bits (335), Expect = 7e-36
 Identities = 30/197 (15%), Positives = 65/197 (32%), Gaps = 37/197 (18%)

Query: 115 SGTGNIFIKNLDKS-IDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQN 173
           + +  + +  LD+S ++   + + F  +GN+   K          G   V+  +  +   
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDR 57

Query: 174 AIDKLNGMLINDKQVFVG-------------------------------HFLRKQERETV 202
           AI  LN   +  +++ V                                 F   ++    
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

Query: 203 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADD 261
            I+   N +   N     T+E+  +I  E G      V +  G  +    G + +++  D
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177

Query: 262 AAKAVEALNGKKFDDRE 278
           A + +  LN  +  +  
Sbjct: 178 ALETLGFLNHYQMKNPN 194

>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 =  118 bits (296), Expect = 1e-30
 Identities = 25/204 (12%), Positives = 59/204 (28%), Gaps = 42/204 (20%)

Query: 29  TTSLYVGDLD-FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
           +  L V  LD   +   +++++F   G V  V+  +        G   V  A+     RA
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRA 58

Query: 88  LDVLNFTPLNNKSIRIMYSHRDPSIRK--------------------------------- 114
           +  LN   +  + + +  S +   +                                   
Sbjct: 59  ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 118

Query: 115 --SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESA 171
               +  +   N    +  +   +     G      +    G  +    G +++++K  A
Sbjct: 119 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDA 178

Query: 172 QNAIDKLNGMLINDKQVFVGHFLR 195
              +  LN   + +      + L+
Sbjct: 179 LETLGFLNHYQMKNPNGPYPYTLK 202

>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 = 79.4 bits (195), Expect = 5e-17
 Identities = 15/119 (12%), Positives = 37/119 (31%), Gaps = 5/119 (4%)

Query: 313 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
            L +  L    ++ +++  +F  +G +   K M+       G+  V  +      RA+  
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITH 61

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQ 430
           +N   +  + + V V+++      +                        P   +    Q
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

>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 = 63.6 bits (154), Expect = 1e-11
 Identities = 15/90 (16%), Positives = 31/90 (34%)

Query: 16  NGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
               A  +  Q  +  L+  +    VT+   +++  ++G      V            G 
Sbjct: 110 TPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGL 169

Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMY 105
           + + + +DA   L  LN   + N +    Y
Sbjct: 170 LEWDSKSDALETLGFLNHYQMKNPNGPYPY 199

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  129 bits (326), Expect = 6e-36
 Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 111 SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKES 170
           S   SG   IF++NL      K L D F+  G++L   I  + +G+SKG G V+FE+ E 
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEV 60

Query: 171 AQNAIDKLNGMLINDKQVFV 190
           A+ A   +NGM ++ +++ V
Sbjct: 61  AERACRMMNGMKLSGREIDV 80

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  113 bits (285), Expect = 3e-30
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
               ++++NL      + LK+ F+E G +    +  + +G SKG G V F +PE A RA 
Sbjct: 7   GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERAC 65

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRA 395
             MNG  +  + + V + +      +
Sbjct: 66  RMMNGMKLSGREIDVRIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  111 bits (279), Expect = 2e-29
 Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
            +    +FV+NL    T + LK  F E G +  A +  + +GKSK  G V FE+ + A +
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAER 63

Query: 265 AVEALNGKKFDDREWYVGKAQKKSERE 291
           A   +NG K   RE  V   +  S   
Sbjct: 64  ACRMMNGMKLSGREIDVRIDRNASGPS 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 85.7 bits (213), Expect = 1e-20
 Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 7/98 (7%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G+SG       ++V +L F+ T   L D F++ G VL   +  +    +S G G V +
Sbjct: 2   SSGSSGA----CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKF 55

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
            +P  A RA  ++N   L+ + I +    R+ S   SG
Sbjct: 56  ESPEVAERACRMMNGMKLSGREIDVRID-RNASGPSSG 92

>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 =  128 bits (324), Expect = 1e-35
 Identities = 29/88 (32%), Positives = 48/88 (54%), Gaps = 4/88 (4%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG----ISKGSGFVAFSTPEEASRA 368
            L+IKNL  S  +E LK +FS+ G I SC + +  +     +S G GFV +  PE+A +A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           L ++ G  +    L V +++R  +  + 
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATKPASG 94

>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 =  117 bits (296), Expect = 1e-31
 Identities = 26/90 (28%), Positives = 48/90 (53%), Gaps = 4/90 (4%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK----SKCFGFVNFENADD 261
           +  + +F+KNL+ STT+E LK +F + G I S  + +  +      S  FGFV ++  + 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 262 AAKAVEALNGKKFDDREWYVGKAQKKSERE 291
           A KA++ L G   D  +  V  +++ ++  
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPA 92

>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 =  103 bits (258), Expect = 1e-26
 Identities = 31/91 (34%), Positives = 47/91 (51%), Gaps = 4/91 (4%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD----GSGQSKGFGFVQFENKES 170
           SG+  +FIKNL+ S   + L   FS  G I SC I+      G   S GFGFV+++  E 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 171 AQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
           AQ A+ +L G  ++  ++ V    R  +  +
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPAS 93

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 87.3 bits (217), Expect = 4e-21
 Identities = 27/102 (26%), Positives = 51/102 (50%), Gaps = 8/102 (7%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLST---RRSLGYGYVN 77
           G+SG    ++ L++ +L+F+ T+  L  +FS+VG + S  + +  +      S+G+G+V 
Sbjct: 1   GSSG----SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVE 56

Query: 78  YANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           Y  P  A +AL  L    ++   + +  S R      SG  +
Sbjct: 57  YKKPEQAQKALKQLQGHTVDGHKLEVRISERATK-PASGPSS 97

>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 =  127 bits (322), Expect = 3e-35
 Identities = 29/93 (31%), Positives = 41/93 (44%), Gaps = 3/93 (3%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
              +   L++  L     +E +  LF  FG I  C V+R P G SKG  FV FS+  EA 
Sbjct: 11  RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQ 70

Query: 367 RALAEMNGKMIV---SKPLYVAVAQRKEERRAR 396
            A+  ++G   +   S  L V  A   +E    
Sbjct: 71  AAIHALHGSQTMPGASSSLVVKFADTDKESGPS 103

>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 =  106 bits (268), Expect = 7e-28
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 3/89 (3%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
             +   +FV  L++  ++ED+ ++F  +G I    V+R  DG SK   FV F +  +A  
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71

Query: 265 AVEALNGKKFDD---REWYVGKAQKKSER 290
           A+ AL+G +          V  A    E 
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFADTDKES 100

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 94.7 bits (236), Expect = 1e-23
 Identities = 25/94 (26%), Positives = 36/94 (38%), Gaps = 3/94 (3%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENK 168
               R      +F+  L+K    + +   F  FG I  C +     G SKG  FV+F + 
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSH 66

Query: 169 ESAQNAIDKLNG---MLINDKQVFVGHFLRKQER 199
             AQ AI  L+G   M      + V      +E 
Sbjct: 67  TEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 20/101 (19%), Positives = 41/101 (40%), Gaps = 4/101 (3%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G+         L+VG L+   ++  +  LF   G +    V R      S G  +V +
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKF 63

Query: 79  ANPADAARALDVLN---FTPLNNKSIRIMYSHRDPSIRKSG 116
           ++  +A  A+  L+     P  + S+ + ++  D     S 
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPSS 104

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score =  127 bits (322), Expect = 3e-35
 Identities = 28/101 (27%), Positives = 54/101 (53%), Gaps = 1/101 (0%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G    +    ++YVG LD  V++  L++LF Q G V++  + +D  T +  GYG+V +
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMY-SHRDPSIRKSGTG 118
            +  DA  A+ +++   L  K IR+   S  + ++    +G
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105

>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 = 90.0 bits (224), Expect = 6e-22
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           V+V  LDE  ++  L ++F + G + +  + +D   G+ + +GFV F + +DA  A++ +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77

Query: 270 NGKKFDDREWYVGKAQKKSERE 291
           +  K   +   V KA   ++  
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNL 99

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 87.3 bits (217), Expect = 5e-21
 Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 1/91 (1%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
           ++ Q   +Y+  L + + +  L ELF + G + +  + +D  +G  +G GFV F + E+A
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
             A+  M+   +  KP+ V  A    +  + 
Sbjct: 71  DYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 76.1 bits (188), Expect = 4e-17
 Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
           P   ++    +++  LD+ +    L + F   G +++  +  D  +GQ +G+GFV+F ++
Sbjct: 8   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67

Query: 169 ESAQNAIDKLNGMLINDKQVFV 190
           E A  AI  ++ + +  K + V
Sbjct: 68  EDADYAIKIMDMIKLYGKPIRV 89

>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 =  126 bits (319), Expect = 6e-35
 Identities = 27/97 (27%), Positives = 50/97 (51%), Gaps = 7/97 (7%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
            K   +FV+NL  + T+E L+K F ++G +     ++D       + F++F+  D A KA
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKA 61

Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 302
           +E +NGK  +     +  A+   ++ +E K Q + A 
Sbjct: 62  MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAAS 98

>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 =  120 bits (304), Expect = 7e-33
 Identities = 28/100 (28%), Positives = 54/100 (54%), Gaps = 11/100 (11%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L+++NL +++ +E L++ FS+FG +   K ++D         F+ F   + A +A+ EM
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEM 65

Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 412
           NGK +  + + +  A+  +++R   +AQ       A GPS
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQRQA----ASGPS 101

>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 = 16/86 (18%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           +    +F++NL  ++  + L   FS FG +   K         K + F+ F+ ++ A  A
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHFDERDGAVKA 61

Query: 175 IDKLNGMLINDKQVFVGHFLRKQERE 200
           ++++NG  +  + + +       ++ 
Sbjct: 62  MEEMNGKDLEGENIEIVFAKPPDQKR 87

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 8/87 (9%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              L+V +L   VT+  L   FSQ G++  V+  +D        Y ++++     A +A+
Sbjct: 11  VKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAM 62

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKS 115
           + +N   L  ++I I+++      RK 
Sbjct: 63  EEMNGKDLEGENIEIVFAKPPDQKRKE 89

>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 =  126 bits (318), Expect = 1e-34
 Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           K   N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K
Sbjct: 6   KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQ 292
            VE  +   F  ++  +G A +K     
Sbjct: 66  IVE--SQINFHGKKLKLGPAIRKQNLST 91

>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 =  112 bits (283), Expect = 5e-30
 Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 2/88 (2%)

Query: 114 KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQN 173
           K     +F+  +D  +D   +   F+ +G++   KI TD +G SKG+GFV F N    Q 
Sbjct: 6   KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQERET 201
            ++  + +  + K++ +G  +RKQ   T
Sbjct: 66  IVE--SQINFHGKKLKLGPAIRKQNLST 91

>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 =  111 bits (279), Expect = 2e-29
 Identities = 21/95 (22%), Positives = 46/95 (48%), Gaps = 6/95 (6%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            +++  +   +D+ +++  F+ +G++   K++ D +G+SKG GFV+F    +  + +   
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV--E 68

Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPV 407
           +      K L +  A RK+           Q RP+
Sbjct: 69  SQINFHGKKLKLGPAIRKQNL----STYHVQPRPL 99

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 70.7 bits (174), Expect = 3e-15
 Identities = 17/75 (22%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +++VG +D  + ++++   F++ G V  V++  D  T  S GYG+V++ N  D  + +
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67

Query: 89  DVLNFTPLNNKSIRI 103
           +  +    + K +++
Sbjct: 68  E--SQINFHGKKLKL 80

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  122 bits (307), Expect = 4e-33
 Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 1/97 (1%)

Query: 191 GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC 250
              + +        K++   + V N+     D DL+++FG++G I    ++ +  G SK 
Sbjct: 12  SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKG 70

Query: 251 FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 287
           FGFV FEN+ DA +A E L+G   + R+  V  A  +
Sbjct: 71  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  118 bits (297), Expect = 9e-32
 Identities = 27/110 (24%), Positives = 51/110 (46%), Gaps = 3/110 (2%)

Query: 281 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 340
           +G +         L  +      E  +K Q   L++ N+     D  L+++F +FG I  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMNTE--NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 341 CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 390
            +++ +  G SKG GFV F    +A RA  +++G ++  + + V  A  +
Sbjct: 59  VEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 90.5 bits (225), Expect = 4e-22
 Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
                +  KS    + + N+        L   F  FG IL  +I  +    SKGFGFV F
Sbjct: 18  GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTF 76

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGH 192
           EN   A  A +KL+G ++  +++ V +
Sbjct: 77  ENSADADRAREKLHGTVVEGRKIEVNN 103

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 78.5 bits (194), Expect = 8e-18
 Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 4/102 (3%)

Query: 2   AQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRV 61
           +     H + +          + +Q     L+V ++ F   D  L  +F Q G++L V +
Sbjct: 4   SHHHHHHSSGLVPRGSHMNTENKSQP--KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI 61

Query: 62  CRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI 103
             +   R S G+G+V + N ADA RA + L+ T +  + I +
Sbjct: 62  IFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1 Length = 92

 Score =  120 bits (303), Expect = 7e-33
 Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 552 PMPITALSTALANASPEQQRTLLGESLYPLVEQLERD--AAAKVTGMLLEMDQTEVLHLL 609
           P+     +        ++QR  LGE LY  V     +  AA K+TGM+L++   EV  LL
Sbjct: 2   PLGSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLL 61

Query: 610 ESPEALKAKVAEAMEVLRSVAQQQANNPAD 639
           ES E  +    EA     S  ++Q      
Sbjct: 62  ESDELFEQHYKEASAAYESFKKEQEQQTEQ 91

>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 =  120 bits (303), Expect = 1e-32
 Identities = 26/105 (24%), Positives = 52/105 (49%), Gaps = 5/105 (4%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            ++++NL    T E++  IFG+YG I    V      +++   +V +E+  DA  AV+ L
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNAVDHL 67

Query: 270 NGKKFDDREWYVGKAQ-KKSEREQELKGQFEQAMKETVDKFQGLN 313
           +G    +R   V      ++ ++ + K + EQ   + + +  G+N
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQ--LKLLKEKYGIN 110

>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 = 94.4 bits (235), Expect = 3e-23
 Identities = 20/94 (21%), Positives = 47/94 (50%), Gaps = 3/94 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            LYI+NL   I  E++ ++F ++G I   +V   P   ++G+ +V +    +A  A+  +
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHL 67

Query: 373 NGKMIVSKPLYVAVAQ-RKEERRARLQAQFSQMR 405
           +G  + ++ L V      +  ++   + +  Q++
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLK 101

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 89.0 bits (221), Expect = 2e-21
 Identities = 24/87 (27%), Positives = 47/87 (54%), Gaps = 3/87 (3%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              LY+ +L + +T  ++YD+F + G +  +RV     TR   G  YV Y +  DA  A+
Sbjct: 8   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAV 64

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKS 115
           D L+   ++N+ + ++Y + + + +K 
Sbjct: 65  DHLSGFNVSNRYLVVLYYNANRAFQKM 91

>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 = 86.7 bits (215), Expect = 1e-20
 Identities = 20/90 (22%), Positives = 48/90 (53%), Gaps = 2/90 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            ++I+NL   I  + ++D F  +G I   ++      +++G  +V +E+   A+NA+D L
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNAVDHL 67

Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKTKF 208
           +G  ++++ + V ++   +  + +  K K 
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKE 97

>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 =  116 bits (294), Expect = 1e-31
 Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 3/90 (3%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G  G+ F    ++VGDL   +T + +   F+  G++   RV +D++T +S GYG+V++ N
Sbjct: 1   GPLGSHF---HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 57

Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDP 110
             DA  A+  +    L  + IR  ++ R P
Sbjct: 58  KWDAENAIQQMGGQWLGGRQIRTNWATRKP 87

>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 = 99.6 bits (249), Expect = 2e-25
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           ++++ +L   I    +   F+ FG I+  +V++D  +G SKG GFV+F    +A  A+ +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 372 MNGKMIVSKPLYVAVAQRK 390
           M G+ +  + +    A RK
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 96.9 bits (242), Expect = 2e-24
 Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           +VFV +L    T   +   F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 269 LNGKKFDDREWYVGKAQKK 287
           + G+    R+     A +K
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 80.7 bits (200), Expect = 8e-19
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           ++F+ +L   I   A+   F+ FG I   ++  D  +G+SKG+GFV F NK  A+NAI +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 178 LNGMLINDKQVFVGHFLRK 196
           + G  +  +Q+      RK
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>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 =  116 bits (294), Expect = 2e-31
 Identities = 26/83 (31%), Positives = 42/83 (50%)

Query: 203 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDA 262
           A +     VFV NL+    +E L ++F + G +T   + +D +GK K FGFV F++ +  
Sbjct: 11  AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70

Query: 263 AKAVEALNGKKFDDREWYVGKAQ 285
           + A+  LNG +   R   V    
Sbjct: 71  SYAIALLNGIRLYGRPINVSGPS 93

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score =  116 bits (293), Expect = 2e-31
 Identities = 25/82 (30%), Positives = 41/82 (50%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
            +     +++ NL   + +E L ELF + G +T   + +D  G  K  GFV F  PE  S
Sbjct: 12  QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS 71

Query: 367 RALAEMNGKMIVSKPLYVAVAQ 388
            A+A +NG  +  +P+ V+   
Sbjct: 72  YAIALLNGIRLYGRPINVSGPS 93

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 93.5 bits (233), Expect = 3e-23
 Identities = 23/90 (25%), Positives = 46/90 (51%), Gaps = 1/90 (1%)

Query: 14  GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
           G +G +      +    +++VG+L+  V +  LY+LF Q G +  V +C+D    +   +
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSF 59

Query: 74  GYVNYANPADAARALDVLNFTPLNNKSIRI 103
           G+V + +P   + A+ +LN   L  + I +
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLYGRPINV 89

>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 = 92.3 bits (230), Expect = 8e-23
 Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           S   P+  ++    +F+ NL+  +  + L++ F   G +    I  D  G+ K FGFV F
Sbjct: 6   SGMFPAQEEADR-TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCF 64

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGH 192
           ++ ES   AI  LNG+ +  + + V  
Sbjct: 65  KHPESVSYAIALLNGIRLYGRPINVSG 91

>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 =  116 bits (292), Expect = 3e-31
 Identities = 29/97 (29%), Positives = 55/97 (56%), Gaps = 6/97 (6%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ-VLSVRVCRDLSTRRSLGYGYVNYA 79
           G+SG+  +  SL++GDL+  + ++ +   F+ +G+ V+SV++ R+  T    GY +V +A
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 80  NPADAARALDVLNFTPLNN----KSIRIMY-SHRDPS 111
           + A A + L  +N  PL      K  ++ Y ++  PS
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 79.7 bits (197), Expect = 2e-18
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
           +L++ +L   +D+  +   F+  G T+ S K++R+  +GI  G  FV F+    A + L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 371 EMNGKMI 377
           ++NGK +
Sbjct: 71  KINGKPL 77

>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 = 77.4 bits (191), Expect = 1e-17
 Identities = 16/74 (21%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFG-NILSCKIATD-GSGQSKGFGFVQFENKESAQNAID 176
           ++++ +L+  +D   +   F++ G  ++S KI  +  +G   G+ FV+F +  +A+  + 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 177 KLNGMLINDKQVFV 190
           K+NG  +       
Sbjct: 71  KINGKPLPGATPAK 84

>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 = 74.7 bits (184), Expect = 1e-16
 Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
           ++++ +L+    +  + + F   G T+ S  ++R+   G    + FV F +   A K + 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 268 ALNGKKFDDRE 278
            +NGK      
Sbjct: 71  KINGKPLPGAT 81

>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 =  111 bits (279), Expect = 2e-29
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  KA+E L
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 77

Query: 270 NGKKFDDREWYVGKAQKKSERE 291
            G K    E  + K + +    
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score =  106 bits (266), Expect = 1e-27
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           NL+I NL  +    +LK   SE        V+   +G ++  G+V F + E+  +AL E+
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-EL 77

Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
            G  +    + +   + ++  R 
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGTRG 100

>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 = 80.0 bits (198), Expect = 2e-18
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 4/97 (4%)

Query: 104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFV 163
           M          +   N+FI NL+ +     L    S         +    +G ++ FG+V
Sbjct: 4   MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 63

Query: 164 QFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
            FE+ E  + A++ L G+ +   ++ +    + + R+
Sbjct: 64  DFESAEDLEKALE-LTGLKVFGNEIKLE---KPKGRD 96

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +L++G+L+ N + ++L    S++     + V  D+ T  +  +GYV++ +  D  +AL+ 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKALE- 76

Query: 91  LNFTPLNNKSIRIMYSH-RDPS 111
           L    +    I++     RD +
Sbjct: 77  LTGLKVFGNEIKLEKPKGRDGT 98

>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 =  110 bits (278), Expect = 2e-29
 Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 6/90 (6%)

Query: 313 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
            +YI NL + I  ++LK+    +FS FG I    V R      +G  FV F     A+ A
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNA 67

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRARLQ 398
           L  M G     KP+ +  A+   +  A+++
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>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 = 99.6 bits (249), Expect = 2e-25
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 6/91 (6%)

Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           + +++ NL+E    ++LKK    IF  +G I   +V R    K +   FV F+    A  
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATN 66

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELK 295
           A+ ++ G  F D+   +  A+  S+   ++K
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>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 = 83.0 bits (206), Expect = 1e-19
 Identities = 29/101 (28%), Positives = 46/101 (45%), Gaps = 9/101 (8%)

Query: 109 DPSIRKSGTGNIFIKNLDKSID----HKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQ 164
            P  R + T  I+I NL++ I      K+LH  FS FG IL   ++     + +G  FV 
Sbjct: 2   VPETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVI 57

Query: 165 FENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIK 205
           F+   SA NA+  + G    DK + +  + +        +K
Sbjct: 58  FKEVSSATNALRSMQGFPFYDKPMRI-QYAKTDSDIIAKMK 97

>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 = 75.0 bits (185), Expect = 8e-17
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 7/83 (8%)

Query: 31  SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
           ++Y+ +L+  +   +L    + +FS+ GQ+L + V R L  R   G  +V +   + A  
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66

Query: 87  ALDVLNFTPLNNKSIRIMYSHRD 109
           AL  +   P  +K +RI Y+  D
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTD 89

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum} Length = 85

 Score =  109 bits (275), Expect = 3e-29
 Identities = 63/82 (76%), Positives = 70/82 (85%)

Query: 551 QPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLE 610
              PI AL++ALAN+ PE QR +LGE+LYPLV+QLE D AAKVTGMLLEMDQTEVLHLLE
Sbjct: 3   LGSPIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLE 62

Query: 611 SPEALKAKVAEAMEVLRSVAQQ 632
           SP+ALKAKVAEAMEVLRS  Q 
Sbjct: 63  SPDALKAKVAEAMEVLRSAQQH 84

>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 =  109 bits (274), Expect = 6e-29
 Identities = 28/80 (35%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL++ +L  ++DDE L+  F +F +  S  VM D  +G S+G GFV+F++ ++A  A+  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 372 MNGKMIVSKPLYVAVAQRKE 391
           M G+ +  +PL +  A + E
Sbjct: 63  MQGQDLNGRPLRINWAAKLE 82

>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 =  108 bits (272), Expect = 1e-28
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
            N+FV +L+ +  DE L+  F ++ +  S  VM D   G S+ +GFV+F + DDA  A++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 268 ALNGKKFDDREWYVGKAQKK 287
           ++ G+  + R   +  A K 
Sbjct: 62  SMQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 95.6 bits (239), Expect = 3e-24
 Identities = 29/82 (35%), Positives = 45/82 (54%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           T +L+VGDL+ NV D  L + F      LS  V  D+ T  S GYG+V++ +  DA  A+
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 89  DVLNFTPLNNKSIRIMYSHRDP 110
           D +    LN + +RI ++ +  
Sbjct: 61  DSMQGQDLNGRPLRINWAAKLE 82

>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 = 88.7 bits (221), Expect = 9e-22
 Identities = 25/82 (30%), Positives = 49/82 (59%), Gaps = 1/82 (1%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
           T N+F+ +L+ ++D + L + F  F + LS  +  D  +G S+G+GFV F +++ AQNA+
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 176 DKLNGMLINDKQVFVGHFLRKQ 197
           D + G  +N + + +    + +
Sbjct: 61  DSMQGQDLNGRPLRINWAAKLE 82

>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 =  109 bits (274), Expect = 1e-28
 Identities = 29/87 (33%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           K+    + V N+     D DL+++FG++G I    ++ +  G SK FGFV FEN+ DA +
Sbjct: 12  KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 70

Query: 265 AVEALNGKKFDDREWYVGKAQKKSERE 291
           A E L+G   + R+  V  A  +    
Sbjct: 71  AREKLHGTVVEGRKIEVNNATARVMTN 97

>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 = 97.7 bits (244), Expect = 1e-24
 Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
            K     L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F    +A 
Sbjct: 11  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADAD 69

Query: 367 RALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           RA  +++G ++  + + V  A  +    + 
Sbjct: 70  RAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 90.0 bits (224), Expect = 6e-22
 Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 1/93 (1%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFEN 167
              S  KS    + + N+        L   F  FG IL  +I  +    SKGFGFV FEN
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFEN 64

Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
              A  A +KL+G ++  +++ V +   +    
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNATARVMTN 97

>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 = 78.5 bits (194), Expect = 7e-18
 Identities = 28/101 (27%), Positives = 51/101 (50%), Gaps = 3/101 (2%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G S ++     L+V ++ F   D  L  +F Q G++L V +  +   R S G+G+V +
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTF 62

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
            N ADA RA + L+ T +  + I +  +     +  SG  +
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNA-TARVMTNSGPSS 102

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1 Length = 85

 Score =  108 bits (270), Expect = 1e-28
 Identities = 41/82 (50%), Positives = 54/82 (65%), Gaps = 2/82 (2%)

Query: 547 ASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVL 606
           +S+       +  T LAN +PEQQ+ +LGE LY  +  +   AAAKVTGMLLEMD  E+L
Sbjct: 2   SSLASQGQNLS--TVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEIL 59

Query: 607 HLLESPEALKAKVAEAMEVLRS 628
           +LL++P  L AKV EA+EVL  
Sbjct: 60  NLLDTPGLLDAKVQEALEVLNR 81

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A Length = 88

 Score =  107 bits (269), Expect = 2e-28
 Identities = 38/87 (43%), Positives = 63/87 (72%)

Query: 552 PMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLES 611
           P+     ++ LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LES
Sbjct: 2   PLGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLES 61

Query: 612 PEALKAKVAEAMEVLRSVAQQQANNPA 638
           PE+L++KV EA+ VL++   ++A   A
Sbjct: 62  PESLRSKVDEAVAVLQAHQAKEAAQKA 88

>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 =  106 bits (267), Expect = 7e-28
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAK 264
           K   V +  L  + T + + +IF  YG I    +  +      SK + +V FEN D+A K
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 265 AVEALNGKKFDDREWYVGKAQKKSER 290
           A++ ++G + D +E           R
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWPR 88

>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 = 90.7 bits (226), Expect = 2e-22
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALA 370
            ++I  L  ++  + + E+FS +G I    +  +     +SKG  +V F  P+EA +AL 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 371 EMNGKMIVSKPLYVAVAQRKEER 393
            M+G  I  + +          R
Sbjct: 66  HMDGGQIDGQEITATAVLAPWPR 88

>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 = 83.0 bits (206), Expect = 1e-19
 Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD--GSGQSKGFGFVQFENKESAQNAID 176
            + I  L +++    + + FS++G I    +  +      SKG+ +V+FEN + A+ A+ 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 177 KLNGMLINDKQVFVGHFLRKQER 199
            ++G  I+ +++     L    R
Sbjct: 66  HMDGGQIDGQEITATAVLAPWPR 88

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 77.2 bits (191), Expect = 1e-17
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD-LSTRRSLGYGYVNYANPADAARA 87
            T +++G L  NVT   + ++FS  G++  + +  + +    S GY YV + NP +A +A
Sbjct: 4   PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63

Query: 88  LDVLNFTPLNNKSIRI 103
           L  ++   ++ + I  
Sbjct: 64  LKHMDGGQIDGQEITA 79

>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 =  106 bits (268), Expect = 9e-28
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             +++KNL    T+ DL  +F  +       +      G+ +   F+ F N + A +A+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQ 292
            +NG K   +   +   + K +R  
Sbjct: 86  LVNGYKLYGKILVIEFGKNKKQRSS 110

>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 =  106 bits (266), Expect = 2e-27
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            LY+KNL   + +  L  LF+ F       +     +G  +G  F+ F   E A +AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 372 MNGKMIVSKPLYVAVAQRKEERRA 395
           +NG  +  K L +   + K++R +
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSS 110

>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 = 85.8 bits (213), Expect = 3e-20
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +++KNL   +  + L   F+ F       I     +G+ +G  F+ F NKE A  A+  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 178 LNGMLINDKQVFVGHFLRKQERE 200
           +NG  +  K + +     K++R 
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRS 109

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 83.5 bits (207), Expect = 2e-19
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 1/88 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              LY+ +L   VT+  L  LF++  +     +   + T R  G  ++ + N   A +AL
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
            ++N   L  K + I +  ++   R SG
Sbjct: 85  HLVNGYKLYGKILVIEFG-KNKKQRSSG 111

>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 =  107 bits (270), Expect = 1e-27
 Identities = 29/90 (32%), Positives = 50/90 (55%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            +LYVG+L F  T+ Q+Y+LFS+ G +  + +  D   + + G+ +V Y + ADA  A+ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
            +N T L+++ IR  +       R+ G G 
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKEGRQYGRGR 129

>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 = 89.1 bits (221), Expect = 6e-21
 Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 5/108 (4%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             ++V NL   TT+E + ++F + G I   ++  D     +  F FV + +  DA  A+ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQ----ELKGQFEQAMKETVDKFQG 311
            +NG + DDR           E  Q       GQ     ++  D  +G
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRG 147

>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 = 83.3 bits (206), Expect = 5e-19
 Identities = 33/154 (21%), Positives = 62/154 (40%), Gaps = 14/154 (9%)

Query: 278 EWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGT 337
           + YV  +Q + +  +    + E+ +K++        LY+ NL     +E++ ELFS+ G 
Sbjct: 12  DSYVELSQYRDQHFRGDNEEQEKLLKKSC------TLYVGNLSFYTTEEQIYELFSKSGD 65

Query: 338 ITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           I    +  D     + G  FV + +  +A  A+  +NG  +  + +        +E R  
Sbjct: 66  IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR-- 123

Query: 397 LQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQ 430
              Q+   R  + G         Y  G  G G+ 
Sbjct: 124 ---QYG--RGRSGGQVRDEYRQDYDAGRGGYGKL 152

>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 = 75.6 bits (186), Expect = 3e-16
 Identities = 17/86 (19%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
            + +       +  +++ NL      + +++ FS  G+I    +  D     + GF FV+
Sbjct: 28  DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           + ++  A+NA+  +NG  ++D+ +  
Sbjct: 88  YYSRADAENAMRYINGTRLDDRIIRT 113

>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 =  107 bits (269), Expect = 2e-27
 Identities = 28/135 (20%), Positives = 54/135 (40%), Gaps = 6/135 (4%)

Query: 165 FENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTK-----FNNVFVKNLDES 219
              KE A++   +  G   N ++    +   + E +               +FV ++ E 
Sbjct: 24  VRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEE 83

Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDRE 278
             ++++++ F +YG I +  +  D   G SK +  V +E    A  A EALNG +   + 
Sbjct: 84  AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT 143

Query: 279 WYVGKAQKKSEREQE 293
             V     K  +  +
Sbjct: 144 IQVDWCFVKGPKRVK 158

>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 = 94.5 bits (235), Expect = 8e-23
 Identities = 29/147 (19%), Positives = 63/147 (42%), Gaps = 5/147 (3%)

Query: 255 NFENADDAAKAVEALN--GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDK--FQ 310
            FE  +D  + +  L    K    R +      +++    E     +    E   +   +
Sbjct: 12  EFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVE 71

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           G  L++ ++ +   +++++E F ++G I +  +  D  +G SKG   V + T ++A  A 
Sbjct: 72  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRAR 396
             +NG  I+ + + V     K  +R +
Sbjct: 132 EALNGAEIMGQTIQVDWCFVKGPKRVK 158

>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 = 84.1 bits (208), Expect = 4e-19
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 1/89 (1%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESA 171
           R      +F+ ++ +      + + F  +G I +  +  D  +G SKG+  V++E  + A
Sbjct: 68  RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 127

Query: 172 QNAIDKLNGMLINDKQVFVGHFLRKQERE 200
             A + LNG  I  + + V     K  + 
Sbjct: 128 LAAKEALNGAEIMGQTIQVDWCFVKGPKR 156

>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 = 78.7 bits (194), Expect = 3e-17
 Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              L+V  +     + ++ + F   G++ ++ +  D  T  S GY  V Y     A  A 
Sbjct: 72  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131

Query: 89  DVLNFTPLNNKSIRIMYSH-RDPSIRKSG 116
           + LN   +  ++I++ +   + P   K  
Sbjct: 132 EALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>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 =  103 bits (260), Expect = 5e-27
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
            ++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV A
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 269 LNGKKFDDREWYVGKAQ 285
           L       +        
Sbjct: 67  LKASGVQAQMAKQSGPS 83

>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 = 97.2 bits (243), Expect = 9e-25
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            LYI+ L     D+ L +L   +G I S K + D  +   KG GFV F +P  A +A+  
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 372 MNGKMIVSKPLYVA 385
           +    + ++    +
Sbjct: 67  LKASGVQAQMAKQS 80

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 92.2 bits (230), Expect = 6e-23
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
           SG+  ++I+ L      + L      +G I+S K   D  + + KG+GFV F++  +AQ 
Sbjct: 3   SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

Query: 174 AIDKLNGMLINDKQVFV 190
           A+  L    +  +    
Sbjct: 63  AVTALKASGVQAQMAKQ 79

>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 = 82.6 bits (205), Expect = 1e-19
 Identities = 19/74 (25%), Positives = 39/74 (52%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           ++ LY+  L    TD  L  L    G+++S +   D +T +  GYG+V++ +P+ A +A+
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64

Query: 89  DVLNFTPLNNKSIR 102
             L  + +  +  +
Sbjct: 65  TALKASGVQAQMAK 78

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score =  104 bits (261), Expect = 6e-27
 Identities = 14/108 (12%), Positives = 43/108 (39%), Gaps = 8/108 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            +    L D++ +  LK++  ++G +   +++  P +    G   V F++   A   +  
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPM 419
           ++   ++   ++  +  + ++R    +        +  G   P  +P 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKYYEL-------IVNGSYTPQTVPT 108

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 95.5 bits (238), Expect = 8e-24
 Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             V    L+++  +  LK +  +YG +    ++      K      V F +   A + V+
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELK 295
            L+         +     K  +R +  +
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQQRMKYYE 94

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 93.2 bits (232), Expect = 6e-23
 Identities = 18/85 (21%), Positives = 33/85 (38%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             +    L+ NV ++ L D+  + G+V  V +     TR+ LG   V + +   A   + 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRK 114
            L+ T +    I      +     K
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQQRMK 91

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 89.0 bits (221), Expect = 2e-21
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 1/83 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
            +    L+ ++    L D    +G +   +I     + +  G   V F +   A+  +  
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 178 LNGMLINDKQVFVGHFLRKQERE 200
           L+   +    +     ++ Q+R 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRM 90

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score =  103 bits (260), Expect = 7e-27
 Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 204 IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 263
             +    ++V+NL  ST++E ++K F          V      K + + FV+F N +DA 
Sbjct: 11  TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAV 65

Query: 264 KAVEALNGKKFDDREWYVGKAQKKSEREQ 292
           +A++ALNGK  D     V  A+   +   
Sbjct: 66  EAMKALNGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 99.7 bits (249), Expect = 2e-25
 Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            LY++NL  S  +E +++ F+        +V +      +   FV FS  E+A  A+  +
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKAL 71

Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
           NGK++   P+ V +A+  ++  +
Sbjct: 72  NGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 78.9 bits (195), Expect = 5e-18
 Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 9/91 (9%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              LYV +L  + ++  +   F+ +      RV      ++   Y +V+++N  DA  A+
Sbjct: 15  VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAM 68

Query: 89  DVLNFTPLNNKSIRIMYS---HRDPSIRKSG 116
             LN   L+   I +  +    +D S   SG
Sbjct: 69  KALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99

>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 = 78.1 bits (193), Expect = 7e-18
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           S  D     S    ++++NL  S   + +   F++       ++      + + + FV F
Sbjct: 5   SSGDEDTMSSVK-ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHF 58

Query: 166 ENKESAQNAIDKLNGMLINDKQVFV 190
            N+E A  A+  LNG +++   + V
Sbjct: 59  SNREDAVEAMKALNGKVLDGSPIEV 83

>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 =  103 bits (260), Expect = 1e-26
 Identities = 31/107 (28%), Positives = 53/107 (49%), Gaps = 4/107 (3%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG +G     S +      ++VGDL   +T   +   F+  G++   RV +D++T +S G
Sbjct: 3   SGSSGQKKDTSNH----FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG 58

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           YG+V++ N  DA  A+  +    L  + IR  ++ R P   KS   +
Sbjct: 59  YGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score =  101 bits (253), Expect = 1e-25
 Identities = 29/113 (25%), Positives = 53/113 (46%), Gaps = 5/113 (4%)

Query: 301 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
           +  +  D     ++++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

Query: 360 STPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 412
               +A  A+ +M G+ +  + +    A RK           ++      GPS
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTK----QSGPS 113

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 99.3 bits (248), Expect = 5e-25
 Identities = 30/84 (35%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 269 LNGKKFDDREWYVGKAQKKSEREQ 292
           + G+    R+     A +K    +
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPK 100

>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 = 83.9 bits (208), Expect = 1e-19
 Identities = 27/91 (29%), Positives = 45/91 (49%), Gaps = 1/91 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
                S   ++F+ +L   I  + +   F+ FG I   ++  D  +G+SKG+GFV F NK
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67

Query: 169 ESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
             A+NAI ++ G  +  +Q+      RK   
Sbjct: 68  WDAENAIQQMGGQWLGGRQIRTNWATRKPPA 98

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  102 bits (255), Expect = 3e-26
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 199 RETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN 258
           R  +    K  +V++K      T +D+K+   + G + +  + R      K   FV F++
Sbjct: 2   RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDS 61

Query: 259 ADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQ 297
            + A K VE   G+K+ + +  +        ++ E + Q
Sbjct: 62  IESAKKFVE-TPGQKYKETDLLILFKDDYFAKKNEERKQ 99

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 97.9 bits (244), Expect = 1e-24
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
           +  +  ++YIK        + +KE   + G + + ++ R      KGS FV F + E A 
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 367 RALAEMNGKMIVSKPLYVA-----VAQRKEERRAR 396
           + + E  G+      L +       A++ EER+  
Sbjct: 67  KFV-ETPGQKYKETDLLILFKDDYFAKKNEERKQN 100

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 73.2 bits (180), Expect = 4e-16
 Identities = 16/92 (17%), Positives = 36/92 (39%), Gaps = 4/92 (4%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +++IK          + +     G +L+ ++        KG  FV F++ ESA+  + + 
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 71

Query: 179 NGMLINDKQVFVGH---FLRKQERETVAIKTK 207
            G    +  + +     +  K+  E    K +
Sbjct: 72  PGQKYKETDLLILFKDDYFAKKNEERKQNKVE 103

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.3 bits (149), Expect = 6e-12
 Identities = 13/80 (16%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 25  NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
           N     S+Y+     + T   + +     GQVL++++ R    +   G  +V + +   A
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESA 65

Query: 85  ARALDVLNFTPLNNKSIRIM 104
            + ++           + I+
Sbjct: 66  KKFVE-TPGQKYKETDLLIL 84

>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 =  102 bits (256), Expect = 3e-26
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 8/108 (7%)

Query: 190 VGHFLRKQERETVAIKTKFN-------NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR 242
           +GH          A+             ++V +L  + T++ L+ IF  +G I S  +M 
Sbjct: 1   MGHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60

Query: 243 DGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSE 289
           D + G+SK +GF+ F +++ A KA+E LNG +   R   VG   ++++
Sbjct: 61  DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 89.3 bits (222), Expect = 1e-21
 Identities = 30/113 (26%), Positives = 51/113 (45%), Gaps = 6/113 (5%)

Query: 281 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 340
           +G                 Q           + LY+ +L  +I ++ L+ +F  FG I S
Sbjct: 1   MGHHHHHHSHMAAAMANNLQKGSAG-----PMRLYVGSLHFNITEDMLRGIFEPFGRIES 55

Query: 341 CKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEE 392
            ++M D  +G SKG GF+ FS  E A +AL ++NG  +  +P+ V     + +
Sbjct: 56  IQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 83.1 bits (206), Expect = 2e-19
 Identities = 27/97 (27%), Positives = 47/97 (48%)

Query: 7   QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS 66
            H         +A            LYVG L FN+T+  L  +F   G++ S+++  D  
Sbjct: 4   HHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE 63

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI 103
           T RS GYG++ +++   A +AL+ LN   L  + +++
Sbjct: 64  TGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 78.5 bits (194), Expect = 8e-18
 Identities = 26/85 (30%), Positives = 48/85 (56%), Gaps = 1/85 (1%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
           +G   +++ +L  +I    L   F  FG I S ++  D  +G+SKG+GF+ F + E A+ 
Sbjct: 24  AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQE 198
           A+++LNG  +  + + VGH   + +
Sbjct: 84  ALEQLNGFELAGRPMKVGHVTERTD 108

>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 =  101 bits (255), Expect = 4e-26
 Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             + V NL E T + DL+++F  +G+I+   + +D   G+SK F F++F   +DAA+A+ 
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
            ++G  +D     V  A+  +  
Sbjct: 76  GVSGFGYDHLILNVEWAKPSTNS 98

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 90.7 bits (226), Expect = 3e-22
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            + + NL +   +  L+ELF  FG+I+   + +D  +G SKG  F++F   E+A+RA+A 
Sbjct: 17  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           ++G       L V  A+        
Sbjct: 77  VSGFGYDHLILNVEWAKPSTNSGPS 101

>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 = 84.2 bits (209), Expect = 6e-20
 Identities = 18/89 (20%), Positives = 45/89 (50%), Gaps = 1/89 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             ++ V +L  +  ++ L +LF   G +  + + +D +T +S G+ ++++    DAARA+
Sbjct: 15  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74

Query: 89  DVLNFTPLNNKSIRIMYSH-RDPSIRKSG 116
             ++    ++  + + ++     S   SG
Sbjct: 75  AGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>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 = 82.7 bits (205), Expect = 2e-19
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
           P+ R      I + NL +      L + F  FG+I    +A D  +GQSKGF F+ F  +
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 169 ESAQNAIDKLNGMLINDKQVFV 190
           E A  AI  ++G   +   + V
Sbjct: 68  EDAARAIAGVSGFGYDHLILNV 89

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A Length = 61

 Score = 98.6 bits (246), Expect = 1e-25
 Identities = 27/59 (45%), Positives = 42/59 (71%)

Query: 570 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRS 628
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++ +
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIA 59

>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 bits (250), Expect = 2e-25
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             ++V  L E   D+ L   F  +G IT   +  D +  K + F FV FE A+DAA A++
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQ 292
            +N  +   R   V  A+    +E 
Sbjct: 73  NMNESELFGRTIRVNLAKPMRIKES 97

>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 = 91.5 bits (228), Expect = 2e-22
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            LY+  L + +DD+ L   F  FG IT  ++  D  +   +G  FV F   E+A+ A+  
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           MN   +  + + V +A+    + + 
Sbjct: 74  MNESELFGRTIRVNLAKPMRIKESG 98

>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 = 85.3 bits (212), Expect = 2e-20
 Identities = 29/100 (29%), Positives = 51/100 (51%), Gaps = 1/100 (1%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G+SG       LYVG L   V D  L+  F   G +  +++  D  T +  G+ +V +
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
               DAA A+D +N + L  ++IR+  + +   I++SG  
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLA-KPMRIKESGPS 100

>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 = 80.7 bits (200), Expect = 1e-18
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
            S   +    +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64

Query: 169 ESAQNAIDKLNG 180
           E A  AID +N 
Sbjct: 65  EDAAAAIDNMNE 76

>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 = 99.2 bits (248), Expect = 3e-25
 Identities = 34/83 (40%), Positives = 52/83 (62%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             +FV  L   T ++ L+++F +YG I+  VV++D +  +S+ FGFV FEN DDA  A+ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
           A+NGK  D R+  V +A K S+ 
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDN 95

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 90.8 bits (226), Expect = 3e-22
 Identities = 24/85 (28%), Positives = 48/85 (56%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L++  L    +++ L+++FS++G I+   V++D  +  S+G GFV F   ++A  A+  
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           MNGK +  + + V  A +  + R+ 
Sbjct: 74  MNGKSVDGRQIRVDQAGKSSDNRSG 98

>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 = 83.4 bits (207), Expect = 1e-19
 Identities = 30/101 (29%), Positives = 53/101 (52%), Gaps = 1/101 (0%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G+SG       L+VG L F+  +  L  +FS+ GQ+  V V +D  T+RS G+G+V +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYS-HRDPSIRKSGTG 118
            N  DA  A+  +N   ++ + IR+  +     +     +G
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102

>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 = 83.1 bits (206), Expect = 1e-19
 Identities = 26/92 (28%), Positives = 47/92 (51%), Gaps = 1/92 (1%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 167
             S   S  G +F+  L    + ++L   FS +G I    +  D  + +S+GFGFV FEN
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
            + A++A+  +NG  ++ +Q+ V    +  + 
Sbjct: 64  IDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 98.8 bits (247), Expect = 4e-25
 Identities = 27/83 (32%), Positives = 51/83 (61%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
           + ++V +L  + T++ L+ IF  +G I + V+M+D D G+SK +GF+ F +++ A +A+E
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
            LNG +   R   VG   ++ + 
Sbjct: 66  QLNGFELAGRPMRVGHVTERLDG 88

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 87.6 bits (218), Expect = 3e-21
 Identities = 28/85 (32%), Positives = 48/85 (56%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            LY+ +L  +I ++ L+ +F  FG I +  +M+D  +G SKG GF+ FS  E A RAL +
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           +NG  +  +P+ V     + +  + 
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGGSG 91

>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 = 81.8 bits (203), Expect = 3e-19
 Identities = 26/86 (30%), Positives = 48/86 (55%), Gaps = 1/86 (1%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
           SG+  +++ +L  +I    L   F  FG I +  +  D  +G+SKG+GF+ F + E A+ 
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQER 199
           A+++LNG  +  + + VGH   + + 
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDG 88

>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 = 81.8 bits (203), Expect = 4e-19
 Identities = 26/75 (34%), Positives = 46/75 (61%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           ++ LYVG L FN+T+  L  +F   G++ ++ + +D  T RS GYG++ +++   A RAL
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64

Query: 89  DVLNFTPLNNKSIRI 103
           + LN   L  + +R+
Sbjct: 65  EQLNGFELAGRPMRV 79

>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 = 98.9 bits (247), Expect = 4e-25
 Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            ++Y G +   +TD  +   FS  GQ++ +RV  +       GY +V ++    AA A+ 
Sbjct: 26  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIV 79

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRKSG 116
            +N T +    ++  +    P +    
Sbjct: 80  SVNGTTIEGHVVKCYWGKESPDMTSGP 106

>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 = 85.5 bits (212), Expect = 3e-20
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 5/87 (5%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            +Y   +   + D+ +++ FS FG I   +V  +     KG  FV FST E A+ A+  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81

Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQA 399
           NG  I    +     +   +  +   +
Sbjct: 82  NGTTIEGHVVKCYWGKESPDMTSGPSS 108

>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 = 78.1 bits (193), Expect = 9e-18
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 266
           K   V+   +    TD+ +++ F  +G I    V  +     K + FV F   + AA A+
Sbjct: 24  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAI 78

Query: 267 EALNGKKFDDREWYVGKAQKKSER 290
            ++NG   +         ++  + 
Sbjct: 79  VSVNGTTIEGHVVKCYWGKESPDM 102

>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 = 75.8 bits (187), Expect = 6e-17
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            ++   +   +  + +  TFS FG I+  ++  +     KG+ FV+F   ESA +AI  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81

Query: 179 NGMLINDKQVFVG 191
           NG  I    V   
Sbjct: 82  NGTTIEGHVVKCY 94

>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 = 98.5 bits (246), Expect = 5e-25
 Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 304 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 363
           E     +G  LY+      +    L+  FS FG I    +        +   FV +   E
Sbjct: 8   ERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKME 60

Query: 364 EASRALAEMNGKMIVSKPLYVAVAQRKEERRA 395
            A +A+AE+NG  + S  L V +A+++    +
Sbjct: 61  SADQAVAELNGTQVESVQLKVNIARKQPMLDS 92

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N ++V   D   T   L+  F  +G I    +        +   FV +E  + A +AV  
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAE 68

Query: 269 LNGKKFDDREWYVGKAQKKSEREQ 292
           LNG + +  +  V  A+K+   + 
Sbjct: 69  LNGTQVESVQLKVNIARKQPMLDS 92

>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 = 83.5 bits (207), Expect = 8e-20
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 8/95 (8%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           S  +    + G   +++   D  +    L   FS FGNI+   +        +   FV +
Sbjct: 5   SSGERRAPRKGN-TLYVYGED--MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTY 56

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           E  ESA  A+ +LNG  +   Q+ V    ++   +
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVNIARKQPMLD 91

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 67.7 bits (166), Expect = 3e-14
 Identities = 22/104 (21%), Positives = 44/104 (42%), Gaps = 12/104 (11%)

Query: 19  AAGASGNQFLT---TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           ++G+SG +       +LYV   D  +T + L   FS  G ++ + +             +
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM------DPPRNCAF 53

Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           V Y     A +A+  LN T + +  +++  + R   +  SG  +
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKVNIA-RKQPMLDSGPSS 96

>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 = 98.5 bits (246), Expect = 6e-25
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 5/88 (5%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
            T+ + +FV NL    T+E+++K+F +YG      + +D     K FGF+  E    A  
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEI 66

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQ 292
           A   L+      ++  V  A   +    
Sbjct: 67  AKVELDNMPLRGKQLRVRFACHSASLTS 94

>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 = 91.9 bits (229), Expect = 1e-22
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++ NL   I +E++++LF ++G      + +D     KG GF+   T   A  A  E+
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 71

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           +   +  K L V  A       + 
Sbjct: 72  DNMPLRGKQLRVRFACHSASLTSG 95

>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 = 79.2 bits (196), Expect = 3e-18
 Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
             +    +F+ NL   I  + +   F  +G      I  D     KGFGF++ E +  A+
Sbjct: 11  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE 65

Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQERET 201
            A  +L+ M +  KQ+ V          +
Sbjct: 66  IAKVELDNMPLRGKQLRVRFACHSASLTS 94

>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 = 78.8 bits (195), Expect = 4e-18
 Identities = 24/104 (23%), Positives = 48/104 (46%), Gaps = 11/104 (10%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG +G     +      + L+VG+L  ++T+ ++  LF + G+   V + +D   +   G
Sbjct: 3   SGSSGGEKTFTQR----SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---K---G 52

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
           +G++       A  A   L+  PL  K +R+ ++    +   SG
Sbjct: 53  FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA-CHSASLTSG 95

>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 = 99.4 bits (248), Expect = 9e-25
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
            N+ V  +  +  +  L+++F  YG I S  ++ D +  +S+ +GFV F++   A +A+ 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
            LNG    ++   V  A    +R
Sbjct: 103 GLNGFNILNKRLKVALAASGHQR 125

>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 = 93.7 bits (233), Expect = 9e-23
 Identities = 29/85 (34%), Positives = 50/85 (58%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  +  ++D+ +L++LF  +G I S K++ D  +  S+G GFV F +   A +A+A 
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           +NG  I++K L VA+A    +R   
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGI 128

>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 = 92.9 bits (231), Expect = 2e-22
 Identities = 37/142 (26%), Positives = 63/142 (44%), Gaps = 7/142 (4%)

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHK 132
              V+  +P      L  L       + I     + +P + +    N+ +  +  ++D  
Sbjct: 4   IPLVSQYDPYGQTAQLQQLQ--QQQQQHIPPTQMNPEPDVLR----NLMVNYIPTTVDEV 57

Query: 133 ALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG 191
            L   F  +G I S KI  D  + QS+G+GFV+F++  SAQ AI  LNG  I +K++ V 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 192 HFLRKQERETVAIKTKFNNVFV 213
                 +R  +A      N ++
Sbjct: 118 LAASGHQRPGIAGAVGDGNGYL 139

>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 = 91.7 bits (228), Expect = 5e-22
 Identities = 31/125 (24%), Positives = 55/125 (44%), Gaps = 4/125 (3%)

Query: 2   AQIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRV 61
              Q+Q   Q    +      +    +  +L V  +   V + QL  LF + G + SV++
Sbjct: 15  QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI 74

Query: 62  CRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY----SHRDPSIRKSGT 117
             D  TR+S GYG+V + + + A +A+  LN   + NK +++        R       G 
Sbjct: 75  VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGD 134

Query: 118 GNIFI 122
           GN ++
Sbjct: 135 GNGYL 139

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 97.7 bits (244), Expect = 1e-24
 Identities = 20/82 (24%), Positives = 39/82 (47%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + +F+  L  S T E+L++I   +GT+    ++ +  GK K   +V +EN   A++AV  
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
           ++G    +    V  +      
Sbjct: 78  MDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 87.3 bits (217), Expect = 5e-21
 Identities = 21/81 (25%), Positives = 41/81 (50%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L+I  L  S   E+L+E+    GT+   +++ + +G  KG  +V +    +AS+A+ +M
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78

Query: 373 NGKMIVSKPLYVAVAQRKEER 393
           +G  I    + VA++      
Sbjct: 79  DGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 85.4 bits (212), Expect = 2e-20
 Identities = 20/74 (27%), Positives = 39/74 (52%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
              +FI  L  S   + L +   + G +   ++ T+ +G+ KG  +V++EN+  A  A+ 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76

Query: 177 KLNGMLINDKQVFV 190
           K++GM I +  + V
Sbjct: 77  KMDGMTIKENIIKV 90

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 80.4 bits (199), Expect = 1e-18
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              L++  L F+ T  +L ++    G V  +R+  +    +  G  YV Y N + A++A+
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAV 75

Query: 89  DVLNFTPLNNKSIRIMYSHRDPS 111
             ++   +    I++  S+  PS
Sbjct: 76  MKMDGMTIKENIIKVAISNSGPS 98

>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 =  102 bits (254), Expect = 1e-24
 Identities = 36/217 (16%), Positives = 64/217 (29%), Gaps = 12/217 (5%)

Query: 251 FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ 310
           +G  +  +  D   +  A NG   +DR+              +  G+            +
Sbjct: 12  YGGHDQIDLYDDVISPSANNGDAPEDRD----YMDTLPPTVGDDVGKGAAPNVVYTYTGK 67

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASR 367
            + LYI NL     DE L E     G   I   K   +  +G SKG   V   +   + +
Sbjct: 68  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 127

Query: 368 ALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF-----SQMRPVAMGPSVPPRMPMYPP 422
            +  +  + +  +   V    ++   +  +Q++              GP        +P 
Sbjct: 128 LMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187

Query: 423 GPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRP 459
           G  G G+             P    G       G   
Sbjct: 188 GGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTH 224

>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 = 88.2 bits (218), Expect = 6e-20
 Identities = 21/101 (20%), Positives = 40/101 (39%), Gaps = 3/101 (2%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENADDAA 263
           K   +++ NL   TTDEDL +     G   I       +   G+SK F  V   +   + 
Sbjct: 67  KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK 126

Query: 264 KAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 304
           K ++ L  ++   +   V    K+   + E++ +      +
Sbjct: 127 KLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQ 167

>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 = 76.7 bits (188), Expect = 7e-16
 Identities = 17/104 (16%), Positives = 41/104 (39%), Gaps = 2/104 (1%)

Query: 7   QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRD 64
                  G                +LY+G+L +  TD  L +    +G   +L ++   +
Sbjct: 46  PTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN 105

Query: 65  LSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR 108
            +  +S G+  V   + A + + +D+L    L+ ++  +   ++
Sbjct: 106 RANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK 149

>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 = 69.7 bits (170), Expect = 1e-13
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 6/89 (6%)

Query: 108 RDPSIRKSGTG---NIFIKNLDKSIDHKALHDTFSSFG--NILSCKIATD-GSGQSKGFG 161
             P++  + TG    ++I NL      + L +   S G  +IL  K   +  +GQSKGF 
Sbjct: 56  AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115

Query: 162 FVQFENKESAQNAIDKLNGMLINDKQVFV 190
            V   ++ S++  +D L    ++ +   V
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVV 144

>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 = 96.1 bits (240), Expect = 3e-24
 Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 266
              + V  L   TT+ DL+++F +YG I    ++ D    +S+ F FV FEN DDA +A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 267 EALNGKKFDDREWYVGKAQ 285
           E  NG + D R   V    
Sbjct: 75  ERANGMELDGRRIRVSGPS 93

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 84.9 bits (211), Expect = 3e-20
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L +  L     +  L+E+FS++G I    ++ D  S  S+G  FV F   ++A  A   
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 372 MNGKMIVSKPLYVAVAQR 389
            NG  +  + + V+    
Sbjct: 77  ANGMELDGRRIRVSGPSS 94

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 82.2 bits (204), Expect = 3e-19
 Identities = 23/78 (29%), Positives = 37/78 (47%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              L V  L    T+  L ++FS+ G +  V +  D  +RRS G+ +V + N  DA  A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 89  DVLNFTPLNNKSIRIMYS 106
           +  N   L+ + IR+   
Sbjct: 75  ERANGMELDGRRIRVSGP 92

>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 = 80.7 bits (200), Expect = 7e-19
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFE 166
                       + +  L      + L + FS +G I    I  D  S +S+GF FV FE
Sbjct: 6   SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65

Query: 167 NKESAQNAIDKLNGMLINDKQVFV 190
           N + A+ A ++ NGM ++ +++ V
Sbjct: 66  NVDDAKEAKERANGMELDGRRIRV 89

>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 = 98.4 bits (245), Expect = 4e-24
 Identities = 30/137 (21%), Positives = 50/137 (36%), Gaps = 5/137 (3%)

Query: 162 FVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKF----NNVFVKNLD 217
            V     E         NG+                E               ++ V NL 
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79

Query: 218 ESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDD 276
             T+ + L+++F +YG +    + RD    +S+ F FV F +  DA  A++A++G   D 
Sbjct: 80  YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 139

Query: 277 REWYVGKAQKKSEREQE 293
           RE  V  A+     +  
Sbjct: 140 RELRVQMARYGRPPDSH 156

>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 = 96.4 bits (240), Expect = 2e-23
 Identities = 31/149 (20%), Positives = 53/149 (35%), Gaps = 8/149 (5%)

Query: 251 FGFVNFENAD--DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDK 308
            G    E  D   A K  +        D EW    A K     +           E    
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEG--- 69

Query: 309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 367
               +L + NL      + L+ +F ++G +    + RD  +  S+G  FV F    +A  
Sbjct: 70  --MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 368 ALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           A+  M+G ++  + L V +A+      + 
Sbjct: 128 AMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>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 = 81.0 bits (200), Expect = 4e-18
 Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
            H    +   G  ++ + NL        L   F  +G +    I  D  + +S+GF FV+
Sbjct: 59  HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           F +K  A++A+D ++G +++ +++ V
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRV 144

>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 = 79.9 bits (197), Expect = 8e-18
 Identities = 22/82 (26%), Positives = 42/82 (51%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
            TSL V +L +  +   L  +F + G+V  V + RD  T+ S G+ +V + +  DA  A+
Sbjct: 70  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129

Query: 89  DVLNFTPLNNKSIRIMYSHRDP 110
           D ++   L+ + +R+  +    
Sbjct: 130 DAMDGAVLDGRELRVQMARYGR 151

>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 = 95.7 bits (239), Expect = 4e-24
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV+NL  ++++EDL+K+F  YG ++      D    K K F FV F   + A KA   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
           +G+ F  R  +V  +  K E  Q
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 85.7 bits (213), Expect = 2e-20
 Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+++NL  +  +E L++LFS +G ++      D  +   KG  FV F  PE A +A AE+
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           +G++   + L+V  +  K+E    
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 83.0 bits (206), Expect = 1e-19
 Identities = 18/91 (19%), Positives = 40/91 (43%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           +  L+V +L +  ++  L  LFS  G +  +    D  T++  G+ +V +  P  A +A 
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
             ++      + + ++ S       +SG  +
Sbjct: 68  AEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 79.6 bits (197), Expect = 2e-18
 Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESA 171
             SG+G +F++NL  +   + L   FS++G +       D  + + KGF FV F   E A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 172 QNAIDKLNGMLINDKQVFVGHFLRKQERE 200
             A  +++G +   + + V     K+E  
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 95.8 bits (239), Expect = 4e-24
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
           + V+V NL  S T+ DL +IF +YG +    +M+D D  KSK   F+ F + D A     
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 268 ALNGKKFDDREWYVGKA 284
           A+N K+   R      A
Sbjct: 77  AINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 85.7 bits (213), Expect = 1e-20
 Identities = 25/91 (27%), Positives = 53/91 (58%), Gaps = 3/91 (3%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG +G++ G + ++   +++YV +L F++T++ LY +FS+ G+V+ V + +D  TR+S G
Sbjct: 3   SGSSGMSGGLAPSK---STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRI 103
             ++ + +   A      +N   L  + I+ 
Sbjct: 60  VAFILFLDKDSAQNCTRAINNKQLFGRVIKA 90

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 80.0 bits (198), Expect = 2e-18
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            +Y+ NL  S+ +  L  +FS++G +    +M+D  +  SKG  F+ F   + A      
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77

Query: 372 MNGKMIVSKPLYVAVA 387
           +N K +  + +  ++A
Sbjct: 78  INNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 80.0 bits (198), Expect = 2e-18
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +++ NL  S+ +  L+  FS +G ++   I  D  + +SKG  F+ F +K+SAQN    
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77

Query: 178 LNGMLINDKQVFVGH 192
           +N   +  + +    
Sbjct: 78  INNKQLFGRVIKASI 92

>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 = 94.2 bits (235), Expect = 2e-23
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
            + V NL   T+ + L+++F +YG +    + R+      + F FV F +  DA  A  A
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
           ++G + D RE  V  A+     
Sbjct: 75  MDGAELDGRELRVQVARYGRRD 96

>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 = 85.4 bits (212), Expect = 2e-20
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L + NL      + L+ +F ++G +    + R+P +   +G  FV F    +A  A A 
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           M+G  +  + L V VA+      + 
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLSG 99

>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 = 81.9 bits (203), Expect = 4e-19
 Identities = 19/103 (18%), Positives = 45/103 (43%), Gaps = 1/103 (0%)

Query: 17  GVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYV 76
           G +  +  +     +L V +L +  +   L  +F + G+V  V + R+  T+   G+ +V
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 77  NYANPADAARALDVLNFTPLNNKSIRIMYSH-RDPSIRKSGTG 118
            + +  DA  A   ++   L+ + +R+  +      +    +G
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103

>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 = 78.4 bits (194), Expect = 6e-18
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 1/86 (1%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
           S         G   + + NL       +L   F  +G +    I  +  +   +GF FV+
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           F ++  AQ+A   ++G  ++ +++ V
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRV 87

>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 = 93.8 bits (234), Expect = 2e-23
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
            V++ ++    T+E +  +    G + +  +M D   G+SK + F+ F + + +A AV  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 269 LNGKKFDDREWYVGKAQKKSEREQE 293
           LNG +   R    G +         
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVS 88

>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 = 85.4 bits (212), Expect = 2e-20
 Identities = 23/83 (27%), Positives = 46/83 (55%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           +  +Y+G + ++ T+ Q+ DL S VG V+++++  D  T RS GY ++ + +   +A A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 89  DVLNFTPLNNKSIRIMYSHRDPS 111
             LN   L ++ ++  YS     
Sbjct: 62  RNLNGYQLGSRFLKCGYSSNSDI 84

>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 = 81.5 bits (202), Expect = 5e-19
 Identities = 18/93 (19%), Positives = 45/93 (48%), Gaps = 1/93 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +++ ++      + + D  S+ G +++ K+  D  +G+SKG+ F++F + ES+ +A+  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
           LNG  +  + +  G+                ++
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHHHHHH 96

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 80.0 bits (198), Expect = 1e-18
 Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            +Y+ ++     +E++ +L S  G + + K+M DP +G SKG  F+ F   E ++ A+  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQ 398
           +NG  + S+ L    +   +     L+
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLE 90

>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 = 94.8 bits (236), Expect = 2e-23
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             + V  L   TT+ DL+++F +YG I    ++ D    +S+ F FV FEN DDA +A E
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 268 ALNGKKFDDREWYVGKAQKK 287
             NG + D R   V  +  K
Sbjct: 107 RANGMELDGRRIRVDFSITK 126

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 85.2 bits (211), Expect = 5e-20
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 1/86 (1%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
            H            + +  L      + L + FS +G I    I  D  S +S+GF FV 
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           FEN + A+ A ++ NGM ++ +++ V
Sbjct: 95  FENVDDAKEAKERANGMELDGRRIRV 120

>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 = 84.4 bits (209), Expect = 1e-19
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L +  L     +  L+E+FS++G I    ++ D  S  S+G  FV F   ++A  A   
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 372 MNGKMIVSKPLYVAVAQRK 390
            NG  +  + + V  +  K
Sbjct: 108 ANGMELDGRRIRVDFSITK 126

>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 = 83.2 bits (206), Expect = 3e-19
 Identities = 24/78 (30%), Positives = 39/78 (50%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              L V  L    T+  L ++FS+ G +  V +  D  +RRS G+ +V + N  DA  A 
Sbjct: 46  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105

Query: 89  DVLNFTPLNNKSIRIMYS 106
           +  N   L+ + IR+ +S
Sbjct: 106 ERANGMELDGRRIRVDFS 123

>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 = 93.0 bits (232), Expect = 3e-23
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             ++V  L E   D+ L   F  +G IT   +  D +  K + F FV FE A+DAA A++
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 268 ALNGKKFDDREWYVGKAQ 285
            +N  +   R   V  A+
Sbjct: 68  NMNESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 84.1 bits (209), Expect = 5e-20
 Identities = 23/74 (31%), Positives = 38/74 (51%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             LYVG L   V D  L+  F   G +  +++  D  T +  G+ +V +    DAA A+D
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 90  VLNFTPLNNKSIRI 103
            +N + L  ++IR+
Sbjct: 68  NMNESELFGRTIRV 81

>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 = 83.3 bits (207), Expect = 7e-20
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            LY+  L + +DD+ L   F  FG IT  ++  D  +   +G  FV F   E+A+ A+  
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 372 MNGKMIVSKPLYVAVAQ 388
           MN   +  + + V +A+
Sbjct: 69  MNESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 77.6 bits (192), Expect = 8e-18
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID 
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 178 LNG 180
           +N 
Sbjct: 69  MNE 71

>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 = 94.4 bits (235), Expect = 4e-23
 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             +FV  + E  T+ED+   F EYG I +  +  D   G  K +  V +E   +A  A+E
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKG 296
            LNG+    +   V     +   + + +G
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRRG 111

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 82.8 bits (205), Expect = 4e-19
 Identities = 21/96 (21%), Positives = 47/96 (48%), Gaps = 1/96 (1%)

Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
           G  L++  + +   +E + + F+E+G I +  +  D  +G  KG   V + T +EA  A+
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMR 405
             +NG+ ++ +P+ V     +   + + +    + R
Sbjct: 82  EGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSR 117

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 79.7 bits (197), Expect = 5e-18
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +F+  + +    + +HD F+ +G I +  +  D  +G  KG+  V++E  + AQ A++ 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 178 LNGMLINDKQVFVGH 192
           LNG  +  + + V  
Sbjct: 84  LNGQDLMGQPISVDW 98

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 76.6 bits (189), Expect = 6e-17
 Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 1/92 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              L+V  +    T+  ++D F++ G++ ++ +  D  T    GY  V Y    +A  A+
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81

Query: 89  DVLNFTPLNNKSIRIMYS-HRDPSIRKSGTGN 119
           + LN   L  + I + +   R P   K   G 
Sbjct: 82  EGLNGQDLMGQPISVDWCFVRGPPKGKRRGGR 113

>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 = 93.5 bits (233), Expect = 4e-23
 Identities = 29/85 (34%), Positives = 47/85 (55%), Gaps = 1/85 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
            +VFV N+    T+E LK IF E G + S  ++ D + GK K +GF  +++ + A  A+ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQ 292
            LNG++F  R   V  A  +  +E+
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEE 93

>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 = 80.4 bits (199), Expect = 1e-18
 Identities = 25/75 (33%), Positives = 44/75 (58%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             S++VG++ +  T+ QL D+FS+VG V+S R+  D  T +  GYG+  Y +   A  A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 89  DVLNFTPLNNKSIRI 103
             LN    + +++R+
Sbjct: 68  RNLNGREFSGRALRV 82

>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 = 78.8 bits (195), Expect = 5e-18
 Identities = 25/93 (26%), Positives = 55/93 (59%), Gaps = 2/93 (2%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 167
           DP++ +S   ++F+ N+      + L D FS  G ++S ++  D  +G+ KG+GF ++++
Sbjct: 1   DPAVDRSLR-SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           +E+A +A+  LNG   + + + V +   ++ +E
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>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 = 78.1 bits (193), Expect = 9e-18
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           ++++ N+     +E+LK++FSE G + S +++ D  +G  KG GF  +   E A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           +NG+    + L V  A  ++ +   
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEEL 94

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A Length = 144

 Score = 94.1 bits (233), Expect = 7e-23
 Identities = 44/139 (31%), Positives = 78/139 (56%), Gaps = 1/139 (0%)

Query: 505 PPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALAN 564
           P    A   P  R +  + +  G  +     ++    +  +  +V         ++ LA+
Sbjct: 2   PLGSAAAATPAVRTVPQYKYAAGVRNP-QQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS 60

Query: 565 ASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME 624
           A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ 
Sbjct: 61  APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA 120

Query: 625 VLRSVAQQQANNPADQLAS 643
           VL++   ++A   A   A+
Sbjct: 121 VLQAHQAKEAAQKAVNSAT 139

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 93.7 bits (233), Expect = 8e-23
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
            ++ V NL   T+ + L+++F +YG +    + RD    +S+ F FV F +  DA  A++
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQ 292
           A++G   D RE  V  A+     + 
Sbjct: 108 AMDGAVLDGRELRVQMARYGRPPDS 132

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 85.9 bits (213), Expect = 3e-20
 Identities = 23/116 (19%), Positives = 46/116 (39%), Gaps = 1/116 (0%)

Query: 282 GKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC 341
           G         Q++        +   D     +L + NL      + L+ +F ++G +   
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 342 KVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
            + RD  +  S+G  FV F    +A  A+  M+G ++  + L V +A+      + 
Sbjct: 78  YIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 79.4 bits (196), Expect = 7e-18
 Identities = 24/94 (25%), Positives = 45/94 (47%)

Query: 10  AQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR 69
            QM   +        +    TSL V +L +  +   L  +F + G+V  V + RD  T+ 
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87

Query: 70  SLGYGYVNYANPADAARALDVLNFTPLNNKSIRI 103
           S G+ +V + +  DA  A+D ++   L+ + +R+
Sbjct: 88  SRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 79.0 bits (195), Expect = 1e-17
 Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 1/94 (1%)

Query: 98  NKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQ 156
            +  R   S+  P     G  ++ + NL        L   F  +G +    I  D  + +
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87

Query: 157 SKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           S+GF FV+F +K  A++A+D ++G +++ +++ V
Sbjct: 88  SRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>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 = 92.7 bits (231), Expect = 8e-23
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV ++ E   ++++++ F +YG I +  +  D   G SK +  V +E    A  A EAL
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           NG +   +   V     K  +
Sbjct: 89  NGAEIMGQTIQVDWCFVKGPK 109

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 80.4 bits (199), Expect = 2e-18
 Identities = 21/86 (24%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +G  L++ ++ +   +++++E F ++G I +  +  D  +G SKG   V + T ++A  A
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERR 394
              +NG  I+ + + V     K  +R
Sbjct: 85  KEALNGAEIMGQTIQVDWCFVKGPKR 110

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 78.9 bits (195), Expect = 6e-18
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 2/96 (2%)

Query: 106 SHRDPSIRKSGTGN-IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFV 163
              +P  ++S  G  +F+ ++ +      + + F  +G I +  +  D  +G SKG+  V
Sbjct: 14  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 73

Query: 164 QFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           ++E  + A  A + LNG  I  + + V     K  +
Sbjct: 74  EYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>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 = 75.4 bits (186), Expect = 8e-17
 Identities = 16/73 (21%), Positives = 33/73 (45%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
            L+V  +     + ++ + F   G++ ++ +  D  T  S GY  V Y     A  A + 
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 91  LNFTPLNNKSIRI 103
           LN   +  ++I++
Sbjct: 88  LNGAEIMGQTIQV 100

>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 = 92.4 bits (230), Expect = 1e-22
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD--GKSKCFGFVNFENADDA 262
           K   + + V+N+       +++++F  +G + +  + +     G  + FGFV+F    DA
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71

Query: 263 AKAVEAL-NGKKFDDREWYVGKAQKKSERE 291
            KA  AL +      R   +  A  +   +
Sbjct: 72  KKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 83.9 bits (208), Expect = 8e-20
 Identities = 19/97 (19%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 303 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFS 360
            +   K     + ++N+    +  +++ELFS FG + + ++ +    +G  +G GFV F 
Sbjct: 7   GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66

Query: 361 TPEEASRALAEM-NGKMIVSKPLYVAVAQRKEERRAR 396
           T ++A +A   + +   +  + L +  A  +   ++ 
Sbjct: 67  TKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>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 = 80.8 bits (200), Expect = 1e-18
 Identities = 20/92 (21%), Positives = 47/92 (51%), Gaps = 3/92 (3%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD--GSGQSKGFGFVQFENKES 170
           +K  T  I ++N+    + + + + FS+FG + + ++     G+G  +GFGFV F  K+ 
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70

Query: 171 AQNAIDKL-NGMLINDKQVFVGHFLRKQERET 201
           A+ A + L +   +  +++ +     +   ++
Sbjct: 71  AKKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102

>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 = 79.3 bits (196), Expect = 4e-18
 Identities = 19/91 (20%), Positives = 49/91 (53%), Gaps = 2/91 (2%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDL-STRRSLGYGYVNYANPADAARA 87
           T+ + V ++ F     ++ +LFS  G++ +VR+ + +  T    G+G+V++    DA +A
Sbjct: 15  TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74

Query: 88  LDVL-NFTPLNNKSIRIMYSHRDPSIRKSGT 117
            + L + T L  + + + ++  + +++   +
Sbjct: 75  FNALCHSTHLYGRRLVLEWADSEVTVQSGPS 105

>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 = 91.5 bits (228), Expect = 1e-22
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N++V NL  S T E +K++F ++G + +  ++ D +  K K FGFV  +  +  ++A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 269 LNGKKFDDREWYVGKAQKKSEREQE 293
           L+   F  R   V +A  K   E  
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHH 86

>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 = 79.9 bits (198), Expect = 2e-18
 Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           N+Y+ NL  S   E++KELFS+FG + + K++ D  +   KG GFV     E  S A+A+
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           ++    + + + V  A  K+     
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHH 86

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 72.6 bits (179), Expect = 6e-16
 Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           ++YVG+L ++ T  Q+ +LFSQ G+V +V++  D  T++  G+G+V        + A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 91  LNFTPLNNKSIRI 103
           L+ T    ++IR+
Sbjct: 62  LDNTDFMGRTIRV 74

>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 = 71.4 bits (176), Expect = 1e-15
 Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
           NI++ NL  S   + + + FS FG + + K+  D  + + KGFGFV+ +  ES   AI K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 178 LNG 180
           L+ 
Sbjct: 62  LDN 64

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 91.9 bits (229), Expect = 1e-22
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             +FV  + E  T+ED+   F EYG I +  +  D   G  K +  V +E   +A  A+E
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 268 ALNGKKFDDREWYVGKAQKK 287
            LNG+    +   V     +
Sbjct: 84  GLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 80.8 bits (200), Expect = 1e-18
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +F+  + +    + +HD F+ +G I +  +  D  +G  KG+  V++E  + AQ A++ 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 178 LNGMLINDKQVFVGH 192
           LNG  +  + + V  
Sbjct: 85  LNGQDLMGQPISVDW 99

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 78.5 bits (194), Expect = 8e-18
 Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           +G  L++  + +   +E + + F+E+G I +  +  D  +G  KG   V + T +EA  A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 369 LAEMNGKMIVSKPLYVAVAQRK 390
           +  +NG+ ++ +P+ V     +
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 76.1 bits (188), Expect = 4e-17
 Identities = 18/74 (24%), Positives = 35/74 (47%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             L+V  +    T+  ++D F++ G++ ++ +  D  T    GY  V Y    +A  A++
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 90  VLNFTPLNNKSIRI 103
            LN   L  + I +
Sbjct: 84  GLNGQDLMGQPISV 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 = 92.0 bits (229), Expect = 1e-22
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 3/84 (3%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
              + + NL  S T+E L+++F +   I    V ++ +GKSK + F+ F + +DA +A+ 
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALN 71

Query: 268 ALNGKKFDDREWYVGKAQKKSERE 291
           + N ++ + R   +     +    
Sbjct: 72  SCNKREIEGRAIRLELQGPRGSPN 95

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 81.6 bits (202), Expect = 5e-19
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L + NL  S  +E L+E+F +   I   KV ++ +G SKG  F+ F++ E+A  AL   N
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74

Query: 374 GKMIVSKPLYVAVAQRKEERRAR 396
            + I  + + + +   +    + 
Sbjct: 75  KREIEGRAIRLELQGPRGSPNSG 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 = 74.6 bits (184), Expect = 1e-16
 Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENK 168
             S     +  + + NL  S   + L + F     I   K+  + +G+SKG+ F++F + 
Sbjct: 7   GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASF 63

Query: 169 ESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           E A+ A++  N   I  + + +     +    
Sbjct: 64  EDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 68.5 bits (168), Expect = 2e-14
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            +L + +L ++ T+  L ++F +   +            +S GY ++ +A+  DA  AL+
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFIEFASFEDAKEALN 71

Query: 90  VLNFTPLNNKSIRI 103
             N   +  ++IR+
Sbjct: 72  SCNKREIEGRAIRL 85

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 92.7 bits (230), Expect = 1e-22
 Identities = 19/117 (16%), Positives = 37/117 (31%), Gaps = 6/117 (5%)

Query: 284 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE----LFSEFGTIT 339
            +  + + +                     + I N+   +  EKL+     L S  G I 
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61

Query: 340 SCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
              V       + G  ++ F+T E A   +    G      PL +  ++  + + A 
Sbjct: 62  DIVVDLSDD--NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE 116

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 85.7 bits (212), Expect = 4e-20
 Identities = 18/100 (18%), Positives = 31/100 (31%), Gaps = 7/100 (7%)

Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
             V + N++     E L+     +    G I   VV       +    ++ F   + A  
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD--DNSGKAYIVFATQESAQA 87

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 304
            VEA  G  F      +  ++    +  E  G  E     
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQSQVAE-DGSLEHHHHH 126

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 75.7 bits (186), Expect = 1e-16
 Identities = 18/119 (15%), Positives = 41/119 (34%), Gaps = 10/119 (8%)

Query: 8   HQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCR 63
            +  M  P+  +         +  + + +++  V   +L    Y L S  G +L + V  
Sbjct: 10  ERQHMDSPDLGSTPPHTEP--SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL 67

Query: 64  DLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP-SIRKSGTGNIF 121
              +  + G  Y+ +A    A   ++     P     + I +S      + + G+    
Sbjct: 68  ---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHH 123

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 74.2 bits (182), Expect = 4e-16
 Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 8/95 (8%)

Query: 109 DPSIRKSGTGNIFIKNLDKSID----HKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQ 164
            P    S    + I N++  +        L+   SS G+IL   +    S  + G  ++ 
Sbjct: 23  PPHTEPSQV--VLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIV 78

Query: 165 FENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           F  +ESAQ  ++   G       + +      Q +
Sbjct: 79  FATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQ 113

>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 = 91.2 bits (227), Expect = 2e-22
 Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 4/84 (4%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 266
              +FVK L E TT+E LK+ F        A ++ D + G SK FGFV+F + +DA  A 
Sbjct: 15  SKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 267 EALNGKKFDDREWYVGKAQKKSER 290
           EA+   + D  +  +  A+ K E 
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKGEG 95

>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 = 76.9 bits (190), Expect = 2e-17
 Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L++K L +   +E LKE F         +++ D  +G SKG GFV F++ E+A  A   
Sbjct: 17  TLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           M    I    + +  A+ K E  + 
Sbjct: 74  MEDGEIDGNKVTLDWAKPKGEGGSG 98

>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 = 73.4 bits (181), Expect = 4e-16
 Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
               P+ R   +  +F+K L +    + L ++F      +  +I TD  +G SKGFGFV 
Sbjct: 4   GSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVD 60

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           F ++E A+ A + +    I+  +V +
Sbjct: 61  FNSEEDAKAAKEAMEDGEIDGNKVTL 86

>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 = 72.7 bits (179), Expect = 7e-16
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           + +L+V  L  + T+  L + F      +  R+  D  T  S G+G+V++ +  DA  A 
Sbjct: 15  SKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 89  DVLNFTPLNNKSIRI 103
           + +    ++   + +
Sbjct: 72  EAMEDGEIDGNKVTL 86

>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 = 91.3 bits (227), Expect = 2e-22
 Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 7/90 (7%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
            VF++NL   + +E L ++  ++G +    V+   D   SK   F  F   + A K + A
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 269 LN------GKKFDDREWYVGKAQKKSEREQ 292
            +      G K D R+  V  A  + E   
Sbjct: 77  ASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>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 = 86.6 bits (215), Expect = 1e-20
 Identities = 27/97 (27%), Positives = 47/97 (48%), Gaps = 7/97 (7%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
           D  +G  ++I+NL    ++E L E+  +FG +   +V+  P +  SKG  F  F T E A
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70

Query: 366 SRALAEMN------GKMIVSKPLYVAVAQRKEERRAR 396
            + LA  +      G  +  + L V +A  ++E  + 
Sbjct: 71  QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>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 = 79.3 bits (196), Expect = 5e-18
 Identities = 20/113 (17%), Positives = 46/113 (40%), Gaps = 11/113 (9%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG +G+ +  +       ++++ +L F+  +  L ++  Q G +  VRV     T  S G
Sbjct: 3   SGSSGLPSDVTEG----KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG 58

Query: 73  YGYVNYANPADAARALDVLNFTP------LNNKSIRIMYSH-RDPSIRKSGTG 118
             +  +     A + L   +         L+ + +++  +  RD +     +G
Sbjct: 59  CAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111

>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 = 77.0 bits (190), Expect = 2e-17
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 1/87 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
                +    +FI+NL    + +AL +    FG++   ++     +  SKG  F QF  +
Sbjct: 8   LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67

Query: 169 ESAQNAIDKLNGMLINDKQVFVGHFLR 195
           E+AQ  +   +           G  L+
Sbjct: 68  EAAQKCLAAASLEAEGGGLKLDGRQLK 94

>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 = 90.7 bits (226), Expect = 3e-22
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 3/84 (3%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 266
            +++ NL   TTDEDL +     G   I       +   G+SK F  V   +   + K +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 267 EALNGKKFDDREWYVGKAQKKSER 290
           + L  ++   +   V  + K    
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHH 86

>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 = 82.2 bits (204), Expect = 2e-19
 Identities = 19/88 (21%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
           + LYI NL     DE L E     G   I   K   +  +G SKG   V   +   + + 
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           +  +  + +  +   V  + + E     
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLEHHHHH 89

>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 = 75.3 bits (186), Expect = 5e-17
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFG--NILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
            ++I NL      + L +   S G  +IL  K   +  +GQSKGF  V   ++ S++  +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 176 DKLNGMLINDKQVFVGHFLRKQER 199
           D L    ++ +   V    + +  
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHH 86

>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 = 74.5 bits (184), Expect = 1e-16
 Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           +LY+G+L +  TD  L +    +G   +L ++   + +  +S G+  V   + A + + +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 89  DVLNFTPLNNKSIRIMYS 106
           D+L    L+ ++  +  S
Sbjct: 63  DLLPKRELHGQNPVVTPS 80

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 91.8 bits (228), Expect = 4e-22
 Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             ++V  L E   D+ L   F  +G IT   +  D +  K + F FV FE A+DAA A++
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123

Query: 268 ALNGKKFDDREWYVGKA 284
            +N  +   R   V  A
Sbjct: 124 NMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 88.7 bits (220), Expect = 6e-21
 Identities = 27/95 (28%), Positives = 48/95 (50%)

Query: 9   QAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR 68
           +  + G +G + G+ G+      LYVG L   V D  L+  F   G +  +++  D  T 
Sbjct: 43  ERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE 102

Query: 69  RSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI 103
           +  G+ +V +    DAA A+D +N + L  ++IR+
Sbjct: 103 KHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 84.8 bits (210), Expect = 1e-19
 Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 1/102 (0%)

Query: 287 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD 346
            +  E+ + G    +            LY+  L + +DD+ L   F  FG IT  ++  D
Sbjct: 39  VNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 98

Query: 347 P-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA 387
             +   +G  FV F   E+A+ A+  MN   +  + + V +A
Sbjct: 99  YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 78.7 bits (194), Expect = 1e-17
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID 
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124

Query: 178 LNG 180
           +N 
Sbjct: 125 MNE 127

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 89.3 bits (222), Expect = 8e-22
 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 265
           + + ++N+   T  + +      Y +  + +  +++D    +++ F FV   +A DA++ 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 266 VEALNGK----KFDDREWYVGKAQK 286
           ++ L       K D +   V  A+ 
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 76.2 bits (188), Expect = 3e-17
 Identities = 13/84 (15%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQ--VLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
             ++ + ++  +     +    S      V ++R+ +D  T+++ G+ +V  ++  DA++
Sbjct: 9   MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQ 68

Query: 87  ALDVLN----FTPLNNKSIRIMYS 106
            L +L        ++ K+I + ++
Sbjct: 69  LLQILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 75.1 bits (185), Expect = 7e-17
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGN--ILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
              I ++N+       ++    S + +  + + ++  D  + Q++GF FVQ  +   A  
Sbjct: 9   MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQ 68

Query: 174 AIDKLNGM----LINDKQVFV 190
            +  L  +     I+ K + V
Sbjct: 69  LLQILQSLHPPLKIDGKTIGV 89

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 74.3 bits (183), Expect = 2e-16
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
            + ++N+      + +    S + +  + + ++++D  +  ++G  FV  S+  +AS+ L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 370 AEMNGK----MIVSKPLYVAVAQR 389
             +        I  K + V  A+ 
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKS 94

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 88.5 bits (220), Expect = 1e-21
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             +  KNL  + T+++LK++F +   I    ++   DGKSK   ++ F++  DA K +E 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEI---RLVSQ-DGKSKGIAYIEFKSEADAEKNLEE 72

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
             G + D R   +    +K   
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGT 94

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 79.2 bits (196), Expect = 3e-18
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L  KNL  +I +++LKE+F +   I   +++    G SKG  ++ F +  +A + L E 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEI---RLVSQ-DGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
            G  I  + + +     K   R 
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 70.4 bits (173), Expect = 3e-15
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            +L   +L FN+T+ +L ++F    ++  V         +S G  Y+ + + ADA + L+
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 71

Query: 90  VLNFTPLNNKSIRIMYS 106
                 ++ +S+ + Y+
Sbjct: 72  EKQGAEIDGRSVSLYYT 88

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
            S +      +  KNL  +I    L + F     I          G+SKG  +++F+++ 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI----RLVSQDGKSKGIAYIEFKSEA 64

Query: 170 SAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
            A+  +++  G  I+ + V + +   K   
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 88.4 bits (220), Expect = 2e-21
 Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + V N+  + T+++L+  F EYG +    +++D       + FV+ E A+DA +A+  
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRG 63

Query: 269 LNGKKFDDREWYVGKAQKKSERE 291
           L+  +F  +  +V  +  +    
Sbjct: 64  LDNTEFQGKRMHVQLSTSRLRTA 86

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 76.9 bits (190), Expect = 2e-17
 Identities = 15/84 (17%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++ N+  +  +++L+  F E+G +  C +++D         FV     E+A  A+  +
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY-------AFVHMERAEDAVEAIRGL 64

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           +      K ++V ++  +    + 
Sbjct: 65  DNTEFQGKRMHVQLSTSRLRTASG 88

>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 = 65.7 bits (161), Expect = 1e-13
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 11/91 (12%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           +T L+VG++    T+ +L   F + G V+   + +         Y +V+     DA  A+
Sbjct: 10  STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAI 61

Query: 89  DVLNFTPLNNKSIRIMYSH---RDPSIRKSG 116
             L+ T    K + +  S    R  S   SG
Sbjct: 62  RGLDNTEFQGKRMHVQLSTSRLRTASGPSSG 92

>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 = 64.9 bits (159), Expect = 3e-13
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
               +  + + N+  +  ++ L   F  +G ++ C I        K + FV  E  E A 
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAV 58

Query: 173 NAIDKLNGMLINDKQVFV 190
            AI  L+      K++ V
Sbjct: 59  EAIRGLDNTEFQGKRMHV 76

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 88.1 bits (219), Expect = 3e-21
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            V+V NL       +L++ F  YG + +  + R+       F FV FE+  DA  AV  L
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           +GK        V  +     R
Sbjct: 58  DGKVICGSRVRVELSTGMPRR 78

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 73.5 bits (181), Expect = 4e-16
 Identities = 26/102 (25%), Positives = 48/102 (47%), Gaps = 6/102 (5%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           + +Y+ NLG      +L+  FS +G + +  + R+P G      FV F  P +A  A+  
Sbjct: 1   MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGF----AFVEFEDPRDAEDAVRG 56

Query: 372 MNGKMIVSKPLYVAVAQ--RKEERRARLQAQFSQMRPVAMGP 411
           ++GK+I    + V ++    +  R  R  A+   +  +  GP
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGP 98

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 66.2 bits (162), Expect = 1e-13
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            +++ NL        L   FS +G + +  IA +      GF FV+FE+   A++A+  L
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 179 NGMLINDKQVFV 190
           +G +I   +V V
Sbjct: 58  DGKVICGSRVRV 69

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 61.9 bits (151), Expect = 4e-12
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
            +YVG+L       +L   FS  G + +V +      R   G+ +V + +P DA  A+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56

Query: 91  LNFTPLNNKSIRIMYSHRDP 110
           L+   +    +R+  S   P
Sbjct: 57  LDGKVICGSRVRVELSTGMP 76

>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 = 87.3 bits (217), Expect = 3e-21
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            +F+ NL    T+++++ +F +YG +    ++++       +GFV+ E+   A  A+  L
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-------YGFVHIEDKTAAEDAIRNL 62

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           +  K       V  ++ KS+ 
Sbjct: 63  HHYKLHGVNINVEASKNKSKA 83

>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 = 75.7 bits (187), Expect = 4e-17
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L+I NL     +++++ LF ++G +  C ++       K  GFV       A  A+  +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           +   +    + V  ++ K +  + 
Sbjct: 63  HHYKLHGVNINVEASKNKSKASSG 86

>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 = 69.9 bits (172), Expect = 5e-15
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 111 SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKES 170
           S   SG   +FI NL +    + +   F  +G +L C I        K +GFV  E+K +
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTA 54

Query: 171 AQNAIDKLNGMLINDKQVFV 190
           A++AI  L+   ++   + V
Sbjct: 55  AEDAIRNLHHYKLHGVNINV 74

>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 = 65.3 bits (160), Expect = 2e-13
 Identities = 25/99 (25%), Positives = 47/99 (47%), Gaps = 10/99 (10%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG+      L++G+L    T+ ++  LF Q G+VL   + +         YG+V+  +
Sbjct: 1   GSSGSS-GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIED 51

Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
              A  A+  L+   L+  +I +  S ++ S   SG  +
Sbjct: 52  KTAAEDAIRNLHHYKLHGVNINVEAS-KNKSKASSGPSS 89

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 86.7 bits (215), Expect = 6e-21
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +   L I+N+   +  E L  L  ++G + SC+ +   S        V +S+ ++A +AL
Sbjct: 14  RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS--ETAVVNVTYSSKDQARQAL 71

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERR 394
            ++NG  + +  L VA    +   +
Sbjct: 72  DKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 84.0 bits (208), Expect = 6e-20
 Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           + +   + ++N+      E L  +  +YG + S   +            V + + D A +
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN--TDSETAVVNVTYSSKDQARQ 69

Query: 265 AVEALNGKKFDDREWYVGKAQKKSERE 291
           A++ LNG + ++    V     +   +
Sbjct: 70  ALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 79.8 bits (197), Expect = 2e-18
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 106 SHRDPSI-RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQ 164
           S    S+ ++     + I+N+   +  + L      +G + SC+     S        V 
Sbjct: 3   SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS--ETAVVNVT 60

Query: 165 FENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           + +K+ A+ A+DKLNG  + +  + V +   +   +
Sbjct: 61  YSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 72.9 bits (179), Expect = 4e-16
 Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 4/92 (4%)

Query: 14  GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
           G +G +      Q     L + ++  ++    L  L  Q G V S   C  ++T      
Sbjct: 1   GSSGSSGSVPKRQ-RIRKLQIRNIPPHLQWEVLDSLLVQYGVVES---CEQVNTDSETAV 56

Query: 74  GYVNYANPADAARALDVLNFTPLNNKSIRIMY 105
             V Y++   A +ALD LN   L N ++++ Y
Sbjct: 57  VNVTYSSKDQARQALDKLNGFQLENFTLKVAY 88

>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 = 88.8 bits (220), Expect = 7e-21
 Identities = 30/145 (20%), Positives = 51/145 (35%), Gaps = 24/145 (16%)

Query: 158 KGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFN-------- 209
           KG    +  +  +A+    +             G +      +T  +    +        
Sbjct: 13  KGETTTEAVDAATAEKVFKQYAN-----DNGVDGEWTYDDATKTFTVTEGSHHHHHHMHR 67

Query: 210 -------NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDA 262
                   V+V NL  +    +L++ FG YG + S  V R+       F FV FE+  DA
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDA 123

Query: 263 AKAVEALNGKKFDDREWYVGKAQKK 287
           A AV  L+G+        V  +  +
Sbjct: 124 ADAVRELDGRTLCGCRVRVELSNGE 148

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 83.0 bits (205), Expect = 7e-19
 Identities = 32/148 (21%), Positives = 59/148 (39%), Gaps = 8/148 (5%)

Query: 247 KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETV 306
             K        +A  A K  +        D EW    A K     +          +++ 
Sbjct: 11  TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC 70

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
                  +Y+ NLG++ +  +L+  F  +G + S  V R+P G      FV F  P +A+
Sbjct: 71  P--LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF----AFVEFEDPRDAA 124

Query: 367 RALAEMNGKMIVSKPLYVAVAQRKEERR 394
            A+ E++G+ +    + V ++    E+R
Sbjct: 125 DAVRELDGRTLCGCRVRVELS--NGEKR 150

>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 = 67.2 bits (164), Expect = 2e-13
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFV 163
           M+    P   K     +++ NL  + +   L   F  +G + S  +A +      GF FV
Sbjct: 65  MHRDSCPLDCK-----VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFV 115

Query: 164 QFENKESAQNAIDKLNGMLINDKQVFVGH 192
           +FE+   A +A+ +L+G  +   +V V  
Sbjct: 116 EFEDPRDAADAVRELDGRTLCGCRVRVEL 144

>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 = 65.3 bits (159), Expect = 8e-13
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 28  LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
           L   +YVG+L  N   ++L   F   G + SV V      R   G+ +V + +P DAA A
Sbjct: 72  LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADA 126

Query: 88  LDVLNFTPLNNKSIRIMYSHRDP 110
           +  L+   L    +R+  S+ + 
Sbjct: 127 VRELDGRTLCGCRVRVELSNGEK 149

>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 = 87.0 bits (216), Expect = 7e-21
 Identities = 23/91 (25%), Positives = 47/91 (51%), Gaps = 4/91 (4%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
             + L+I  +  ++D++ LK LF EFG I    V++D  +G+ KG  F+ +   E A +A
Sbjct: 12  DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 369 LAEMNGKMIV---SKPLYVAVAQRKEERRAR 396
            + ++ +  +   ++P+ V  A  +    + 
Sbjct: 72  QSALHEQKTLPGMNRPIQVKPADSESRGGSG 102

>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 = 82.0 bits (203), Expect = 4e-19
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
            +F+  +  +  ++DLK +F E+G I    V++D   G  K   F+ +   + A KA  A
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 269 LNGKK---FDDREWYVGKAQKKSER 290
           L+ +K     +R   V  A  +S  
Sbjct: 75  LHEQKTLPGMNRPIQVKPADSESRG 99

>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 = 77.4 bits (191), Expect = 2e-17
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
             ++      +FI  + +++D K L   F  FG I    +  D  +G  KG  F+ +  +
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 169 ESAQNAIDKLNGMLIND 185
           ESA  A   L+      
Sbjct: 66  ESALKAQSALHEQKTLP 82

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 73.1 bits (180), Expect = 5e-16
 Identities = 23/106 (21%), Positives = 43/106 (40%), Gaps = 6/106 (5%)

Query: 17  GVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYV 76
           G +  +         L++G +  N+ +  L  LF + G++  + V +D  T    G  ++
Sbjct: 1   GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 77  NYANPADAARALDVLN---FTPLNNKSIRIMYS---HRDPSIRKSG 116
            Y     A +A   L+     P  N+ I++  +    R  S   SG
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106

>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 = 86.5 bits (215), Expect = 7e-21
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           +FV N+  + T ++L+ +F   G +    V++D       + FV+ E   DA  A+  LN
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64

Query: 271 GKKFDDREWYVGKAQKKSER 290
           GK+   +   V  + K  ++
Sbjct: 65  GKEVKGKRINVELSTKGQKK 84

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 76.1 bits (188), Expect = 3e-17
 Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +++ N+  +   ++L+ LF   G +  C V++D         FV      +A  A+A++N
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY-------AFVHMEKEADAKAAIAQLN 64

Query: 374 GKMIVSKPLYVAVAQRKEERRA 395
           GK +  K + V ++ + +++  
Sbjct: 65  GKEVKGKRINVELSTKGQKKSG 86

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 8/98 (8%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG+   T  ++VG++    T  +L  LF + G+V+   V +         Y +V+   
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEK 52

Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
            ADA  A+  LN   +  K I +  S +        +G
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPSSG 90

>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 = 67.2 bits (165), Expect = 3e-14
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
               T  IF+ N+  +   + L   F   G ++ C +        K + FV  E +  A+
Sbjct: 5   SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAK 57

Query: 173 NAIDKLNGMLINDKQVFV 190
            AI +LNG  +  K++ V
Sbjct: 58  AAIAQLNGKEVKGKRINV 75

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N +++ NL  + T +DL+++FG+     +  V          + FV++ + + A +A+E 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIET 63

Query: 269 LNGK-KFDDREWYVGKAQKKSERE 291
           L+GK +   +   V  +  K  R 
Sbjct: 64  LSGKVELHGKIMEVDYSVSKKLRS 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 = 74.6 bits (184), Expect = 1e-16
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LYI NL  ++  + L++LF +     + +V+        G  FV +     A RA+  ++
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLS 65

Query: 374 GKM-IVSKPLYVAVAQRKEERRA 395
           GK+ +  K + V  +  K+ R +
Sbjct: 66  GKVELHGKIMEVDYSVSKKLRSS 88

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 70.0 bits (172), Expect = 5e-15
 Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG   ++I NL  ++    L   F      L+ ++         G+ FV + ++  A  A
Sbjct: 6   SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRA 60

Query: 175 IDKLNGML-INDKQVFVGHFLRKQERET 201
           I+ L+G + ++ K + V + + K+ R +
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRSS 88

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 70.0 bits (172), Expect = 5e-15
 Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 8/88 (9%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             LY+G+L   VT   L  LF      L+ +           GY +V+Y +   A RA++
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE 62

Query: 90  VLN-FTPLNNKSIRIMYSHRDPSIRKSG 116
            L+    L+ K + + YS     +R SG
Sbjct: 63  TLSGKVELHGKIMEVDYS-VSKKLRSSG 89

>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 = 86.0 bits (213), Expect = 2e-20
 Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 14/102 (13%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             +  KNL   T   ++++ F  +G++   ++      +      V F    +A KA   
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRH 65

Query: 269 LNGKKFDDREWYVGKA---------QKKSEREQELKGQFEQA 301
           L   KF     Y+  A         QKK  + ++   + E  
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESG 107

>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 = 68.3 bits (167), Expect = 3e-14
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +  KNL       +++E FS FG++    +          +  V F  P EA +A   + 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLA 67

Query: 374 GKMIVSKPLYV 384
                  PLY+
Sbjct: 68  YSKFHHVPLYL 78

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 62.9 bits (153), Expect = 2e-12
 Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
            S  +S T  I  KNL        + +TFS FG++    +      +      V+F    
Sbjct: 4   GSSGRSKT-VILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPL 57

Query: 170 SAQNAIDKLNGMLINDKQVFV 190
            A+ A   L     +   +++
Sbjct: 58  EARKAFRHLAYSKFHHVPLYL 78

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 11/74 (14%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T +   +L      +++ + FS+ G +  V +              V +  P +A +A  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFR 64

Query: 90  VLNFTPLNNKSIRI 103
            L ++  ++  + +
Sbjct: 65  HLAYSKFHHVPLYL 78

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 85.5 bits (212), Expect = 3e-20
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAV--------VMRDGD-GKSKCFGFVNFENA 259
           N +FV+ L E+ T E +   F + G I +          +  D + GK K    V+F++ 
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 260 DDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
             A  A++  +GK+F      V  A ++++  +
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 75.1 bits (185), Expect = 1e-16
 Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 9/97 (9%)

Query: 306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGF 356
            D      ++++ LG+++  E + + F + G I +          +  D  +G  KG   
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 357 VAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 393
           V+F  P  A  A+   +GK     P+ V+ A R+ + 
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF 98

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 70.5 bits (173), Expect = 5e-15
 Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 9/97 (9%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS--------CKIATDG-SGQSKGFGFV 163
             S    IF++ L +++  +++ D F   G I +          + TD  +G+ KG   V
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 164 QFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
            F++  SA+ AID  +G   +   + V    R+ +  
Sbjct: 63  SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 67.4 bits (165), Expect = 6e-14
 Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 8/98 (8%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANP 81
            +++V  L  NVT   + D F Q+G + +        + +  D  T +  G   V++ +P
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 82  ADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
             A  A+D  +    +   I++ ++ R     + G   
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNG 105

>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 = 85.1 bits (211), Expect = 3e-20
 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NL      +D++ +F +YG I    +          F FV FE+  DA  AV   +
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAEDAVYGRD 82

Query: 271 GKKFDDREWYVGKAQKKSER 290
           G  +D     V   +     
Sbjct: 83  GYDYDGYRLRVEFPRSGRGT 102

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 69.7 bits (171), Expect = 1e-14
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 2/83 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y+ NL   I  + ++++F ++G I    +     G      FV F  P +A  A+   +
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAVYGRD 82

Query: 374 GKMIVSKPLYVAVAQRKEERRAR 396
           G       L V   +      + 
Sbjct: 83  GYDYDGYRLRVEFPRSGRGTGSG 105

>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 = 68.9 bits (169), Expect = 2e-14
 Identities = 20/107 (18%), Positives = 41/107 (38%), Gaps = 6/107 (5%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG +G              +YVG+L  ++    + D+F + G +  + +      R    
Sbjct: 6   SGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPP 62

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH---RDPSIRKSG 116
           + +V + +P DA  A+   +    +   +R+ +        S   SG
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSSG 109

>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 = 68.5 bits (168), Expect = 3e-14
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 4/83 (4%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFEN 167
           R P+        I++ NL   I  K + D F  +G I    +     G    F FV+FE+
Sbjct: 15  RGPAGNNDCR--IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFED 70

Query: 168 KESAQNAIDKLNGMLINDKQVFV 190
              A++A+   +G   +  ++ V
Sbjct: 71  PRDAEDAVYGRDGYDYDGYRLRV 93

>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 = 84.1 bits (209), Expect = 4e-20
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           +++V N+D   T E+L+  F   G++    ++ D   G  K F ++ F + +    ++ A
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66

Query: 269 LNGKKFDDREWYVGKAQKK 287
           L+   F  R+  V   +  
Sbjct: 67  LDESLFRGRQIKVIPKRTN 85

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 76.0 bits (188), Expect = 3e-17
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             S+YVG++D+  T  +L   F   G V  V +  D  +    G+ Y+ +++      +L
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

Query: 89  DVLNFTPLNNKSIRIMY 105
             L+ +    + I+++ 
Sbjct: 66  -ALDESLFRGRQIKVIP 81

>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 = 73.3 bits (181), Expect = 3e-16
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           ++Y+ N+      E+L+  F   G++    ++ D  SG  KG  ++ FS  E    +LA 
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66

Query: 372 MNGKMIVSKPLYVAVAQ 388
           ++  +   + + V   +
Sbjct: 67  LDESLFRGRQIKVIPKR 83

>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 = 73.3 bits (181), Expect = 3e-16
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           +I++ N+D     + L   F   G++    I  D  SG  KGF +++F +KES + ++  
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66

Query: 178 LNGMLINDKQVFV 190
           L+  L   +Q+ V
Sbjct: 67  LDESLFRGRQIKV 79

>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 = 84.7 bits (210), Expect = 5e-20
 Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 2/92 (2%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 264
           T F  +FV  L   TTD  L+K F  +G I  AVV+ D   GKS+ +GFV   +   A +
Sbjct: 15  TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKG 296
           A +  N    D R+  V  A   ++      G
Sbjct: 75  ACKDPN-PIIDGRKANVNLAYLGAKPRSLQTG 105

>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 = 77.7 bits (192), Expect = 2e-17
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +++  L     D  L++ F  FG I    V+ D  +G S+G GFV  +    A RA  + 
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 373 N----GKMIVSKPLYVAVAQRKEERRA 395
           N    G+          +A    + R+
Sbjct: 80  NPIIDGRKANVN-----LAYLGAKPRS 101

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 68.5 bits (168), Expect = 3e-14
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
           S +D +  K     IF+  L       +L   F  FG+I    + TD  +G+S+G+GFV 
Sbjct: 11  SQKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
             ++ +A+ A    N + I+ ++  V
Sbjct: 66  MADRAAAERACKDPNPI-IDGRKANV 90

>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 = 64.6 bits (158), Expect = 6e-13
 Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 1/87 (1%)

Query: 16  NGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
                  S      T ++VG L ++ TD+ L   F   G +    V  D  T +S GYG+
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 76  VNYANPADAARALDVLNFTPLNNKSIR 102
           V  A+ A A RA    N   ++ +   
Sbjct: 64  VTMADRAAAERACKDPNPI-IDGRKAN 89

>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 = 83.9 bits (208), Expect = 6e-20
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR-DGDGKSKCFGFVNFENADDAA 263
           K     + V+N+  + + +++   F  Y  I  +V ++ +  G       V FE+ D+A 
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 264 KAVEALNGKKFDDREWYVGKAQK 286
            AV  LN +    R+  +     
Sbjct: 72  AAVIDLNDRPIGSRKVKLSGPSS 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 69.3 bits (170), Expect = 1e-14
 Identities = 14/75 (18%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR-DPSGISKGSGFVAFSTPEEASRALAEM 372
           + ++N+  ++  +++ + F  +  I     ++ +  G+  G   VAF + +EA+ A+ ++
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 373 NGKMIVSKPLYVAVA 387
           N + I S+ + ++  
Sbjct: 78  NDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 66.2 bits (162), Expect = 1e-13
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 6/95 (6%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQV-LSVRVCRDLSTRRSL 71
           SG +G ++G  G     T + V ++ F V+  ++ D F     +  SV +  +       
Sbjct: 3   SGSSGSSSGKPGP----TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPT 57

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS 106
           G   V + +  +A  A+  LN  P+ ++ +++   
Sbjct: 58  GEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 66.2 bits (162), Expect = 1e-13
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 114 KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQ 172
           K G   I ++N+  ++    + D F  +  I     +  +  G   G   V FE+++ A 
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 173 NAIDKLNGMLINDKQVFV 190
            A+  LN   I  ++V +
Sbjct: 72  AAVIDLNDRPIGSRKVKL 89

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 86.1 bits (213), Expect = 7e-20
 Identities = 19/105 (18%), Positives = 45/105 (42%), Gaps = 3/105 (2%)

Query: 203 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENA 259
            ++ +   V+V +    TTD+ L ++    G   +       +   G+SK +  V   + 
Sbjct: 50  GLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASE 109

Query: 260 DDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 304
           +   K +E L GK  +  +  V  A +++  + E + +  + ++ 
Sbjct: 110 NSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRV 154

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 81.5 bits (201), Expect = 3e-18
 Identities = 24/148 (16%), Positives = 51/148 (34%), Gaps = 8/148 (5%)

Query: 267 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGL-----NLYIKNLGD 321
              +G        Y    +      QE   +        +  + GL      +Y+ +   
Sbjct: 6   HHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSW 65

Query: 322 SIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV 378
              D++L ++    G   +   K   +  +G SKG   V  ++     + L  + GK++ 
Sbjct: 66  WTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN 125

Query: 379 SKPLYVAVAQRKEERRARLQAQFSQMRP 406
            + + V  A R+   +   QA+  +   
Sbjct: 126 GEKVDVRPATRQNLSQFEAQARKRECVR 153

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 76.5 bits (188), Expect = 1e-16
 Identities = 20/100 (20%), Positives = 42/100 (42%), Gaps = 2/100 (2%)

Query: 9   QAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLS 66
               +    +    SG +    ++YVG   +  TD QL  +   +G   V+ ++   + +
Sbjct: 35  PKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS 106
             +S GY  V  A+     + L++L    LN + + +  +
Sbjct: 95  NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 72.6 bits (178), Expect = 3e-15
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFG--NILSCKIATD-GSGQSKGFGFVQFENKESA 171
           +    +++ +       + L     S G  +++  K A +  +GQSKG+  V   ++ S 
Sbjct: 53  NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSV 112

Query: 172 QNAIDKLNGMLINDKQVFV 190
              ++ L G ++N ++V V
Sbjct: 113 HKLLELLPGKVLNGEKVDV 131

>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 = 83.6 bits (207), Expect = 1e-19
 Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 9/93 (9%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAV--------VMRDGD-GKSKCFGFVNFENA 259
           + ++V+ L++S T +DL   F + G +            +  D + GK K    V++E+ 
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 260 DDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
             A  AVE  +GK F   +  V  A+KK     
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>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 = 78.2 bits (193), Expect = 1e-17
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 9/99 (9%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGFV 357
           +      +Y++ L DS+  + L + F + G +            +  D  +G  KG   V
Sbjct: 11  EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

Query: 358 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           ++  P  A  A+   +GK      L V++A++K    + 
Sbjct: 71  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSG 109

>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 = 70.9 bits (174), Expect = 4e-15
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 9/92 (9%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS--------CKIATDG-SGQSK 158
                  S    I+++ L+ S+    L D F   G +            I  D  +G+ K
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65

Query: 159 GFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           G   V +E+  +A+ A++  +G      ++ V
Sbjct: 66  GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKV 97

>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 = 66.7 bits (163), Expect = 1e-13
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 8/82 (9%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANP 81
           +++YV  L+ +VT   L D F Q G V          + +  D  T +  G   V+Y +P
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 82  ADAARALDVLNFTPLNNKSIRI 103
             A  A++  +        +++
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKV 97

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 83.1 bits (206), Expect = 1e-19
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAA 263
           K     + V+N+  + + +++   F  Y  I  +V +  +  G       V FE+ D+A 
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 264 KAVEALNGKKFDDREWYVGKAQKKS 288
            AV  LN +    R+  +      S
Sbjct: 72  AAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 74.3 bits (183), Expect = 2e-16
 Identities = 14/79 (17%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEASRALAEM 372
           + ++N+  ++  +++ + F  +  I     +  +  G+  G   VAF + +EA+ A+ ++
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 373 NGKMIVSKPLYVAVAQRKE 391
           N + I S+ + + +     
Sbjct: 78  NDRPIGSRKVKLVLGSGPS 96

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 21/100 (21%), Positives = 44/100 (44%), Gaps = 6/100 (6%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQV-LSVRVCRDLSTRRSL 71
           SG +G ++G  G     T + V ++ F V+  ++ D F     +  SV +  +       
Sbjct: 3   SGSSGASSGKPGP----TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPT 57

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPS 111
           G   V + +  +A  A+  LN  P+ ++ ++++      S
Sbjct: 58  GEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSS 97

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 67.7 bits (166), Expect = 3e-14
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI-LSCKIATDGSGQSKGFGFVQFENK 168
            S  K G   I ++N+  ++    + D F  +  I  S  +  +  G   G   V FE++
Sbjct: 8   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 169 ESAQNAIDKLNGMLINDKQVFV 190
           + A  A+  LN   I  ++V +
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKL 89

>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 = 83.0 bits (206), Expect = 2e-19
 Identities = 19/87 (21%), Positives = 45/87 (51%), Gaps = 2/87 (2%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 264
           +K N +FV  +  +  + +L++ F ++G +T  V++ D +  + + FGF+ FE+     +
Sbjct: 8   SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQ 67

Query: 265 AVEALNGKKFDDREWYVGKAQKKSERE 291
           AV   +      ++  V +A+ +  + 
Sbjct: 68  AVNM-HFHDIMGKKVEVKRAEPRDSKS 93

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 74.2 bits (183), Expect = 2e-16
 Identities = 17/84 (20%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +++  +  +  + +L+E F +FG +T   ++ D      +G GF+ F   +   +A+  M
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           +   I+ K + V  A+ ++ + + 
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSKSSG 95

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 66.4 bits (163), Expect = 1e-13
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
           +  IF+  +  +     L + F  FG +    +  D    + +GFGF+ FE+++S   A+
Sbjct: 10  SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69

Query: 176 DKLNGMLINDKQV 188
             ++   I  K+V
Sbjct: 70  -NMHFHDIMGKKV 81

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 15/82 (18%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 22  ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP 81
           +  +   +  ++VG +  N  +++L + F + G V  V +  D   +R  G+G++ + + 
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 82  ADAARALDVLNFTPLNNKSIRI 103
               +A++ ++F  +  K + +
Sbjct: 63  QSVDQAVN-MHFHDIMGKKVEV 83

>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 = 84.8 bits (209), Expect = 2e-19
 Identities = 30/137 (21%), Positives = 55/137 (40%), Gaps = 10/137 (7%)

Query: 77  NYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIF---IKNLDKSIDHKA 133
           ++ +   A  AL  +N     N ++    +  D  +  +G   +    ++NL   +    
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62

Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHF 193
           LH  FS FG +L     T  +        +Q+ +  SAQ+A   L+G  I +        
Sbjct: 63  LHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDGQNIYNA----CCT 115

Query: 194 LRKQERETVAIKTKFNN 210
           LR    +  ++  K+NN
Sbjct: 116 LRIDFSKLTSLNVKYNN 132

>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 = 58.6 bits (141), Expect = 3e-10
 Identities = 19/115 (16%), Positives = 44/115 (38%), Gaps = 4/115 (3%)

Query: 164 QFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDE 223
              +  SAQ A+  +N +   +  +             +A ++    + V+NL    T +
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLAL-AASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLD 61

Query: 224 DLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE 278
            L +IF ++GT+   +     +        + + +   A  A  +L+G+   +  
Sbjct: 62  VLHQIFSKFGTVLKIITFTKNNQFQ---ALLQYADPVSAQHAKLSLDGQNIYNAC 113

>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 = 54.7 bits (131), Expect = 5e-09
 Identities = 19/123 (15%), Positives = 44/123 (35%), Gaps = 16/123 (13%)

Query: 255 NFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNL 314
           +  +   A  A++A+N  +  +       A   +      +                L +
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPV-------------LRI 49

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 374
            ++NL   +  + L ++FS+FGT+         +        + ++ P  A  A   ++G
Sbjct: 50  IVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDG 106

Query: 375 KMI 377
           + I
Sbjct: 107 QNI 109

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 49.7 bits (118), Expect = 3e-07
 Identities = 26/114 (22%), Positives = 48/114 (42%), Gaps = 13/114 (11%)

Query: 2   AQIQVQHQAQMSGPNGVAAGASGNQFLTTS-------LYVGDLDFNVTDSQLYDLFSQVG 54
           A +Q  +  Q       A+ A+ +  +  +       + V +L + VT   L+ +FS+ G
Sbjct: 12  AALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFG 71

Query: 55  QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS--IRIMYS 106
            VL +       T+ +     + YA+P  A  A   L+   + N    +RI +S
Sbjct: 72  TVLKIITF----TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121

>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 = 82.8 bits (205), Expect = 3e-19
 Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           VF   L       DL+  F   G +    ++ D +  +SK   +V F        A+  L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
            G++       V  +Q +  R  
Sbjct: 87  TGQRLLGVPIIVQASQAEKNRLS 109

>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 = 80.4 bits (199), Expect = 2e-18
 Identities = 22/112 (19%), Positives = 46/112 (41%), Gaps = 5/112 (4%)

Query: 286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR 345
             S  +  ++   +    E  D      ++   L   I    L++ FS  G +   +++ 
Sbjct: 3   SGSSGKSPVREPVDNLSPEERDA---RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIIS 59

Query: 346 DP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
           D  S  SKG  +V F   +    A+  + G+ ++  P+ V  +Q ++ R + 
Sbjct: 60  DRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLSG 110

>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 = 77.4 bits (191), Expect = 2e-17
 Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +++   L   +    L D FS VG+V  VR+  D ++RRS G  YV +        A+  
Sbjct: 27  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG- 85

Query: 91  LNFTPLNNKSIRIMYSH-RDPSIRKSGTG 118
           L    L    I +  S      +    +G
Sbjct: 86  LTGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>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 = 74.7 bits (184), Expect = 2e-16
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 2/86 (2%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
              + S  +     +F   L   I  + L D FS+ G +   +I +D  S +SKG  +V+
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           F   +S   AI  L G  +    + V
Sbjct: 74  FCEIQSVPLAI-GLTGQRLLGVPIIV 98

>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 = 81.8 bits (202), Expect = 5e-19
 Identities = 26/83 (31%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N V V  L  S + +DLK    E G +  A V RDG       G V F   +D   AV  
Sbjct: 16  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVEFVRKEDMTYAVRK 69

Query: 269 LNGKKFDDREWYVGKAQKKSERE 291
           L+  KF   E      + K +  
Sbjct: 70  LDNTKFRSHEGETAYIRVKVDGP 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 = 71.0 bits (174), Expect = 3e-15
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +  L  S   + LK+   E G +    V RD      G+G V F   E+ + A+ +++
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 71

Query: 374 GKMIVSKPLYVAVAQRKEERRAR 396
                S     A  + K +    
Sbjct: 72  NTKFRSHEGETAYIRVKVDGPRS 94

>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 = 66.4 bits (162), Expect = 1e-13
 Identities = 18/96 (18%), Positives = 31/96 (32%), Gaps = 7/96 (7%)

Query: 106 SHRDPSIRKSGTGN-IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQ 164
           S          + N + +  L  S   + L D     G++    +  DG       G V+
Sbjct: 3   SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVE 56

Query: 165 FENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           F  KE    A+ KL+       +    +   K +  
Sbjct: 57  FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP 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 = 66.0 bits (161), Expect = 2e-13
 Identities = 21/105 (20%), Positives = 36/105 (34%), Gaps = 8/105 (7%)

Query: 14  GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
           G +G ++G   ++     + V  L  + +   L D   + G V    V RD       G 
Sbjct: 1   GSSG-SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GT 52

Query: 74  GYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
           G V +    D   A+  L+ T   +      Y        +S + 
Sbjct: 53  GVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 97

>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 = 82.1 bits (203), Expect = 7e-19
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           +V+V N+D  +T +DL+  F   G+I    ++ D   G  K + ++ F   +    AV A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
           ++   F  R   V   +     
Sbjct: 97  MDETVFRGRTIKVLPKRTNMPG 118

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 74.8 bits (184), Expect = 2e-16
 Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 1/102 (0%)

Query: 3   QIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC 62
             ++   A   GP    +     +    S+YVG++D+  T   L   FS  G +  + + 
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 63  RDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM 104
            D  +    GY Y+ +A       A+  ++ T    ++I+++
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVL 110

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 74.0 bits (182), Expect = 4e-16
 Identities = 20/113 (17%), Positives = 42/113 (37%), Gaps = 2/113 (1%)

Query: 285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM 344
             K       +G  +    E   +    ++Y+ N+      + L+  FS  G+I    ++
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 345 RDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
            D  SG  KG  ++ F+       A+A M+  +   + + V   +      + 
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRTNMPGISS 121

>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 = 71.7 bits (176), Expect = 3e-15
 Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAI 175
             ++++ N+D     + L   FSS G+I    I  D  SG  KG+ +++F  + S   A+
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95

Query: 176 DKLNGMLINDKQVFVGHFLRKQERE 200
             ++  +   + + V   L K+   
Sbjct: 96  -AMDETVFRGRTIKV---LPKRTNM 116

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 80.9 bits (200), Expect = 8e-19
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 10/93 (10%)

Query: 191 GHFLRKQERETVAIKTKFNNVFVKNL---DESTTD---EDLKKIFGEYGTITSAVVMRDG 244
           G  L+ + +E   I    + + V N+        +     + KIF ++G IT+     + 
Sbjct: 1   GDVLKDRPQEADGID---SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE- 56

Query: 245 DGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           DGK+K + F+ + +   A  AV+  +G K D +
Sbjct: 57  DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 64.0 bits (156), Expect = 9e-13
 Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 7/86 (8%)

Query: 120 IFIKNL------DKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQN 173
           I + N+              +H  FS FG I +     +  G++KG+ F+++ +   A +
Sbjct: 18  IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVD 76

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQER 199
           A+   +G  ++ +  F  +     ++
Sbjct: 77  AVKNADGYKLDKQHTFRVNLFTDFDK 102

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 61.3 bits (149), Expect = 7e-12
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 9/84 (10%)

Query: 302 MKETVDKFQGLN--LYIKNLGDSIDD------EKLKELFSEFGTITSCKVMRDPSGISKG 353
           +K+   +  G++  + + N+     D        + ++FS+FG IT+     +  G +KG
Sbjct: 4   LKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKG 62

Query: 354 SGFVAFSTPEEASRALAEMNGKMI 377
             F+ +++P  A  A+   +G  +
Sbjct: 63  YIFLEYASPAHAVDAVKNADGYKL 86

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 50.9 bits (122), Expect = 4e-08
 Identities = 13/81 (16%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 25 NQFLTTSLYVGDL------DFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
             + + + V ++            + ++ +FS+ G++ +     +    ++ GY ++ Y
Sbjct: 11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEY 68

Query: 79 ANPADAARALDVLNFTPLNNK 99
          A+PA A  A+   +   L+ +
Sbjct: 69 ASPAHAVDAVKNADGYKLDKQ 89

>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 = 80.0 bits (198), Expect = 2e-18
 Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             ++V  L  +T+   L + F  +G+I +   ++        F ++ +E+ D A  A   
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAK 72

Query: 269 LNGKKFD 275
           + G    
Sbjct: 73  MRGFPLG 79

>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 = 73.4 bits (181), Expect = 3e-16
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 11/88 (12%)

Query: 97  NNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ 156
           +  S +I Y   +P+ R      +++  L  +    AL   F  FG+I +          
Sbjct: 3   SGSSGKIGYGKANPTTR------LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---- 52

Query: 157 SKGFGFVQFENKESAQNAIDKLNGMLIN 184
              F ++Q+E+ ++AQ A  K+ G  + 
Sbjct: 53  -DSFAYIQYESLDAAQAACAKMRGFPLG 79

>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 = 71.9 bits (177), Expect = 1e-15
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++  LG +     L   F  FG+I +   ++          ++ + + + A  A A+M
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKM 73

Query: 373 NGKMI--VSKPLYVAVAQRK 390
            G  +    + L V  A+  
Sbjct: 74  RGFPLGGPDRRLRVDFAKSG 93

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 66.9 bits (164), Expect = 6e-14
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           TT L+VG L  N + + L   F + G + ++         +   + Y+ Y +   A  A 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYESLDAAQAAC 70

Query: 89  DVLNFTPLNNKSIRIM--YSHRDPS 111
             +   PL     R+   ++   PS
Sbjct: 71  AKMRGFPLGGPDRRLRVDFAKSGPS 95

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 79.0 bits (195), Expect = 2e-18
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 7/75 (9%)

Query: 209 NNVFVKNL---DESTTD---EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDA 262
           + + V N+        +     + KIF ++G IT+     + DGK+K + F+ + +   A
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHA 60

Query: 263 AKAVEALNGKKFDDR 277
             AV+  +G K D +
Sbjct: 61  VDAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 63.2 bits (154), Expect = 7e-13
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 11/78 (14%)

Query: 120 IFIKNL--------DKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESA 171
           I + N+        +K      +H  FS FG I +     +  G++KG+ F+++ +   A
Sbjct: 4   IVVDNVPQVGPDRLEKLK--NVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHA 60

Query: 172 QNAIDKLNGMLINDKQVF 189
            +A+   +G  ++ +  F
Sbjct: 61  VDAVKNADGYKLDKQHTF 78

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 62.0 bits (151), Expect = 2e-12
 Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
             + ++FS+FG IT+     +  G +KG  F+ +++P  A  A+   +G  +  +
Sbjct: 22  NVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 49.7 bits (119), Expect = 6e-08
 Identities = 14/66 (21%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 34 VGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF 93
          VG        + ++ +FS+ G++ +     +    ++ GY ++ YA+PA A  A+   + 
Sbjct: 12 VGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADG 69

Query: 94 TPLNNK 99
            L+ +
Sbjct: 70 YKLDKQ 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 79.0 bits (196), Expect = 2e-18
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 268
           +FV  L  +TT ED+K  F ++G +  A++M D    + + FGFV FE+ D   K  E  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 269 ---LNGKKFD 275
              +N K  +
Sbjct: 62  FHEINNKMVE 71

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 69.4 bits (171), Expect = 5e-15
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           +++  L  +   E +K  F +FG +    +M D  +   +G GFV F + +   +     
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 371 --EMNGKMI 377
             E+N KM+
Sbjct: 62  FHEINNKMV 70

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 64.4 bits (158), Expect = 2e-13
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  L  +   + +   F  FG +    +  D  + + +GFGFV FE+++  +    ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 179 NGMLINDKQV 188
           +   IN+K V
Sbjct: 61  HFHEINNKMV 70

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 59.0 bits (144), Expect = 2e-11
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG L  N T   +   F Q G+V    +  D +T R  G+G+V + +     +  ++ 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 92  NFTPLNNKSIRI 103
           +F  +NNK +  
Sbjct: 61  HFHEINNKMVEC 72

>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 = 79.6 bits (197), Expect = 3e-18
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 268
           + V  L   TT++DLK+ F  +G +    V +D   G SK FGFV F   +   K +   
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 269 --LNGKKFDDREWYVGKAQKKSEREQ 292
             ++G+  D           K  ++ 
Sbjct: 78  HMIDGRWCD-----CKLPNSKQSQDS 98

>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 = 74.6 bits (184), Expect = 1e-16
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L +  L     ++ LKE FS FG +   +V +D  +G SKG GFV F+  E   + +++ 
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 373 ---NGKMIVSKPLYVAVAQRKEERRA 395
              +G+    K         K+ + +
Sbjct: 78  HMIDGRWCDCKL-----PNSKQSQDS 98

>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 = 64.9 bits (159), Expect = 3e-13
 Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
           T ++ +  L      + L + FS+FG +L  ++  D  +G SKGFGFV+F   E+    +
Sbjct: 15  TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74

Query: 176 DKLNGMLINDKQVFVGHFLRKQERET 201
            + +  +I+ +         KQ +++
Sbjct: 75  SQRH--MIDGRWCDCKLPNSKQSQDS 98

>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 = 60.3 bits (147), Expect = 2e-11
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 16  NGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           +  ++G       T+ L V  L +  T+  L + FS  G+VL V+V +DL T  S G+G+
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 76  VNYANPADAARALDVLNFTPLNNKSIRI 103
           V +       + +   +   ++ +    
Sbjct: 62  VRFTEYETQVKVMSQRHM--IDGRWCDC 87

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 79.5 bits (196), Expect = 4e-18
 Identities = 26/83 (31%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N V V  L  S + +DLK    E G +  A V RDG       G V F   +D   AV  
Sbjct: 17  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVEFVRKEDMTYAVRK 70

Query: 269 LNGKKFDDREWYVGKAQKKSERE 291
           L+  KF   E      + K +  
Sbjct: 71  LDNTKFRSHEGETAYIRVKVDGP 93

>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 = 69.5 bits (170), Expect = 1e-14
 Identities = 21/99 (21%), Positives = 37/99 (37%), Gaps = 6/99 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +  L  S   + LK+   E G +    V RD      G+G V F   E+ + A+ +++
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 72

Query: 374 GKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 412
                S     A  + K +         S+ R  +   S
Sbjct: 73  NTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRS 111

>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 = 63.3 bits (154), Expect = 2e-12
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + +  L  S   + L D     G++    +  DG       G V+F  KE    A+ KL+
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVEFVRKEDMTYAVRKLD 72

Query: 180 GMLINDKQVFVGHFLRKQERE 200
                  +    +   K +  
Sbjct: 73  NTKFRSHEGETAYIRVKVDGP 93

>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 = 61.4 bits (149), Expect = 9e-12
 Identities = 18/87 (20%), Positives = 28/87 (32%), Gaps = 7/87 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           + V  L  + +   L D   + G V    V RD       G G V +    D   A+  L
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 71

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGTG 118
           + T   +      Y        +S + 
Sbjct: 72  DNTKFRSHEGETAYIRVKVDGPRSPSY 98

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 78.9 bits (195), Expect = 5e-18
 Identities = 19/97 (19%), Positives = 35/97 (36%), Gaps = 10/97 (10%)

Query: 95  PLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS 154
            +N +++  +     P +        +I N+        L   F +FG IL  K   +  
Sbjct: 10  QVNPQAVDHIIRSAPPRVT-----TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-- 62

Query: 155 GQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG 191
              KG  F++++  E A   I  L       + +  G
Sbjct: 63  ---KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 78.9 bits (195), Expect = 5e-18
 Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
             ++ N+    T+ DL  +F  +G I       +     K   F+ ++  + AA  + AL
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83

Query: 270 NGKKFDDRE 278
               F  R 
Sbjct: 84  ANFPFQGRN 92

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 78.5 bits (194), Expect = 6e-18
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+ Y+G++    T++ L  LF   G +L  +   +       G  ++ Y     AA  + 
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIV 81

Query: 90  VLNFTPLNNKSIRIMY 105
            L   P   +++R  +
Sbjct: 82  ALANFPFQGRNLRTGW 97

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 75.0 bits (185), Expect = 9e-17
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 5/70 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
             YI N+     +  L  LF  FG I   K   +     KG  F+ + T E+A+  +  +
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83

Query: 373 NGKMIVSKPL 382
                  + L
Sbjct: 84  ANFPFQGRNL 93

>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 = 77.5 bits (192), Expect = 5e-18
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 268
           +FV  L   T +E +++ FG +G + S  +  D    K + F F+ F+  +   K +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 269 ---LNGKK 273
              +   K
Sbjct: 62  YHNVGLSK 69

>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 = 67.5 bits (166), Expect = 2e-14
 Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           +++  L     +EK++E F  FG + S ++  D  +   +G  F+ F   E   + +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 371 --EMNGKMI 377
              +     
Sbjct: 62  YHNVGLSKC 70

>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 = 61.7 bits (151), Expect = 2e-12
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  L      + + + F  FG + S ++  D  + + +GF F+ F+ +E  +  ++K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 179 NGMLINDKQV 188
               +   + 
Sbjct: 61  KYHNVGLSKC 70

>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 = 54.4 bits (132), Expect = 1e-09
 Identities = 11/72 (15%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG L  +  + ++ + F   G+V S+ +  D  T +  G+ ++ +       + ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 92  NFTPLNNKSIRI 103
            +  +      I
Sbjct: 61  KYHNVGLSKCEI 72

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 76.8 bits (190), Expect = 1e-17
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 268
           +F+  L   TT E L++ FG++G +   +VMRD    +S+ FGFV F +     K +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 269 ---LNGKKFD 275
              L+ K  D
Sbjct: 63  RHELDSKTID 72

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 74.4 bits (184), Expect = 7e-17
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 371 --EMNGKMIVSK 380
             E++ K I  K
Sbjct: 63  RHELDSKTIDPK 74

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 60.2 bits (147), Expect = 8e-12
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI  L      + L + F  FG +  C +  D  + +S+GFGFV F ++      +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 179 NGMLINDKQV 188
           +   ++ K +
Sbjct: 62  SRHELDSKTI 71

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 58.7 bits (143), Expect = 3e-11
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++G L +  T   L + F Q G+V    V RD  T+RS G+G+V + + A   + L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 92  NFTPLNNKSIR 102
           +   L++K+I 
Sbjct: 62  SRHELDSKTID 72

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 77.7 bits (192), Expect = 1e-17
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAV--------VMRDGD-GKSKCFGFVNFENA 259
           N +FV+ L E+ T E +   F + G I +          +  D + GK K    V+F++ 
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 260 DDAAKAVEALNGKKFDDREWYVGKA 284
             A  A++  +GK+F      V  A
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 72.3 bits (178), Expect = 7e-16
 Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 9/93 (9%)

Query: 107 HRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS--------CKIATDG-SGQS 157
           H       S    IF++ L +++  +++ D F   G I +          + TD  +G+ 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 158 KGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           KG   V F++  SA+ AID  +G   +   + V
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95

>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 = 68.5 bits (168), Expect = 2e-14
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGFVAFSTPE 363
            ++++ LG+++  E + + F + G I +          +  D  +G  KG   V+F  P 
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 364 EASRALAEMNGKMIVSKPLYVAVA 387
            A  A+   +GK     P+ V+ A
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 67.3 bits (165), Expect = 5e-14
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANP 81
            +++V  L  NVT   + D F Q+G + +        + +  D  T +  G   V++ +P
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 82  ADAARALDVLNFTPLNNKSIRI 103
             A  A+D  +    +   I++
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKV 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 = 77.3 bits (191), Expect = 2e-17
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV  LD STT E L+  F +YG +   V+M+D    +S+ FGFV F++ +     + + 
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS- 77

Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
                D R         +  +  
Sbjct: 78  RPHTLDGRNIDPKPCTPRGMQPS 100

>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 = 71.5 bits (176), Expect = 2e-15
 Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 10/87 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           L++  L  S   E L+  FS++G +  C +M+D  +  S+G GFV F  P      LA  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78

Query: 371 --EMNGKMIVSKPLYVAVAQRKEERRA 395
              ++G+ I  KP        +  + +
Sbjct: 79  PHTLDGRNIDPKP-----CTPRGMQPS 100

>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 = 58.8 bits (143), Expect = 6e-11
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 5/86 (5%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
           S    +      G +F+  LD S   + L   FS +G ++ C I  D  + QS+GFGFV+
Sbjct: 5   SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVK 64

Query: 165 FENKESAQNAID----KLNGMLINDK 186
           F++       +      L+G  I+ K
Sbjct: 65  FKDPNCVGTVLASRPHTLDGRNIDPK 90

>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 = 58.4 bits (142), Expect = 7e-11
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 14  GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
           G +G +   +        L+VG LD++ T   L   FSQ G+V+   + +D +T +S G+
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60

Query: 74  GYVNYANPADAARALDVLNFTPLNNKSIR 102
           G+V + +P      L       L+ ++I 
Sbjct: 61  GFVKFKDPNCVGTVLAS-RPHTLDGRNID 88

>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 = 76.9 bits (190), Expect = 3e-17
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FGFV F +  +   A+ A 
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88

Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
                D R     +A  + E   
Sbjct: 89  RPHSIDGRVVEPKRAVAREESGS 111

>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 = 72.7 bits (179), Expect = 1e-15
 Identities = 29/87 (33%), Positives = 46/87 (52%), Gaps = 10/87 (11%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS+  E   A+A  
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 371 --EMNGKMIVSKPLYVAVAQRKEERRA 395
              ++G+++  K      A  +EE  +
Sbjct: 90  PHSIDGRVVEPKR-----AVAREESGS 111

>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 = 58.8 bits (143), Expect = 7e-11
 Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
                   K     +FI  L      ++L + +  +G +  C +  D  S +S+GFGFV 
Sbjct: 16  PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75

Query: 165 FENKESAQNAID----KLNGMLINDK 186
           F +      A+      ++G ++  K
Sbjct: 76  FSSMAEVDAAMAARPHSIDGRVVEPK 101

>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 = 57.3 bits (139), Expect = 2e-10
 Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  T+  L + + Q G++    V RD +++RS G+G+V +++ A+   A+   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88

Query: 92  NFTPLNNKSIR 102
               ++ + + 
Sbjct: 89  RPHSIDGRVVE 99

>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 = 76.8 bits (189), Expect = 4e-17
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 209 NNVFVKNLDESTTDEDL---KKIFGEYGTITSAVVMRD----GDGKSKCFGFVNFENADD 261
           N VFV  L +   D ++    + FG++G I   V+       G        +V +  ++D
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 262 AAKAVEALNGKKFDDR 277
           A +A++ +N    D R
Sbjct: 76  ALRAIQCVNNVVVDGR 91

>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 = 64.5 bits (157), Expect = 6e-13
 Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 12/92 (13%)

Query: 32  LYVGDLDFNVTDSQL---YDLFSQVGQVLSVRVCRDLST---RRSLGYGYVNYANPADAA 85
           ++V  L   + D ++    + F + G++  V +    S    +      YV Y    DA 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 86  RALDVLNFTPLNNKSIRIMY------SHRDPS 111
           RA+  +N   ++ ++++         S+  PS
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTKYCSYSGPS 109

>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 = 63.7 bits (155), Expect = 1e-12
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 120 IFIKNLDKSI---DHKALHDTFSSFGNILSCKIATD----GSGQSKGFGFVQFENKESAQ 172
           +F+  L + +   +     + F  FG I    I       GS       +V +   E A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 173 NAIDKLNGMLINDKQVFVGH 192
            AI  +N ++++ + +    
Sbjct: 78  RAIQCVNNVVVDGRTLKASL 97

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 63.3 bits (154), Expect = 2e-12
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 314 LYIKNLGDSIDDE---KLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTPEEAS 366
           +++  L   + D    K  E F +FG I    +        S     S +V +   E+A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 367 RALAEMNGKMIVSKPLYVAVAQRK 390
           RA+  +N  ++  + L  ++   K
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 75.3 bits (186), Expect = 5e-17
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 268
           +FV  L   T+ +DLK  F ++G +    +  D + G+S+ FGF+ F++A    K ++  
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 269 ---LNGKKFD 275
              L+G+  D
Sbjct: 74  EHRLDGRVID 83

>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 = 73.4 bits (181), Expect = 3e-16
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +++  L      + LK+ F++FG +  C +  DP +G S+G GF+ F       + L + 
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 373 ----NGKMI 377
               +G++I
Sbjct: 74  EHRLDGRVI 82

>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 = 61.8 bits (151), Expect = 3e-12
 Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 167
           + S  +   G +F+  L      K L D F+ FG ++ C I  D  +G+S+GFGF+ F++
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 168 KESAQNAIDKLNGMLINDKQV 188
             S +  +D+     ++ + +
Sbjct: 63  AASVEKVLDQKEHR-LDGRVI 82

>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 = 60.7 bits (148), Expect = 7e-12
 Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 1/81 (1%)

Query: 22  ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP 81
           AS N+     ++VG L ++ +   L D F++ G+V+   +  D +T RS G+G++ + + 
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63

Query: 82  ADAARALDVLNFTPLNNKSIR 102
           A   + LD      L+ + I 
Sbjct: 64  ASVEKVLDQKEHR-LDGRVID 83

>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 = 75.8 bits (187), Expect = 6e-17
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L   TT E L++ FG++G +   +VMRD    +S+ FGFV F +     K +   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 86

Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
           +  + D +      A  +  + +
Sbjct: 87  SRHELDSKTIDPKVAFPRRAQPK 109

>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 = 71.1 bits (175), Expect = 3e-15
 Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA  
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87

Query: 371 --EMNGKMIVSKPLYVAVAQRKEER 393
             E++ K I  K    A  +R + +
Sbjct: 88  RHELDSKTIDPKV---AFPRRAQPK 109

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 62.7 bits (153), Expect = 3e-12
 Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 7/95 (7%)

Query: 95  PLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-G 153
             ++  +    SH   S  K     +FI  L      + L + F  FG +  C +  D  
Sbjct: 8   HHHSSGLVPRGSHMGSSGCK-----MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62

Query: 154 SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV 188
           + +S+GFGFV F ++      +   +   ++ K +
Sbjct: 63  TKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTI 96

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 58.4 bits (142), Expect = 8e-11
 Identities = 24/97 (24%), Positives = 42/97 (43%), Gaps = 1/97 (1%)

Query: 7   QHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS 66
                    +G+    S        +++G L +  T   L + F Q G+V    V RD  
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI 103
           T+RS G+G+V + + A   + L   +   L++K+I  
Sbjct: 63  TKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDP 98

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 76.0 bits (187), Expect = 7e-17
 Identities = 14/101 (13%), Positives = 39/101 (38%), Gaps = 5/101 (4%)

Query: 202 VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT-ITSAVVMRDGD--GKSKCFGFVNFEN 258
            +  +    +F+  + +    E++ +   +    +   +V        K++ F FV +E+
Sbjct: 2   SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61

Query: 259 ADDAAKAVEALNGKKF--DDREWYVGKAQKKSEREQELKGQ 297
              AA A   L   +      +  V  A+ + + ++++   
Sbjct: 62  HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>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 = 68.3 bits (167), Expect = 3e-14
 Identities = 12/92 (13%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGT-ITSCKVMRDP--SGISKGSGFVAFSTPEEASRALA 370
           L+I  +      E++ E  ++    +    V         ++G  FV + +   A+ A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 371 EMNGK--MIVSKPLYVAVAQRKEERRARLQAQ 400
           ++      +    + V  A+ + +    +   
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>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 = 61.3 bits (149), Expect = 8e-12
 Identities = 18/95 (18%), Positives = 38/95 (40%), Gaps = 8/95 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVG-QVLSVRVCRDL-STRRSLGYGYVNYANPADAARALD 89
           L++G +       ++ +  ++V   VL V V        ++ G+ +V Y +   AA A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 90  VLN--FTPLNNKSIRIMYS----HRDPSIRKSGTG 118
            L      L    I + ++      D  + ++ +G
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSG 105

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.4 bits (144), Expect = 4e-11
 Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFG-NILSCKIATDG--SGQSKGFGFVQFENKESAQNAID 176
           +FI  + K    + + +  +     +L   +        +++GF FV++E+  +A  A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 177 KLN--GMLINDKQVFV 190
           KL    + +   Q+ V
Sbjct: 71  KLMPGRIQLWGHQIAV 86

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 75.9 bits (187), Expect = 7e-17
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
             + N+  S T  D+ +         +AV V+ D +G+      V F+N DDA K+   L
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-L 76

Query: 270 NGKKFDDREWYVGKAQKKSEREQE 293
           + KK + RE +V     +  RE E
Sbjct: 77  HRKKLNGREAFVHVVTLEDMREIE 100

>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 = 64.8 bits (158), Expect = 6e-13
 Identities = 20/104 (19%), Positives = 39/104 (37%), Gaps = 9/104 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            +I N+  SI    + +          +  V+ D +G   G   V F   ++A ++   +
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RL 76

Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPR 416
           + K +  +  +V V   ++ R         +  P A G S P  
Sbjct: 77  HRKKLNGREAFVHVVTLEDMREI-------EKNPPAQGKSGPSS 113

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 61.7 bits (150), Expect = 7e-12
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 2/95 (2%)

Query: 107 HRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNIL-SCKIATDGSGQSKGFGFVQF 165
                   S      I N+  SI    +            +  +  D +GQ  G   VQF
Sbjct: 5   SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQF 64

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           +N++ A+ +  +L+   +N ++ FV     +  RE
Sbjct: 65  KNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMRE 98

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.2 bits (141), Expect = 1e-10
 Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 3/83 (3%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVL-SVRVCRDLSTRRSLGYGYVNYANPADAARA 87
               ++ ++ F++T   +      +     +V V  D +  + LG   V + N  DA ++
Sbjct: 15  KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKNEDDARKS 73

Query: 88  LDVLNFTPLNNKSIRIMYSHRDP 110
              L+   LN +   +     + 
Sbjct: 74  ER-LHRKKLNGREAFVHVVTLED 95

>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 = 74.6 bits (184), Expect = 8e-17
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 11/85 (12%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFEN 167
            D +I       +++  L  +I    L + F  FG I +  +        +   F+QF  
Sbjct: 8   EDKTIT-----TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFAT 57

Query: 168 KESAQNAIDK-LNGMLINDKQVFVG 191
           +++A+ A +K  N +++N +++ V 
Sbjct: 58  RQAAEVAAEKSFNKLIVNGRRLNVK 82

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 73.5 bits (181), Expect = 2e-16
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 10/89 (11%)

Query: 21  GASGNQFL---TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN 77
           G+SG+       T+LYVG L   +T++ L + F Q G++ ++ V +           ++ 
Sbjct: 1   GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54

Query: 78  YANPADAARAL-DVLNFTPLNNKSIRIMY 105
           +A    A  A     N   +N + + + +
Sbjct: 55  FATRQAAEVAAEKSFNKLIVNGRRLNVKW 83

>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 = 71.2 bits (175), Expect = 1e-15
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 6/70 (8%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA- 268
            ++V  L ++ T+ DL+  F ++G I +  V++      +   F+ F     A  A E  
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKS 68

Query: 269 LNGKKFDDRE 278
            N    + R 
Sbjct: 69  FNKLIVNGRR 78

>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 = 71.2 bits (175), Expect = 2e-15
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            LY+  LGD+I +  L+  F +FG I +  V++      +   F+ F+T + A  A  + 
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKS 68

Query: 373 -NGKMIVSKPLYV 384
            N  ++  + L V
Sbjct: 69  FNKLIVNGRRLNV 81

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 75.4 bits (186), Expect = 8e-17
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
            +V NL  +T   D+  IF +   I S  ++RD D  K K F +V F+  D   +A+   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75

Query: 270 NGKKFDDREWYVGKAQKKSERE 291
           +G    DR   V  A+ + + +
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDK 97

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 69.6 bits (171), Expect = 8e-15
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
            Y+ NL  +     +  +F +   I S +++RD  +   KG  +V F   +    AL   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-Y 75

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           +G ++  + L V +A+ +++ ++ 
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDKSG 99

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 66.9 bits (164), Expect = 7e-14
 Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           + YVG+L FN     +  +F  +  + SVR+ RD  T +  G+ YV +        AL  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74

Query: 91  LNFTPLNNKSIRIMYSH---RDPSIRKSG 116
            +   L ++S+R+  +    +D S   SG
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKSGPSSG 103

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 61.5 bits (150), Expect = 7e-12
 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
            ++ NL  +     +   F     I S ++  D  + + KGF +V+F+  +S + A+   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75

Query: 179 NGMLINDKQVFV 190
           +G L+ D+ + V
Sbjct: 76  DGALLGDRSLRV 87

>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 = 75.0 bits (185), Expect = 1e-16
 Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEA 268
            F+ NL    T+E +K+ F     I++  + R+     + K FG+  FE+ D    A+ +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 269 LNGKKFDDREWYVGKAQKKSERE 291
           LN +   ++   V  A +  +++
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAE 371
            ++ NL   + +E +KE F     I++ ++ R+P      KG G+  F   +    AL+ 
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 372 MNGKMIVSKPLYVAVAQRKEERR 394
           +N + + +K + V VA + +++ 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>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 = 64.6 bits (158), Expect = 6e-13
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR-RSLGYGYVNYANPADAARALD 89
           + ++G+L ++VT+  + + F  +  + +VR+ R+ S   R  G+GY  + +      AL 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   L NK IR+  +
Sbjct: 76  -LNEESLGNKRIRVDVA 91

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG--SGQSKGFGFVQFENKESAQNAIDK 177
            F+ NL   +  +++ + F     I + ++  +     + KGFG+ +FE+ +S  +A+  
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 178 LNGMLINDKQVFV 190
           LN   + +K++ V
Sbjct: 76  LNEESLGNKRIRV 88

>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 = 74.2 bits (183), Expect = 1e-16
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VFV    E  T E+L++ F +YG +    + +      + F FV F +   A        
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCG--E 67

Query: 271 GKKFDDREWYVGKAQKKSER 290
                    ++  A+ K  +
Sbjct: 68  DLIIKGISVHISNAEPKHNK 87

>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 = 64.6 bits (158), Expect = 4e-13
 Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM- 372
           +++    + +  E+L++ F ++G +    + +      +   FV F+  + A     E  
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDL 69

Query: 373 --NGKMIVSKPLYVAVAQRKEERR 394
              G  +         A+ K  + 
Sbjct: 70  IIKGISVHISN-----AEPKHNKL 88

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 6/72 (8%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
              +F+    + +  + L   F  +G ++   I        + F FV F + + AQ+   
Sbjct: 11  GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCG 66

Query: 177 KLNGMLINDKQV 188
           +    +I    V
Sbjct: 67  EDL--IIKGISV 76

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+  +    + ++VG    ++T  +L   F Q G+V+ V +      +    + +V +A+
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFAD 57

Query: 81  PADAARALDVLNFTPLNNKSIRI 103
              A           +   S+ I
Sbjct: 58  DKVAQSLCG--EDLIIKGISVHI 78

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 74.8 bits (184), Expect = 1e-16
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALN 270
            + +       + L  +F + G + +     D   GK+K F FV   + +DA K +++ +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 271 GKKFDDR 277
           GK+ D +
Sbjct: 76  GKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 64.4 bits (157), Expect = 5e-13
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
            I +    +  + L  LFS+ G + + +   D  +G +KG  FV   +  +A + +   +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 374 GKMI 377
           GK +
Sbjct: 76  GKRL 79

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 62.8 bits (153), Expect = 2e-12
 Identities = 15/67 (22%), Positives = 31/67 (46%)

Query: 33 YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN 92
           +      V    L  LFS+ G+V+++    D +T ++ G+ +V   +  DA + +   +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 93 FTPLNNK 99
             L+ K
Sbjct: 76 GKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 61.7 bits (150), Expect = 4e-12
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 118 GNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
                I +    +  KAL   FS  G +++ +   D  +G++KGF FV+  +   A+  I
Sbjct: 12  NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71

Query: 176 DKLNGMLINDKQVF 189
              +G  ++ K   
Sbjct: 72  KSFHGKRLDLKHRL 85

>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 = 74.6 bits (184), Expect = 1e-16
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEA 268
            F+ NL    T+E +K+ F     I++  + R+     + K FG+  FE+ D    A+  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 79

Query: 269 LNGKKFDDREWYVGKAQKKSE 289
           LN +   +R   V  A +  +
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAE 371
            ++ NL   + +E +KE F     I++ ++ R+P      KG G+  F   +    AL  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 372 MNGKMIVSKPLYVAVAQRKEE 392
           +N + + ++ + V VA + ++
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 65.3 bits (160), Expect = 2e-13
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR-RSLGYGYVNYANPADAARALD 89
           + ++G+L ++VT+  + + F  +  + +VR+ R+ S   R  G+GY  + +      AL 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 90  VLNFTPLNNKSIRI 103
            LN   L N+ IR+
Sbjct: 80  -LNEESLGNRRIRV 92

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 16/73 (21%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG--SGQSKGFGFVQFENKESAQNAIDK 177
            F+ NL   +  +++ + F     I + ++  +     + KGFG+ +FE+ +S  +A+  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 178 LNGMLINDKQVFV 190
           LN   + ++++ V
Sbjct: 80  LNEESLGNRRIRV 92

>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 = 73.4 bits (181), Expect = 2e-16
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           VFV       T+++L++ F +YG +    + +      + F FV F +   A        
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--E 61

Query: 271 GKKFDDREWYVGKAQKKSEREQ 292
                    ++  A+ K     
Sbjct: 62  DLIIKGISVHISNAEPKHNSNS 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 12/83 (14%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM- 372
           +++      + +++L+E FS++G +    + +      +   FV F+  + A     E  
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGEDL 63

Query: 373 --NGKMIVSKPLYVAVAQRKEER 393
              G  +         A+ K   
Sbjct: 64  IIKGISVHISN-----AEPKHNS 81

>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 = 58.4 bits (142), Expect = 5e-11
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG+  +F+      +    L + FS +G+++   I        + F FV F + + AQ+ 
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSL 58

Query: 175 IDKLNGMLINDKQV 188
                 ++I    V
Sbjct: 59  CG--EDLIIKGISV 70

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 7/75 (9%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           ++ ++VG    ++T+ +L + FSQ G V+ V +      +    + +V +A+   A    
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLC 59

Query: 89  DVLNFTPLNNKSIRI 103
                  +   S+ I
Sbjct: 60  G--EDLIIKGISVHI 72

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 73.0 bits (180), Expect = 5e-16
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +F+ NL  ++ + EDL +IF  YG I    +          FGF+ F+N      A+E  
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA-------FGFIQFDNPQSVRDAIECE 65

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           + +    ++  +  +   +  
Sbjct: 66  SQEMNFGKKLILEVSSSNARP 86

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 314 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L+I NL   ++  E L  +FS +G I    +           GF+ F  P+    A+   
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIECE 65

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           + +M   K L + V+      +  
Sbjct: 66  SQEMNFGKKLILEVSSSNARPQFD 89

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 120 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI NL  K++  + L   FS +G+I+   I          FGF+QF+N +S ++AI+  
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECE 65

Query: 179 NGMLINDKQVFV 190
           +  +   K++ +
Sbjct: 66  SQEMNFGKKLIL 77

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 9/83 (10%)

Query: 29  TTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
            + L++G+L   NV+   L+ +FS  G ++ + +           +G++ + NP     A
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDA 61

Query: 88  LDVLNFTPLNNKSIRIMYSHRDP 110
           ++  +      K + +  S  + 
Sbjct: 62  IECESQEMNFGKKLILEVSSSNA 84

>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 = 72.4 bits (178), Expect = 7e-16
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + + VKNL + +  +++  +  +Y      V       ++K   FV   N + A  A++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV------DRNKRTAFVTLLNGEQAQNAIQM 59

Query: 269 LNGKKFDDREWYVGKAQKKS 288
            +   F  ++  V      +
Sbjct: 60  FHQYSFRGKDLIVQLQPTDA 79

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 67.8 bits (166), Expect = 2e-14
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG+  I +KNL +  + + +HD    +  +  C +      ++K   FV   N E AQNA
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNA 56

Query: 175 IDKLNGMLINDKQVFV 190
           I   +      K + V
Sbjct: 57  IQMFHQYSFRGKDLIV 72

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 64.4 bits (157), Expect = 4e-13
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +KNL    + +++ +L  ++  +  C V       +K + FV     E+A  A+   +
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 374 GKMIVSKPLYVAVAQRK 390
                 K L V +    
Sbjct: 62  QYSFRGKDLIVQLQPTD 78

>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 = 60.1 bits (146), Expect = 1e-11
 Identities = 17/99 (17%), Positives = 38/99 (38%), Gaps = 12/99 (12%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG    ++ + V +L  +    +++DL         ++ C      R+    +V   N
Sbjct: 1   GSSG----SSGILVKNLPQDSNCQEVHDLLKDYD----LKYCY---VDRNKRTAFVTLLN 49

Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
              A  A+ + +      K + +     D ++  SG  +
Sbjct: 50  GEQAQNAIQMFHQYSFRGKDLIVQLQPTD-ALLCSGPSS 87

>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 = 74.5 bits (182), Expect = 1e-15
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
             +V++K      T +D+K+   + G + +  + R      K   FV F++ + A K VE
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 168

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQE 293
              G+K+ + +  +        ++ E
Sbjct: 169 TP-GQKYKETDLLILFKDDYFAKKNE 193

>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 = 71.4 bits (174), Expect = 2e-14
 Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 9/102 (8%)

Query: 297 QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF 356
              +   E  +  +  ++YIK        + +KE   + G + + ++ R      KGS F
Sbjct: 95  PLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIF 154

Query: 357 VAFSTPEEASRALAEMNGK------MIVSKPLYVAVAQRKEE 392
           V F + E A + +     K      +I+ K  Y A   +K E
Sbjct: 155 VVFDSIESAKKFVETPGQKYKETDLLILFKDDYFA---KKNE 193

>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 = 61.8 bits (149), Expect = 4e-11
 Identities = 12/61 (19%), Positives = 26/61 (42%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +++IK          + +     G +L+ ++        KG  FV F++ ESA+  ++  
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170

Query: 179 N 179
            
Sbjct: 171 G 171

>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 = 49.1 bits (116), Expect = 7e-07
 Identities = 13/83 (15%), Positives = 32/83 (38%), Gaps = 2/83 (2%)

Query: 25  NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
           N     S+Y+     + T   + +     GQVL++++ R    +   G  +V + +   A
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESA 163

Query: 85  ARALDVLNFTPLNNKSIRIMYSH 107
            + ++           + I++  
Sbjct: 164 KKFVETPGQK-YKETDLLILFKD 185

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 71.0 bits (174), Expect = 3e-15
 Identities = 16/89 (17%), Positives = 39/89 (43%), Gaps = 7/89 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL--AE 371
           ++I+ L   + + ++  L   FG +T+  +++      K   F+  +T E A+  +    
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQ 400
               ++  +P+Y+  +  KE +      Q
Sbjct: 74  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 60.3 bits (146), Expect = 2e-11
 Identities = 11/89 (12%), Positives = 31/89 (34%), Gaps = 7/89 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL- 269
           + ++ L    T+ ++  +   +G +T+ ++++      K   F+     + A   V    
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 270 -NGKKFDDREWYVGKAQKKSEREQELKGQ 297
                   +  Y+  +  K  +      Q
Sbjct: 74  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 53.3 bits (128), Expect = 5e-09
 Identities = 12/90 (13%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++  L  +VT+ ++  L    G+V ++ + +           ++       A   ++  
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72

Query: 92  NFTP--LNNKSIRIMYSHRDPSIRKSGTGN 119
                 L  + I I +S+       S    
Sbjct: 73  TSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 52.2 bits (125), Expect = 1e-08
 Identities = 12/84 (14%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL- 178
           I I+ L   +    +      FG + +  +        K   F++   +E+A   ++   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 179 -NGMLINDKQVFVGHFLRKQERET 201
               ++  + +++  F   +E +T
Sbjct: 74  SVTPVLRGQPIYI-QFSNHKELKT 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 70.6 bits (173), Expect = 3e-15
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
            +V+V NL       DLK+   E G++   +  +      +   F+++ ++  A +AV  
Sbjct: 20  ADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ----GPRRRAFLHYPDSAAAQQAVSC 75

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
           L G +       V  A+++ ++
Sbjct: 76  LQGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 61.0 bits (148), Expect = 7e-12
 Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG +G  +       L   +YVG+L  +   S L     ++G      V   L+ +    
Sbjct: 3   SGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-----SVPLRLTWQGPRR 57

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH 107
             +++Y + A A +A+  L    L   ++R+  + 
Sbjct: 58  RAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 57.5 bits (139), Expect = 1e-10
 Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           ++Y+ NL        LK    E G++      + P    +   F+ +     A +A++ +
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP----RRRAFLHYPDSAAAQQAVSCL 76

Query: 373 NGKMIVSKPLYVAVAQRKEER 393
            G  + +  L VA+A+++ ++
Sbjct: 77  QGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 4/72 (5%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           ++++ NL +      L       G  +  ++   G    +   F+ + +  +AQ A+  L
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQGP---RRRAFLHYPDSAAAQQAVSCL 76

Query: 179 NGMLINDKQVFV 190
            G+ +    + V
Sbjct: 77  QGLRLGTDTLRV 88

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 70.4 bits (173), Expect = 4e-15
 Identities = 17/88 (19%), Positives = 30/88 (34%), Gaps = 5/88 (5%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +VFV           L + F  +G + S V+ +D       F  V   +   A +AV + 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDV-GAREAVLSQ 64

Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQ 297
           +          V   ++K  +    K  
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQSPASKSP 92

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 5/84 (5%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           ++++      +D  +L E F  FG + S  + +D          V           L+  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAVLS-Q 64

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           +   +    L V   ++KE +   
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQSPA 88

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.5 bits (142), Expect = 5e-11
 Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG  ++F+    + +D   L + F +FG + S  +  D       F  V+  +  + +  
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAV 61

Query: 175 IDKLNGMLINDKQVFV 190
           +   +   +   ++ V
Sbjct: 62  L-SQSQHSLGGHRLRV 76

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG+  L  S++V      V  +QL + F   G V SV + +D        +  V   +
Sbjct: 1   GSSGSSGLR-SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGD 54

Query: 81  PADAARALDVLNFTPLNNKSIRI 103
                  L   +   L    +R+
Sbjct: 55  VGAREAVLS-QSQHSLGGHRLRV 76

>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 = 69.7 bits (171), Expect = 8e-15
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 8/68 (11%)

Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           VF+ NL+       D++ IF +YG +    V +        + FV + N   A  AV   
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG-------YAFVQYSNERHARAAVLGE 82

Query: 270 NGKKFDDR 277
           NG+    +
Sbjct: 83  NGRVLAGQ 90

>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 = 66.2 bits (162), Expect = 1e-13
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 11/86 (12%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKS-IDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQ 164
           +  DP    S    +FI NL+ + +    +   FS +G +  C +        KG+ FVQ
Sbjct: 19  NKNDPKSINS---RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQ 68

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           + N+  A+ A+   NG ++  + + +
Sbjct: 69  YSNERHARAAVLGENGRVLAGQTLDI 94

>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 = 65.9 bits (161), Expect = 2e-13
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 314 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           ++I NL    +    ++ +FS++G +  C        + KG  FV +S    A  A+   
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCS-------VHKGYAFVQYSNERHARAAVLGE 82

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           NG+++  + L + +A   +  R+ 
Sbjct: 83  NGRVLAGQTLDINMAGEPKPDRSG 106

>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 = 59.3 bits (144), Expect = 4e-11
 Identities = 22/89 (24%), Positives = 42/89 (47%), Gaps = 10/89 (11%)

Query: 29  TTSLYVGDLDFN-VTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
            + +++G+L+   V  S +  +FS+ G+V    V +        GY +V Y+N   A  A
Sbjct: 27  NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAA 78

Query: 88  LDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
           +   N   L  +++ I  +  +P   +SG
Sbjct: 79  VLGENGRVLAGQTLDINMA-GEPKPDRSG 106

>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 = 69.9 bits (171), Expect = 1e-14
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 269
           V++K L     ++ +   F +   +  ++ +    +GK+   GFV F N  D   A+   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-R 86

Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
           + +   +R   V    KK   E+
Sbjct: 87  HKQYMGNRFIQVHPITKKGMLEK 109

>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 = 59.5 bits (144), Expect = 5e-11
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           +Y+K L    +++ + + F +   +     +   P+G + G GFV F    +   AL   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CR 86

Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
           + + + ++ + V    +K     
Sbjct: 87  HKQYMGNRFIQVHPITKKGMLEK 109

>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 = 54.8 bits (132), Expect = 2e-09
 Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +++K L    ++K + D F     +     IA   +G++ G GFV+F N+   + A+ + 
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR- 86

Query: 179 NGMLINDKQVFV 190
           +   + ++ + V
Sbjct: 87  HKQYMGNRFIQV 98

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVL-SVRVCRDLSTRRSLGYGYVNYANPADAARA 87
              +Y+  L F   +  + D F ++  V  S+ +    + + + G G+V + N AD   A
Sbjct: 25  GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT-GEGFVEFRNEADYKAA 83

Query: 88  LDVLNFTPLNNKSIRIMYSHRD 109
           L   +   + N+ I++    + 
Sbjct: 84  LC-RHKQYMGNRFIQVHPITKK 104

>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 = 68.5 bits (168), Expect = 2e-14
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 8/68 (11%)

Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +F+ NL  ++ + EDL +IF  YG I    +          FGF+ F+N      A+E  
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA-------FGFIQFDNPQSVRDAIEXE 77

Query: 270 NGKKFDDR 277
           + +    +
Sbjct: 78  SQEMNFGK 85

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 11/91 (12%)

Query: 104 MYSHRDPSIRKSGTGN---IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKG 159
            + H    +   G+     +FI NL  K++  + L   FS +G+I+   I          
Sbjct: 6   HHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NA 58

Query: 160 FGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           FGF+QF+N +S ++AI+  +  +   K++ +
Sbjct: 59  FGFIQFDNPQSVRDAIEXESQEMNFGKKLIL 89

>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 = 61.2 bits (149), Expect = 6e-12
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 10/82 (12%)

Query: 314 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L+I NL   ++  E L  +FS +G I    +           GF+ F  P+    A+   
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXE 77

Query: 373 NGKMIVSKPLYVAVAQRKEERR 394
           + +M   K L + V+      R
Sbjct: 78  SQEMNFGKKLILEVS--SSNAR 97

>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 = 59.3 bits (144), Expect = 3e-11
 Identities = 18/101 (17%), Positives = 39/101 (38%), Gaps = 13/101 (12%)

Query: 8   HQAQMSGPNGVAAGASGNQFLTTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLS 66
           H         V  G+       + L++G+L   NV+   L+ +FS  G ++ + +     
Sbjct: 5   HHHHHHSSGLVPRGSHMK----SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--- 57

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH 107
                 +G++ + NP     A++  +      K + +  S 
Sbjct: 58  -----AFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSS 93

>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 = 68.4 bits (167), Expect = 4e-14
 Identities = 16/89 (17%), Positives = 39/89 (43%), Gaps = 7/89 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL--AE 371
           ++I+ L   + + ++  L   FG +T+  +++      K   F+  +T E A+  +    
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 88

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQ 400
               ++  +P+Y+  +  KE +      Q
Sbjct: 89  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117

>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 = 59.2 bits (143), Expect = 5e-11
 Identities = 10/81 (12%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE- 267
             + ++ L    T+ ++  +   +G +T+ ++++      K   F+     + A   V  
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNY 86

Query: 268 -ALNGKKFDDREWYVGKAQKK 287
                     +  Y+  +  K
Sbjct: 87  YTSVTPVLRGQPIYIQFSNHK 107

>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 = 53.4 bits (128), Expect = 6e-09
 Identities = 15/105 (14%), Positives = 37/105 (35%), Gaps = 9/105 (8%)

Query: 7   QHQAQMSGPNGVAAG-ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDL 65
            H +    P G   G +      +  +++  L  +VT+ ++  L    G+V ++ + +  
Sbjct: 8   HHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG- 66

Query: 66  STRRSLGYGYVNYANPADAARALDVLNFTP--LNNKSIRIMYSHR 108
                    ++       A   ++        L  + I I +S+ 
Sbjct: 67  -----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 52.2 bits (125), Expect = 2e-08
 Identities = 12/84 (14%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID--K 177
           I I+ L   +    +      FG + +  +      + K   F++   +E+A   ++   
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYT 88

Query: 178 LNGMLINDKQVFVGHFLRKQERET 201
               ++  + +++  F   +E +T
Sbjct: 89  SVTPVLRGQPIYI-QFSNHKELKT 111

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 67.5 bits (165), Expect = 6e-14
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + +KNL E  + +DLK +  E    T               G + F + +   +A+E 
Sbjct: 29  YRITMKNLPEGCSWQDLKDLARENSLET--TFSSVNTRDFDGTGALEFPSEEILVEALER 86

Query: 269 LNGKKFDDREWYV 281
           LN  +F      V
Sbjct: 87  LNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 62.5 bits (152), Expect = 3e-12
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           I +KNL +    + L D        L    ++  +    G G ++F ++E    A+++LN
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENS--LETTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88

Query: 180 GMLINDKQVFV 190
            +      + V
Sbjct: 89  NIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 59.8 bits (145), Expect = 3e-11
 Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 3/83 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +KNL +    + LK+L  E             +    G+G + F + E    AL  +N
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88

Query: 374 GKMIVSKPLYVAVA-QRKEERRA 395
                   + V         RR+
Sbjct: 89  NIEFRGSVITVERDDNPPPIRRS 111

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 58.7 bits (142), Expect = 8e-11
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 3/84 (3%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           + + +L    +   L DL  +            ++TR   G G + + +      AL+ L
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENS---LETTFSSVNTRDFDGTGALEFPSEEILVEALERL 87

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKS 115
           N        I +      P IR+S
Sbjct: 88  NNIEFRGSVITVERDDNPPPIRRS 111

>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 = 66.4 bits (162), Expect = 1e-13
 Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 7/80 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA--E 371
           L+I+ L   + + ++  L   FG +T+  +++      K   F+  +T E A   +    
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 372 MNGKMIVSKPLYVAVAQRKE 391
                + ++P+Y+  +  KE
Sbjct: 73  AVTPHLRNQPIYIQYSNHKE 92

>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 = 59.4 bits (144), Expect = 3e-11
 Identities = 10/79 (12%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE--A 268
           + ++ L    T+ ++  +   +G +T+ ++++      K   F+     + A   V   +
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 269 LNGKKFDDREWYVGKAQKK 287
                  ++  Y+  +  K
Sbjct: 73  AVTPHLRNQPIYIQYSNHK 91

>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 = 52.9 bits (127), Expect = 6e-09
 Identities = 10/84 (11%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID--K 177
           + I+ L   +    +      FG + +  +      + K   F++   +E+A   ++   
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYS 72

Query: 178 LNGMLINDKQVFVGHFLRKQERET 201
                + ++ +++  +   +E +T
Sbjct: 73  AVTPHLRNQPIYI-QYSNHKELKT 95

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 8/79 (10%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++  L   VT++++  L    G+V ++ + +           ++  A    A   ++  
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYY 71

Query: 92  NFTP--LNNKSIRIMYSHR 108
           +     L N+ I I YS+ 
Sbjct: 72  SAVTPHLRNQPIYIQYSNH 90

>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 = 65.9 bits (161), Expect = 2e-13
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 269
           V ++ L    + E++ + F     + + + +  D  G+S    FV F + + A KA++  
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-K 76

Query: 270 NGKKFDDREWYVGKAQKKSERE 291
           + ++   R   + K+ +   R 
Sbjct: 77  HKERIGHRYIEIFKSSRAEVRT 98

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 60.9 bits (148), Expect = 9e-12
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEASRALAEM 372
           + ++ L      E++ + FS    + +   +  D  G S G  FV F++ E A +AL + 
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KK 76

Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
           + + I  + + +  + R E R +
Sbjct: 77  HKERIGHRYIEIFKSSRAEVRTS 99

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQ 164
           S   P     G   + ++ L      + +   FS    + +   +  D  G+S G  FVQ
Sbjct: 6   SGNSPDTANDGF--VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
           F ++E A+ A+ K +   I  + + +
Sbjct: 64  FASQEIAEKALKK-HKERIGHRYIEI 88

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 52.8 bits (127), Expect = 6e-09
 Identities = 21/106 (19%), Positives = 43/106 (40%), Gaps = 7/106 (6%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVL-SVRVCRDLSTRRSL 71
           SG +G +   + + F+     +  L F  +  ++   FS +  V   + +  D   R + 
Sbjct: 3   SGSSGNSPDTANDGFV----RLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRST- 57

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGT 117
           G  +V +A+   A +AL   +   + ++ I I  S R        +
Sbjct: 58  GEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGPS 102

>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 = 71.8 bits (175), Expect = 2e-13
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 266
           F  +FV  ++  TT+  L++ F  YG I    ++     GK + + F+ +E+  D   A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161

Query: 267 EALNGKKFDDRE 278
           +  +GKK D R 
Sbjct: 162 KHADGKKIDGRR 173

>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 = 65.6 bits (159), Expect = 2e-11
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 107 HRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQF 165
           H DP+ +      +F+  ++       L   F  +G I    +     SG+ +G+ F+++
Sbjct: 92  HNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151

Query: 166 ENKESAQNAIDKLNGMLINDKQVFV 190
           E++    +A    +G  I+ ++V V
Sbjct: 152 EHERDMHSAYKHADGKKIDGRRVLV 176

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 65.3 bits (158), Expect = 2e-11
 Identities = 31/176 (17%), Positives = 64/176 (36%), Gaps = 8/176 (4%)

Query: 255 NFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQG--- 311
            FE+  DA     A   ++  +R+    + +K   R+QE++ + +          QG   
Sbjct: 47  EFEDPRDAPPPTRAETREERMERK----RREKIERRQQEVETELKMWDPHNDPNAQGDAF 102

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
             L++  +     + KL+  F  +G I    ++    SG  +G  F+ +    +   A  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 371 EMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSG 426
             +GK I  + + V V + +  +  R +     +     G +            S 
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSR 218

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 59.9 bits (144), Expect = 1e-09
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 22  ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP 81
           A G+ F T  L+V  ++++ T+S+L   F   G +  + +     + +  GY ++ Y + 
Sbjct: 97  AQGDAFKT--LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154

Query: 82  ADAARALDVLNFTPLNNKSIRIMYSHRD 109
            D   A    +   ++ + + +      
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLVDVERGR 182

>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 = 66.4 bits (162), Expect = 2e-13
 Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 269
           V ++ L    T E++ + F     + + + +  D +GK     FV F + + A KA+   
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-K 103

Query: 270 NGKKFDDR 277
           + ++   R
Sbjct: 104 HKERIGHR 111

>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 = 61.4 bits (149), Expect = 1e-11
 Identities = 23/108 (21%), Positives = 43/108 (39%), Gaps = 2/108 (1%)

Query: 288 SEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RD 346
           S       GQ       + D      + ++ L      E++ + FS    + +   +  D
Sbjct: 19  SHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVD 78

Query: 347 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 394
           P G   G  FV F++ E A +AL   + + I  + + V  + ++E R 
Sbjct: 79  PEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEEVRS 125

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 54.9 bits (132), Expect = 2e-09
 Identities = 19/103 (18%), Positives = 42/103 (40%), Gaps = 2/103 (1%)

Query: 8   HQAQMSGPNGVAAGAS-GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS 66
           H A M+G   +  G++  +      + +  L F  T  ++   FS +  V +        
Sbjct: 20  HMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDP 79

Query: 67  TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD 109
             +  G  +V +A+   A +AL   +   + ++ I +  S ++
Sbjct: 80  EGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQE 121

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 54.5 bits (131), Expect = 3e-09
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFEN 167
             S   +  G + ++ L      + +   FS    + +   +  D  G+  G  FVQF +
Sbjct: 34  SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93

Query: 168 KESAQNAIDKLNGMLINDKQVFV 190
           +E A+ A+ K +   I  + + V
Sbjct: 94  QELAEKALGK-HKERIGHRYIEV 115

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 11/67 (16%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V ++    + T++++ +         +  ++R+  G    + FV+F N ++  +A++  N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN 70

Query: 271 GKKFDDR 277
            +    R
Sbjct: 71  REYMGGR 77

>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 = 57.7 bits (140), Expect = 9e-11
 Identities = 14/78 (17%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + ++    ++ ++ + E  +      + +++R+  G   G  FV FS  EE  +AL + N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-KCN 70

Query: 374 GKMIVSKPLYVAVAQRKE 391
            + +  + + V   +   
Sbjct: 71  REYMGGRYIEVFREKSGP 88

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 12/71 (16%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + ++    ++  K + +  +     ++ +I  +  G   G+ FV F N+E  + A+   N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC-N 70

Query: 180 GMLINDKQVFV 190
              +  + + V
Sbjct: 71  REYMGGRYIEV 81

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 20/93 (21%), Positives = 46/93 (49%), Gaps = 5/93 (5%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G+SG    T  + +    FNVT+  + +  + +   +++R+ R+    ++ GY +V++
Sbjct: 2   SSGSSGTTCHT--VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKT-GYIFVDF 57

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYSHRDPS 111
           +N  +  +AL   N   +  + I +      PS
Sbjct: 58  SNEEEVKQALK-CNREYMGGRYIEVFREKSGPS 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 = 65.2 bits (159), Expect = 3e-13
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 7/90 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            ++++ L +S+ +  L E   +FGTI    +M       K    V F   + A   +   
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFA 71

Query: 373 --NGKMIVSKPLYVAVAQRKEERRARLQAQ 400
                 I  +  +   +  K   R      
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>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 = 61.4 bits (149), Expect = 6e-12
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 7/91 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             V V+ L ES  + DL +   ++GTI   ++M       K    V FEN D A + V  
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTF 70

Query: 269 LNGKKF--DDREWYVGKAQKKSEREQELKGQ 297
                     ++ +   +  K        G 
Sbjct: 71  AADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>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 = 57.1 bits (138), Expect = 2e-10
 Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID-- 176
            + ++ L +S+    L +    FG I    +        K    V+FEN +SA+  +   
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFA 71

Query: 177 KLNGMLINDKQVFV 190
               + I  +Q F 
Sbjct: 72  ADVPVYIAGQQAFF 85

>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 = 56.0 bits (135), Expect = 5e-10
 Identities = 14/89 (15%), Positives = 28/89 (31%), Gaps = 8/89 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++V  L  +V ++ L +   + G +  V +              V + N   A   +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71

Query: 92  NFTP--LNNKSIRIMYSHRDPSIRKSGTG 118
              P  +  +     YS      R   +G
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRITRPGNSG 100

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 64.4 bits (157), Expect = 5e-13
 Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           ++I+ L D + +  L E   EFG I+   VM       K    V F     A  A+    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAA 78

Query: 374 GK--MIVSKPLYVAVAQRKE 391
                I   P +V  +  ++
Sbjct: 79  DNQIYIAGHPAFVNYSTSQK 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 5/66 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             V ++ L +   + DL +   E+G I+  VVM       K    V FE+   A  AV  
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNY 76

Query: 269 LNGKKF 274
               + 
Sbjct: 77  AADNQI 82

>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 = 1e-10
 Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + I+ L   +    L +    FG I    +        K    V+FE+   A NA++   
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAA 78

Query: 180 GM--LINDKQVFV 190
                I     FV
Sbjct: 79  DNQIYIAGHPAFV 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 53.6 bits (129), Expect = 3e-09
 Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 8/79 (10%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++  L   V ++ L +   + G +  V V              V + +   A  A++  
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77

Query: 92  NFTP--LNNKSIRIMYSHR 108
                 +      + YS  
Sbjct: 78  ADNQIYIAGHPAFVNYSTS 96

>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 = 64.4 bits (157), Expect = 6e-13
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 2/81 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V V  +  S  + D++  F     + +  +++D  G++   G V F +  D  +A++  N
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RN 76

Query: 271 GKKFDDREWYVGKAQKKSERE 291
                 R   V  A ++    
Sbjct: 77  RMLMIQRYVEVSPATERQWVA 97

>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 = 61.7 bits (150), Expect = 7e-12
 Identities = 15/83 (18%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +  +  S  +  +++ F     + +  +++D  G + G+G V F +P++   AL + N
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRN 76

Query: 374 GKMIVSKPLYVAVAQRKEERRAR 396
             +++ + + V+ A  ++   A 
Sbjct: 77  RMLMIQRYVEVSPATERQWVAAG 99

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 56.7 bits (137), Expect = 3e-10
 Identities = 20/107 (18%), Positives = 43/107 (40%), Gaps = 6/107 (5%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG +G     + +      + V  + F+  ++ + D F  + +V +V + +D   R + G
Sbjct: 3   SGSSGKPLPINPDDL---YVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNN-G 57

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
            G V + +P D   AL   N   +  + + +  +     +   G   
Sbjct: 58  NGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVAAGGHIT 103

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 56.7 bits (137), Expect = 4e-10
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           S   P         + +  +  S     + D F     + +  +  D  G++ G G V+F
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKF 63

Query: 166 ENKESAQNAIDKLNGMLINDKQVFV 190
            + +    A+ + N ML+  + V V
Sbjct: 64  LSPQDTFEALKR-NRMLMIQRYVEV 87

>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 = 64.2 bits (156), Expect = 1e-12
 Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 10/98 (10%)

Query: 194 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGF 253
           LR +  ETV+  T+   V    L    +   L  +  + G + + ++  +     K + F
Sbjct: 13  LRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSF 67

Query: 254 VNFENADDAAKAVEALNGKKFDDRE-----WYVGKAQK 286
             +   +++ +A   LNGK+  D        Y+   +K
Sbjct: 68  ARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 63.0 bits (153), Expect = 2e-12
 Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 7/93 (7%)

Query: 97  NNKSIRIMYSHRDPSIRKSGTGNIFIKN--LDKSIDHKALHDTFSSFGNILSCKIATDGS 154
           ++ +   +  H         T ++ + N  L   +    L       G + +  +  +  
Sbjct: 5   SSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-- 62

Query: 155 GQSKGFGFVQFENKESAQNAIDKLNGMLINDKQ 187
              K + F ++   E ++ A   LNG  + D  
Sbjct: 63  ---KPYSFARYRTTEESKRAYVTLNGKEVVDDL 92

>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 = 61.9 bits (150), Expect = 6e-12
 Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 12/89 (13%)

Query: 313 NLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           +L + N  LG+ +   +L  +  + G + +  +  +     K   F  + T EE+ RA  
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYV 81

Query: 371 EMNGKMIV-----SKPLYVAVAQRKEERR 394
            +NGK +V        LY+   ++ +   
Sbjct: 82  TLNGKEVVDDLGQKITLYLNFVEKVQWSG 110

>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 = 51.9 bits (124), Expect = 2e-08
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 29 TTSLYV--GDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
          T SL V  G L   V+ +QL  +  + G V ++ +  +        Y +  Y    ++ R
Sbjct: 25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKR 78

Query: 87 ALDVLN 92
          A   LN
Sbjct: 79 AYVTLN 84

>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 = 62.8 bits (153), Expect = 2e-12
 Identities = 13/67 (19%), Positives = 22/67 (32%), Gaps = 2/67 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V ++ L    T+ D+   F          +    DG+      V F   +DA  A+   +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KD 75

Query: 271 GKKFDDR 277
                 R
Sbjct: 76  KANMQHR 82

>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 = 56.6 bits (137), Expect = 3e-10
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           ++++ L     +  +   FS         +   P G   G   V F+T E+A  A+   +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKD 75

Query: 374 GKMIVSKPLYVAVAQRKEERRA 395
              +  + + + +        +
Sbjct: 76  KANMQHRYVELFLNSTAGTSGS 97

>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 = 52.8 bits (127), Expect = 7e-09
 Identities = 21/104 (20%), Positives = 48/104 (46%), Gaps = 9/104 (8%)

Query: 19  AAGASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           ++G+SG+ F +T+   +++  L +  T++ +Y+ FS +   + V +      R + G   
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVT-GEAD 59

Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP---SIRKSG 116
           V +A   DA  A+   +   + ++ + +  +       S   SG
Sbjct: 60  VEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGSGPSSG 102

>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 = 52.0 bits (125), Expect = 1e-08
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 3/87 (3%)

Query: 105 YSHRDPSIRKSGTGN-IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFV 163
            S    S  +S TG+ + ++ L        +++ FS   N +   I     G+  G   V
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADV 60

Query: 164 QFENKESAQNAIDKLNGMLINDKQVFV 190
           +F   E A  A+ K +   +  + V +
Sbjct: 61  EFATHEDAVAAMAK-DKANMQHRYVEL 86

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 61.8 bits (150), Expect = 7e-12
 Identities = 19/89 (21%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAV----VMRDGDGKSKCFGFVNFENADDAAKAV 266
           V ++ L  + T E++   FG++  IT        +   DG+     FV F   + A  A+
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 267 EALNGKKFDDREWYVGKAQKKSEREQELK 295
              +      R   + ++   +E +Q L 
Sbjct: 86  R-KHKDLLGKRYIELFRS-TAAEVQQVLN 112

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 51.8 bits (124), Expect = 2e-08
 Identities = 20/103 (19%), Positives = 38/103 (36%), Gaps = 11/103 (10%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTIT----SCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           + ++ L  +   E++   F +   IT        +  P G   G  FV F+  E A  AL
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 412
              +  ++  + + +  +   E ++             A GPS
Sbjct: 86  -RKHKDLLGKRYIELFRSTAAEVQQVL------NRFSSASGPS 121

>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 = 9e-07
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNIL----SCKIATDGSGQSKGFGFVQFENK 168
            K     + ++ L  +   + +   F     I          T   G+  G  FV F  +
Sbjct: 19  SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACE 78

Query: 169 ESAQNAIDKLNGMLINDKQVFV 190
           E AQNA+ K +  L+  + + +
Sbjct: 79  EYAQNALRK-HKDLLGKRYIEL 99

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 46.0 bits (109), Expect = 3e-06
 Identities = 22/107 (20%), Positives = 38/107 (35%), Gaps = 13/107 (12%)

Query: 14  GPNGVAAGASGN---QFLTTS----LYVGDLDFNVTDSQLYDLFSQVGQVL----SVRVC 62
           G +G + G + N   QFL+      + +  L F  T  ++   F Q   +      +   
Sbjct: 1   GSSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFV 60

Query: 63  RDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD 109
                R + G  +V +A    A  AL   +   L  + I +  S   
Sbjct: 61  TYPDGRPT-GDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRSTAA 105

>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 = 61.4 bits (149), Expect = 1e-11
 Identities = 12/67 (17%), Positives = 22/67 (32%), Gaps = 2/67 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V ++ L    T+ D+   F          +    DG+      V F   ++A  A+   +
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS-KD 106

Query: 271 GKKFDDR 277
                 R
Sbjct: 107 RANMQHR 113

>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 = 57.2 bits (138), Expect = 5e-10
 Identities = 19/108 (17%), Positives = 37/108 (34%), Gaps = 2/108 (1%)

Query: 296 GQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSG 355
           G+     + TV    G  ++++ L     +  +   FS         +   P G   G  
Sbjct: 31  GRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEA 89

Query: 356 FVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 403
            V F+T EEA  A+   +   +  + + + +            +Q  Q
Sbjct: 90  DVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136

>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 = 53.7 bits (129), Expect = 8e-09
 Identities = 15/109 (13%), Positives = 41/109 (37%), Gaps = 3/109 (2%)

Query: 10  AQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR 69
            Q  G     +  +        +++  L +  T++ +Y+ FS +   + V +      R 
Sbjct: 27  GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRV 85

Query: 70  SLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
           + G   V +A   +A  A+   +   + ++ I +  +    +   + + 
Sbjct: 86  T-GEADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAYSS 132

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.9 bits (127), Expect = 2e-08
 Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + ++ L        +++ FS     +   I     G+  G   V+F   E A  A+ K +
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK-D 106

Query: 180 GMLINDKQVFV 190
              +  + + +
Sbjct: 107 RANMQHRYIEL 117

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 60.4 bits (146), Expect = 3e-11
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 97  NNKSIRIMYSHRDPSIRKSGTGNI---FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG 153
            N ++    +  D  +  +G   +    ++NL   +    LH  FS FG +L     T  
Sbjct: 5   GNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 64

Query: 154 SGQSKGFGFVQFENKESAQNAIDKLNGMLIND 185
           +        +Q+ +  SAQ+A   L+G  I +
Sbjct: 65  NQ---FQALLQYADPVSAQHAKLSLDGQNIYN 93

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 53.5 bits (128), Expect = 7e-09
 Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V+NL    T + L +IF ++GT+   +     +        + + +   A  A  +L+
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ---ALLQYADPVSAQHAKLSLD 87

Query: 271 GKKFDD 276
           G+   +
Sbjct: 88  GQNIYN 93

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 52.0 bits (124), Expect = 2e-08
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           L + ++NL   +  + L ++FS+FGT+         +        + ++ P  A  A   
Sbjct: 29  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLS 85

Query: 372 MNGKMI 377
           ++G+ I
Sbjct: 86  LDGQNI 91

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 51.2 bits (122), Expect = 4e-08
 Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 13/108 (12%)

Query: 11  QMSGPNGVAAGASGNQFLTTS-------LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCR 63
           Q       A+ A+ +  +  +       + V +L + VT   L+ +FS+ G VL +    
Sbjct: 3   QSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF- 61

Query: 64  DLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS--IRIMYSHRD 109
              T+ +     + YA+P  A  A   L+   + N    +RI +S   
Sbjct: 62  ---TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 106

>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 = 57.8 bits (140), Expect = 8e-11
 Identities = 11/78 (14%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRV-----CRDLSTRRSLGYGYVNYANPADAA 85
            LYVG++ F +T+  + D F+   ++  +          +   +   + ++ + +  +  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 86  RALDVLNFTPLNNKSIRI 103
           +A+   +      +S++I
Sbjct: 68  QAMA-FDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 7/73 (9%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG------DGKSKCFGFVNFENADDAAK 264
           ++V N+    T+E +   F     +                 + K F F+ F + D+  +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 265 AVEALNGKKFDDR 277
           A+ A +G  F  +
Sbjct: 69  AM-AFDGIIFQGQ 80

>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 = 53.6 bits (129), Expect = 2e-09
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCK------VMRDPSGISKGSGFVAFSTPEEASR 367
           LY+ N+   I +E + + F+    +          V+       K   F+ F + +E ++
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 368 ALAEMNGKMIVSKPLYV 384
           A+A  +G +   + L +
Sbjct: 69  AMA-FDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG------SGQSKGFGFVQFENKESAQN 173
           +++ N+   I  +A+ D F++   +     A           Q K F F++F + +    
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 174 AIDKLNGMLINDKQVFVG 191
           A+   +G++   + + + 
Sbjct: 69  AM-AFDGIIFQGQSLKIR 85

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 57.6 bits (139), Expect = 2e-10
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMR---DGDGKSKCFGFVNFENADDAAKAVE 267
           +  + L  S T ED+   F +         +    + DGK +    +  E+  D  KA+E
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELK 295
             +      R   V +     + +  +K
Sbjct: 74  -KHRMYMGQRYVEVYEI-NNEDVDALMK 99

>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 = 50.2 bits (120), Expect = 6e-08
 Identities = 12/90 (13%), Positives = 30/90 (33%), Gaps = 4/90 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           +  + L  S   E +   FS+            + +  G  +G   +   + ++  +AL 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL- 72

Query: 371 EMNGKMIVSKPLYVAVAQRKEERRARLQAQ 400
           E +   +  + + V     ++        Q
Sbjct: 73  EKHRMYMGQRYVEVYEINNEDVDALMKSLQ 102

>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 = 48.3 bits (115), Expect = 3e-07
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSF---GNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
           I  + L  S   + + + FS               +  G+ +G   ++ E+++  Q A++
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73

Query: 177 KLNGMLINDKQVFV 190
           K + M +  + V V
Sbjct: 74  K-HRMYMGQRYVEV 86

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 9/81 (11%), Positives = 28/81 (34%), Gaps = 5/81 (6%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQ---VGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           +    L ++ T   + + FS          +    +   +R  G   +   +  D  +AL
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRR-GDALIEMESEQDVQKAL 72

Query: 89  DVLNFTPLNNKSIRIMYSHRD 109
           +  +   +  + + +   + +
Sbjct: 73  E-KHRMYMGQRYVEVYEINNE 92

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 57.7 bits (139), Expect = 2e-10
 Identities = 11/84 (13%), Positives = 28/84 (33%), Gaps = 6/84 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD---GKSKCFGFVNFENADDAAKA 265
             VFV  L     ++++   F  +G +      +         K + F+ F+        
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQA- 67

Query: 266 VEALNGKKFDDREWYVGKAQKKSE 289
              ++    +D + Y+  +    +
Sbjct: 68  --LIDACLEEDGKLYLCVSSPTIK 89

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 47.3 bits (112), Expect = 9e-07
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSC---KIATDGSGQSKGFGFVQFENKESAQNAID 176
           +F+  L   ID   +  +F  FG ++     K  +      KG+ F+ F+ + S Q  ID
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 177 K 177
            
Sbjct: 71  A 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 45.4 bits (107), Expect = 4e-06
 Identities = 15/96 (15%), Positives = 31/96 (32%), Gaps = 12/96 (12%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPEEASRALA 370
           +++  L   ID++++   F  FG +      +  S      KG  F+ F         + 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 371 EMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 406
                    K      +   +++         Q+RP
Sbjct: 71  --ACLEEDGKLYLCVSSPTIKDKPV-------QIRP 97

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.7 bits (95), Expect = 2e-04
 Identities = 10/70 (14%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDL--STRRSLGYGYVNYA 79
           S     +  ++VG L  ++ + ++   F + G ++     +    S     GY ++ + 
Sbjct: 1  GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 80 NPADAARALD 89
            +     +D
Sbjct: 61 EESSVQALID 70

>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 = 55.7 bits (134), Expect = 8e-10
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEY---GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           V ++ L  S + ED++    +      +     +   +G+     FV  E+ DD   A++
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELK 295
             + +    R   V K+  ++E +  LK
Sbjct: 80  -KDRESMGHRYIEVFKS-HRTEMDWVLK 105

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 51.8 bits (124), Expect = 2e-08
 Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 4/85 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           + ++ L  S   E ++   S+      +     +    G   G  FV   + ++   AL 
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL- 78

Query: 371 EMNGKMIVSKPLYVAVAQRKEERRA 395
           + + + +  + + V  + R E    
Sbjct: 79  KKDRESMGHRYIEVFKSHRTEMDWV 103

>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 = 49.9 bits (119), Expect = 9e-08
 Identities = 23/110 (20%), Positives = 43/110 (39%), Gaps = 10/110 (9%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQ---VGQVLSVRVCRDLSTRR 69
           SG +G+  G  G +     + +  L ++ +   + +  S       V  V        R+
Sbjct: 3   SGSSGMMLGPEGGEGYV--VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60

Query: 70  SLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR---DPSIRKSG 116
           S G  +V   +  D   AL   +   + ++ I +  SHR   D  ++ SG
Sbjct: 61  S-GEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTEMDWVLKHSG 108

>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 = 49.9 bits (119), Expect = 1e-07
 Identities = 11/74 (14%), Positives = 29/74 (39%), Gaps = 4/74 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSF---GNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
           + ++ L  S   + + +  S       +          G+  G  FV+ E+++  + A+ 
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 177 KLNGMLINDKQVFV 190
           K +   +  + + V
Sbjct: 80  K-DRESMGHRYIEV 92

>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 = 53.3 bits (128), Expect = 4e-09
 Identities = 14/56 (25%), Positives = 25/56 (44%)

Query: 222 DEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           +E   ++  +YG +    V  +         +V F   +DA KAV  LN + F+ +
Sbjct: 41  EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

>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 = 48.7 bits (116), Expect = 2e-07
 Identities = 13/64 (20%), Positives = 30/64 (46%)

Query: 321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
           D   +E   E+  ++G +    V  +      G+ +V F   E+A +A+ ++N +    +
Sbjct: 37  DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

Query: 381 PLYV 384
           P++ 
Sbjct: 97  PIHA 100

>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 = 45.6 bits (108), Expect = 2e-06
 Identities = 10/50 (20%), Positives = 21/50 (42%)

Query: 141 FGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           +G +    +  +      G  +V+F  +E A+ A+  LN    N + +  
Sbjct: 51  YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

>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 = 58.3 bits (140), Expect = 6e-09
 Identities = 60/453 (13%), Positives = 127/453 (28%), Gaps = 165/453 (36%)

Query: 55  QVLSVRVCRDLSTRRSLGYG--YVNYANPADAARALDVL---------NFTPLNNKSIRI 103
             +++ VC     +  + +   ++N  N       L++L         N+T  ++ S  I
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223

Query: 104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKA----LHD-----TFSSFGNILSCKI----- 149
               R  SI+        ++ L KS  ++     L +      +++F   LSCKI     
Sbjct: 224 --KLRIHSIQAE------LRRLLKSKPYENCLLVLLNVQNAKAWNAFN--LSCKILLTTR 273

Query: 150 ---ATDGSGQSKGF---------GFVQFENKE----SAQNAIDKL-------NGMLINDK 186
               TD    +                 E K             L       N   ++  
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS-- 331

Query: 187 QVFVGHFLR---------KQ---ERETVAIKTKFNNVFVKNLDESTTDEDLKK------I 228
              +   +R         K    ++ T  I+       +  L+      + +K      +
Sbjct: 332 --IIAESIRDGLATWDNWKHVNCDKLTTIIE-----SSLNVLEP----AEYRKMFDRLSV 380

Query: 229 FGEYGTITSAVVMR-----------------------DGDGKSKCFGF------VNFENA 259
           F     I + ++                         +   K            +  +  
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLE 440

Query: 260 DDAA---KAVEALNG-KKFDDRE-----------WYVG---KAQKKSEREQELKGQF--- 298
           ++ A     V+  N  K FD  +            ++G   K  +  ER    +  F   
Sbjct: 441 NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDF 500

Query: 299 ---EQAMKET----------VDKFQGLNLYIKNLGDS--IDDEKLKELFSEFGTITSCKV 343
              EQ ++            ++  Q L  Y   + D+    +  +  +  +F       +
Sbjct: 501 RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAIL-DFLPKIEENL 559

Query: 344 MRDP-SGISKGSGFVAFSTP-----EEASRALA 370
           +    + + +    +A         EEA + + 
Sbjct: 560 ICSKYTDLLR----IALMAEDEAIFEEAHKQVQ 588

>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 = 56.4 bits (135), Expect = 2e-08
 Identities = 61/487 (12%), Positives = 135/487 (27%), Gaps = 142/487 (29%)

Query: 33  YVGDLDFN-VTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +V + D   V D            +LS      +          +   +       L   
Sbjct: 29  FVDNFDCKDVQDMPK--------SILSKEEIDHI----------IMSKDAVSGTLRL--- 67

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGTGNI-FIKNL--DKSIDHKALHDTFSSFGNILSCK 148
            F  L +K   ++    +  +R     N  F+ +    +      +   +    +    +
Sbjct: 68  -FWTLLSKQEEMVQKFVEEVLRI----NYKFLMSPIKTEQRQPSMMTRMYIEQRD----R 118

Query: 149 IATDGSGQSKGFGFVQ-FENKESAQNAIDKLN--------GMLINDKQVFVGHFLRKQER 199
           +  D    +K    V   +     + A+ +L         G+L + K           + 
Sbjct: 119 LYNDNQVFAKYN--VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK- 175

Query: 200 ETVAIKTKF-NNVFVKNLDESTTDEDLKKI-----------FGEYGTITSAVVMRDGDGK 247
               ++ K    +F  NL    + E + ++           +      +S + +R    +
Sbjct: 176 ----VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231

Query: 248 SKCFGFV---NFENA----DDA--AKAVEALNGK------------------------KF 274
           ++    +    +EN      +   AKA  A N                            
Sbjct: 232 AELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISL 291

Query: 275 DDREWYVGKAQKKS-------EREQELK--------------GQFEQAMKETVDKFQGLN 313
           D     +   + KS        R Q+L                +  +    T D ++ +N
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVN 351

Query: 314 LY-----IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS-----GFVAFSTPE 363
                  I++  + ++  + +++F          V    + I           V  S   
Sbjct: 352 CDKLTTIIESSLNVLEPAEYRKMFDRLS------VFPPSAHIPTILLSLIWFDVIKSDVM 405

Query: 364 E-----ASRALAEMNGK-MIVSKP-LYVAVAQRKEERRA---RLQAQFSQMRPVAMGPSV 413
                    +L E   K   +S P +Y+ +  + E   A    +   ++  +       +
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI 465

Query: 414 PPRMPMY 420
           PP +  Y
Sbjct: 466 PPYLDQY 472

>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 = 44.5 bits (104), Expect = 1e-04
 Identities = 32/241 (13%), Positives = 71/241 (29%), Gaps = 57/241 (23%)

Query: 192 HFLRKQERETVAIKTKFNNV-------FVKNLDESTTDEDLKKIFG--EYGTITSAVVMR 242
           H     + ET   + ++ ++       FV N D     +  K I    E   I   ++ +
Sbjct: 2   HHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI---IMSK 58

Query: 243 DGDGKS-KCFGFVNFENADDAAKAVE-ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 300
           D    + + F  +  +  +   K VE  L      + ++ +   + +  +   +   + +
Sbjct: 59  DAVSGTLRLFWTLLSKQEEMVQKFVEEVLR----INYKFLMSPIKTEQRQPSMMTRMYIE 114

Query: 301 A---MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS----KG 353
               +      F   N+        +  + L EL             R    +      G
Sbjct: 115 QRDRLYNDNQVFAKYNVSRLQPYLKL-RQALLEL-------------RPAKNVLIDGVLG 160

Query: 354 SG---FVAFSTPEEASRA---LAEMNGKMIVSKPLYVAVAQRKEERR--ARLQAQFSQMR 405
           SG           +   +     +M+ K+      ++ +            LQ    Q+ 
Sbjct: 161 SGKTWVAL-----DVCLSYKVQCKMDFKI-----FWLNLKNCNSPETVLEMLQKLLYQID 210

Query: 406 P 406
           P
Sbjct: 211 P 211

>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 = 57.9 bits (139), Expect = 8e-09
 Identities = 32/171 (18%), Positives = 52/171 (30%), Gaps = 14/171 (8%)

Query: 386 VAQRKEERRARLQAQFSQMRPVAMGPS--VPPRMPMYPPGPSGLGQQFLYGQAPPAIIPP 443
           ++  K+    + Q Q+ Q       P+  +PP+ P       G         A P++   
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYG-QMGMPPQGAVPSMGQQ 59

Query: 444 QAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQ 503
           Q     Q+QL   +  A   M +  +  V                P    Q   P+   Q
Sbjct: 60  QFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNA------YMQPQVPVQMGTPLQQQQ 113

Query: 504 MPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMP 554
            P    AY  P     Q+             P+D+   +P     +  P P
Sbjct: 114 QPMAAPAYGQPSAAMGQNMRPMNQ-----LYPIDLLTELPPPITDLTLPPP 159

>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 = 55.2 bits (132), Expect = 6e-08
 Identities = 24/157 (15%), Positives = 37/157 (23%), Gaps = 10/157 (6%)

Query: 398 QAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGM 457
           Q     M P     +      M  P    +          PA              +  M
Sbjct: 24  QQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDM 83

Query: 458 RPAGAPM--PNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAY---- 511
                P+  PN ++      Q G     ++         QP   M   M P    Y    
Sbjct: 84  HLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDL 143

Query: 512 ----RYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPR 544
                 P+       P  +     + VP ++    P 
Sbjct: 144 LTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD 180

>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 = 51.7 bits (124), Expect = 2e-08
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 223 EDLKKIFGEYGTITSAVVMRDGDGKS---KCFGFVNFENADDAAKAVEALNGKKFDDR 277
           ED++    +YG + S  + R  DG         FV F +  D  KA++ L G+KF +R
Sbjct: 30  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANR 87

>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 = 43.6 bits (103), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 13/74 (17%)

Query: 314 LYIKNL---GDSIDDEKLKELFSE-------FGTITSCKVMRDPSGIS---KGSGFVAFS 360
           L + N+    + +DDE+ +E+  +       +G + S ++ R   G+     G  FV F+
Sbjct: 8   LCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFT 67

Query: 361 TPEEASRALAEMNG 374
           +  +  +A+  + G
Sbjct: 68  SVFDCQKAMQGLTG 81

>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 = 43.2 bits (102), Expect = 2e-05
 Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 3/63 (4%)

Query: 134 LHDTFSSFGNILSCKI---ATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           + D  S +G + S +I            G  FV+F +    Q A+  L G    ++ V  
Sbjct: 32  VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 91

Query: 191 GHF 193
            + 
Sbjct: 92  KYC 94

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 54.8 bits (131), Expect = 2e-08
 Identities = 16/93 (17%), Positives = 37/93 (39%), Gaps = 14/93 (15%)

Query: 119 NIFIKNLDKSIDHKA---------LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
            +++  +D +++ K          +   FS  G+I   +       +SK  GFV+F+ + 
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQA 190

Query: 170 SAQNAIDKLNGMLINDKQVFVGHFLRKQERETV 202
           +A+ A + ++   +           R+     V
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLV 223

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 54.8 bits (131), Expect = 2e-08
 Identities = 18/103 (17%), Positives = 39/103 (37%), Gaps = 17/103 (16%)

Query: 313 NLYIKNLGDSID---------DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 363
            LY+  +  +++         + +++ +FS  G I   + +      SK  GFV F    
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQA 190

Query: 364 EASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 406
            A  A   M+ + ++         +R+      L  +++   P
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREGT---GLLVKWANEDP 230

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 54.4 bits (130), Expect = 2e-08
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             +  K+L  +  +  ++ +F   G I     +     +SK  GFV F+   +A  A EA
Sbjct: 144 GALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQANAEFAKEA 198

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
           ++ +            +++   
Sbjct: 199 MSNQTLLLPSDKEWDDRREGTG 220

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.4 bits (117), Expect = 1e-06
 Identities = 20/101 (19%), Positives = 41/101 (40%), Gaps = 15/101 (14%)

Query: 21  GASGNQFLTTSLYVGDLDFNVT---------DSQLYDLFSQVGQVLSVRVCRDLSTRRSL 71
           G    +    +LYVG +D  +          +S++  +FS++G +  +R         S 
Sbjct: 126 GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SK 179

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSI 112
             G+V +   A+A  A + ++   L   S +     R+ + 
Sbjct: 180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>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 = 51.5 bits (123), Expect = 3e-08
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 314 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA-- 370
           +++ NL      D  + +L   +G I +  +MR      K   F+   T E+A   +   
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHC 82

Query: 371 EMNGKMIVSKPLYVAVAQRKEE 392
                    + + V ++++ ++
Sbjct: 83  LKKALWFQGRCVKVDLSEKYKK 104

>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 = 48.4 bits (115), Expect = 3e-07
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 12/88 (13%)

Query: 211 VFVKNL-DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE-- 267
           + + NL     +D  + K+   YG I + ++M     + K   F+  E  +DA   V+  
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-----RMKSQAFIEMETREDAMAMVDHC 82

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELK 295
                 F  R   V      SE+ ++L 
Sbjct: 83  LKKALWFQGRCVKV----DLSEKYKKLV 106

>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 = 51.5 bits (123), Expect = 4e-08
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMR---DGDGKSKCFGFVNFENADDAAKAVE 267
           V ++ L  S + ED++    +      A  +      +G+     FV   + DD   A++
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELK 295
             + +    R   V K+  ++E +  LK
Sbjct: 107 -KDRESMGHRYIEVFKS-HRTEMDWVLK 132

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 50.4 bits (120), Expect = 9e-08
 Identities = 15/100 (15%), Positives = 35/100 (35%), Gaps = 4/100 (4%)

Query: 299 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSG 355
             +M    +  +G  + ++ L  S   E ++   S+            +    G   G  
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91

Query: 356 FVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRA 395
           FV   + ++   AL + + + +  + + V  + R E    
Sbjct: 92  FVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRTEMDWV 130

>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 = 49.6 bits (118), Expect = 2e-07
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 8/91 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQ---VGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           + +  L ++ +   + +  S          V        R+S G  +V   +  D   AL
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQS-GEAFVELGSEDDVKMAL 105

Query: 89  DVLNFTPLNNKSIRIMYSHR---DPSIRKSG 116
              +   + ++ I +  SHR   D  ++ SG
Sbjct: 106 K-KDRESMGHRYIEVFKSHRTEMDWVLKHSG 135

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 45.8 bits (108), Expect = 5e-06
 Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSF---GNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
           + ++ L  S   + + +  S                  G+  G  FV+  +++  + A+ 
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106

Query: 177 KLNGMLINDKQVFV 190
           K +   +  + + V
Sbjct: 107 K-DRESMGHRYIEV 119

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 51.2 bits (122), Expect = 5e-08
 Identities = 17/68 (25%), Positives = 24/68 (35%), Gaps = 4/68 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + I+N    I    L+   +  G +    I      Q      V+FE+   AQ A   LN
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ----AMVEFESVLCAQKAKAALN 83

Query: 180 GMLINDKQ 187
           G  I    
Sbjct: 84  GADIYAGC 91

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 45.1 bits (106), Expect = 6e-06
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 4/67 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + ++N     T + L  +    G +   V+ +    +      V FE+   A KA  ALN
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ----AMVEFESVLCAQKAKAALN 83

Query: 271 GKKFDDR 277
           G      
Sbjct: 84  GADIYAG 90

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 45.1 bits (106), Expect = 7e-06
 Identities = 21/101 (20%), Positives = 40/101 (39%), Gaps = 15/101 (14%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L + +  + +T   LY + + VG+V      R +  +R+     V + +   A +A   L
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQ-----RIVIFKRNGIQAMVEFESVLCAQKAKAAL 82

Query: 92  NFTPLNNKS--IRIMYSHRDPSIRKSGTGNIFIKNLDKSID 130
           N   +      ++I Y+          T    I+N + S D
Sbjct: 83  NGADIYAGCCTLKIEYARP--------TRLNVIRNDNDSWD 115

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.1 bits (101), Expect = 3e-05
 Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 4/66 (6%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           L L I+N    I  + L  + +  G +    + +     +     V F +   A +A A 
Sbjct: 26  LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR----NGIQAMVEFESVLCAQKAKAA 81

Query: 372 MNGKMI 377
           +NG  I
Sbjct: 82  LNGADI 87

>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 = 50.0 bits (119), Expect = 5e-08
 Identities = 14/87 (16%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 311 GLNLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
           G ++ + N+   +  ++L++     F+  G + S ++        +    V     ++A 
Sbjct: 9   GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAI 66

Query: 367 RALAEMNGKMIVSKPLYVAVAQRKEER 393
            A+  ++   I SK + V++A      
Sbjct: 67  GAVNSLHRYKIGSKKILVSLATGASGP 93

>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 = 49.6 bits (118), Expect = 7e-08
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 7/85 (8%)

Query: 111 SIRKSGTG-NIFIKNLDKSIDHK----ALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           S   SG G ++ + N+D  +  K     L + F+  G + S +++     Q      VQ 
Sbjct: 2   SSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ--LKAVVQM 59

Query: 166 ENKESAQNAIDKLNGMLINDKQVFV 190
           EN + A  A++ L+   I  K++ V
Sbjct: 60  ENLQDAIGAVNSLHRYKIGSKKILV 84

>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 = 49.6 bits (118), Expect = 7e-08
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 210 NVFVKNLDESTTDEDLKKI----FGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
           +V V N+D   + ++L+++    F  +G + S  +    D + K    V  EN  DA  A
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKA--VVQMENLQDAIGA 68

Query: 266 VEALNGKKFDDREWYVGKAQKKSERE 291
           V +L+  K   ++  V  A   S   
Sbjct: 69  VNSLHRYKIGSKKILVSLATGASGPS 94

>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 = 45.4 bits (107), Expect = 3e-06
 Identities = 22/100 (22%), Positives = 44/100 (44%), Gaps = 8/100 (8%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQ----LYDLFSQVGQVLSVRVCRDLSTRRSLGYGYV 76
           G+SG+      + V ++D+ ++  +    L + F++ G+V SV +      +       V
Sbjct: 1   GSSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ---LKAVV 57

Query: 77  NYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
              N  DA  A++ L+   + +K I +  +    S   SG
Sbjct: 58  QMENLQDAIGAVNSLHRYKIGSKKILVSLA-TGASGPSSG 96

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L +KNL   ID   L+ L  + G + S         +++G     ++T EEA++A   +N
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-----YLNQGIALCKYTTREEANKAQMALN 64

Query: 374 GKMIVSKPLYVAVAQRKEERR 394
             ++ +  ++       E + 
Sbjct: 65  NCVLANTTIFAESPSENEVQS 85

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 47.7 bits (114), Expect = 6e-07
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 10/74 (13%)

Query: 210 NVF-VKNLDESTTDEDLKK-IFGE---YGTITSAVVMRD-GDGKSKCFGFVNFENADDAA 263
           N+F  +  +E   D ++K  +  E   +G +    V ++   G      +V   +   A 
Sbjct: 14  NMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAI 69

Query: 264 KAVEALNGKKFDDR 277
            AV AL+G+ F  +
Sbjct: 70  AAVNALHGRWFAGK 83

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 6/58 (10%)

Query: 320 GDSIDDEKLKELFSE---FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 374
               D E   ++  E    G +    V ++ +    G+ +V   +   A  A+  ++G
Sbjct: 23  EVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHG 77

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 47.1 bits (112), Expect = 1e-06
 Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 17/93 (18%)

Query: 194 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK-IFGE---YGTITSAVVMRDGDGKSK 249
           LRKQE   + ++    N+     D    D+DL+  +  E   +G +   ++ ++  G+ +
Sbjct: 15  LRKQESTVMVLR----NMV----DPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEE 66

Query: 250 CFG-----FVNFENADDAAKAVEALNGKKFDDR 277
                   FV F  A +  KA++ALNG+ F  R
Sbjct: 67  DAEIIVKIFVEFSIASETHKAIQALNGRWFAGR 99

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 41.7 bits (98), Expect = 7e-05
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 10/71 (14%)

Query: 314 LYIKNL--GDSIDDEKLKELFSE---FGTITSCKVMRDPSGISK-----GSGFVAFSTPE 363
           + ++N+     IDD+   E+  E   FG +    + ++  G  +        FV FS   
Sbjct: 23  MVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIAS 82

Query: 364 EASRALAEMNG 374
           E  +A+  +NG
Sbjct: 83  ETHKAIQALNG 93

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 12/60 (20%), Positives = 19/60 (31%), Gaps = 5/60 (8%)

Query: 139 SSFGNILSCKI-----ATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHF 193
             FG +    I       +   +     FV+F        AI  LNG     ++V    +
Sbjct: 47  GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVY 106

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 96

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 4/79 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+ NL  + D + +             KV+     I+  S  + F   + A RA   M 
Sbjct: 12  LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLS----ITGCSAILRFINQDSAERAQKRME 67

Query: 374 GKMIVSKPLYVAVAQRKEE 392
            + +    + V+   +  E
Sbjct: 68  NEDVFGNRIIVSFTPKNRE 86

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A Length = 624

 Score = 49.6 bits (118), Expect = 2e-06
 Identities = 33/166 (19%), Positives = 50/166 (30%), Gaps = 30/166 (18%)

Query: 311 GLNLYIKNL--GDSIDDEKLKELFSEFGTITSCKVMRDPS----------GISKGSGFVA 358
              L+  N     S++  K   L+ +   +      +D               K   F A
Sbjct: 460 AAYLFKGNNRWKQSVELCKKDSLYKD--AMQYASESKDTELAEELLQWFLQEEKRECFGA 517

Query: 359 -------FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGP 411
                     P+      A  +  M  + P ++ V +    +  +L A  S  +      
Sbjct: 518 CLFTCYDLLRPDVVLE-TAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASESLRKEEEQAT 576

Query: 412 SVPPRMP-----MYPPGPSGL---GQQFLYGQAPPAIIPPQAGFGY 449
              P +      M   GPS        F YG   PA   PQ GFGY
Sbjct: 577 ETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGY 622

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 194 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG- 252
           + K   + V ++    N+      +   + + K+   +YG +   V+             
Sbjct: 3   MGKCPTKVVLLR----NMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVR 58

Query: 253 -FVNFENADDAAKAVEALNGKKFDDR 277
            F+ FE  + A KAV  LNG+ F  R
Sbjct: 59  IFLEFERVESAIKAVVDLNGRYFGGR 84

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 7/69 (10%)

Query: 314 LYIKNL--GDSIDDEKLKELFSE---FGTITSCKVMRDPSGISKGSG--FVAFSTPEEAS 366
           + ++N+     +D++   E   E   +G +  C +   P      +   F+ F   E A 
Sbjct: 11  VLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAI 70

Query: 367 RALAEMNGK 375
           +A+ ++NG+
Sbjct: 71  KAVVDLNGR 79

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 44.7 bits (106), Expect = 6e-06
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 19/92 (20%)

Query: 195 RKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGE--------YGTITSAVVM-RDGD 245
           R +    V IK    N+F  +  +   D  +     E        +G I   ++  R  D
Sbjct: 11  RMRHERVVIIK----NMF--HPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPD 64

Query: 246 GKSKCFGFVNFENADDAAKAVEALNGKKFDDR 277
           G       V+F + ++A   ++ L+G+ F  R
Sbjct: 65  GV----ASVSFRDPEEADYCIQTLDGRWFGGR 92

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 3/49 (6%)

Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 374
           E L+   S+FG I    +         G   V+F  PEEA   +  ++G
Sbjct: 41  EDLRVECSKFGQIRKLLLFDRHP---DGVASVSFRDPEEADYCIQTLDG 86

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 3/55 (5%)

Query: 139 SSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHF 193
           S FG I    +         G   V F + E A   I  L+G     +Q+    +
Sbjct: 48  SKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 99

>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 = 44.3 bits (104), Expect = 5e-05
 Identities = 24/112 (21%), Positives = 27/112 (24%), Gaps = 8/112 (7%)

Query: 405 RPVAMGPSVPPRMPMYPPGPSG-------LGQQFLYGQAPPAIIPPQAGFGYQQQLVPGM 457
           R    G      MP  P G +G         QQ +  Q    +    A         P  
Sbjct: 108 RAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQ 167

Query: 458 RPAGAPMPN-FFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRG 508
            P G   P                P G R          P    P  MPP G
Sbjct: 168 YPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPG 219

>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 = 40.8 bits (95), Expect = 6e-04
 Identities = 24/134 (17%), Positives = 31/134 (23%), Gaps = 10/134 (7%)

Query: 406 PVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMP 465
             A GP +        P    + Q      AP  +  P  G G   Q V   +  G    
Sbjct: 99  GAAGGPGIGRAAGRGIPAGVPMPQ------APAGLAGPVRGVGGPSQQVMTPQGRGTVAA 152

Query: 466 NFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFD 525
                  +       P                   P  M       R P+G  M   P  
Sbjct: 153 A---AAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPP-G 208

Query: 526 MGAGSMLPVPVDMG 539
            G    +P P    
Sbjct: 209 RGTPMGMPPPGMRP 222

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE--- 267
           V V+ L  +  DE L   F          V+     +  C G + F    DA + +    
Sbjct: 11  VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--RLGCGGVLTFREPADAERVLAQAD 68

Query: 268 -ALNGKKFDDR 277
             L+G +   R
Sbjct: 69  HELHGAQLSLR 79

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 6/61 (9%)

Query: 211 VFVKNL-DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           V + +          L ++   +G I++ +++           F+     +DA  AV+  
Sbjct: 18  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-----NKINEAFIEMATTEDAQAAVDYY 72

Query: 270 N 270
            
Sbjct: 73  T 73

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 320 GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS 379
                 + L  L  ++G + +  +    S    G+  V F+T + A  A+    G +   
Sbjct: 26  KGGYSKDVLLRLLQKYGEVLNLVL----SSKKPGTAVVEFATVKAAELAVQNEVGLV--D 79

Query: 380 KPLYVAVAQRKEERRA 395
            PL ++  + + +  +
Sbjct: 80  NPLKISWLEGQPQDAS 95

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 41.3 bits (96), Expect = 8e-04
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 12/94 (12%)

Query: 313 NLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
           +L + N  LG+ +   +L  +  + G + +  +M      +K   F  + T EE+ RA  
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDAL-LMPP----NKPYSFARYRTTEESKRAYV 74

Query: 371 EMNGKMIVSK-----PLYVAVAQRKEERRARLQA 399
            +NGK +V        LY+   ++ + +  R QA
Sbjct: 75  TLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQA 108

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	652
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.98
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	99.97
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	99.97
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.94
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.94
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.94
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.93
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.83
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.83
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.81
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.8
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.78
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.77
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.77
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.76
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.76
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.76
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.75
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.75
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.75
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.75
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.75
2div_A	99	TRNA selenocysteine associated protein; structural	99.75
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.75
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.75
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.74
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.74
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.74
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.74
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.74
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.74
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.74
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.73
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.73
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.73
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.73
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.73
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.73
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.73
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.73
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.73
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.72
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.72
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.72
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.72
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.72
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.71
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.71
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.71
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.71
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.71
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.71
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.7
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.7
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.7
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.7
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.7
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.7
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.7
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.7
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.7
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.7
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.7
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.7
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.69
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.69
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.69
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.69
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.69
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.69
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.69
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.69
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.69
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.69
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.69
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.69
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.69
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.69
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.69
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.69
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.69
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.68
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.68
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.68
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.68
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.68
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.68
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.68
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.67
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.67
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.67
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.67
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.67
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.67
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.67
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.67
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.67
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.67
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.67
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.67
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.67
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.67
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.67
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.67
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.66
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.66
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.66
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.66
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.66
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.66
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.66
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.66
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.66
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.66
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.66
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.66
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.66
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.66
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.66
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.66
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.66
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.66
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.66
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.65
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.65
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.65
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.65
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.65
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.65
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.65
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.65
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.65
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.65
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.65
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.65
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.65
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.65
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.64
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.64
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.64
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.64
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.64
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.64
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.64
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.64
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.64
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.64
2div_A	99	TRNA selenocysteine associated protein; structural	99.64
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.64
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.64
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.64
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.64
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.64
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.63
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.63
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.63
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.63
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.63
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.63
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.63
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.63
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.62
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.62
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.62
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.62
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.62
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.62
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.62
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.62
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.62
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.62
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.62
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.62
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.62
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.62
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.62
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.62
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.62
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.61
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.61
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.61
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.61
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.61
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.61
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.61
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.61
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.61
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.4
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.61
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.6
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.6
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.6
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.6
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.6
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.6
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.6
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.6
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.6
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.6
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.6
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.6
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.6
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.59
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.59
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.59
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.59
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.59
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.59
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.59
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.59
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.58
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.58
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.58
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.58
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.58
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.58
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.58
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.58
1x5p_A	97	Negative elongation factor E; structure genomics,	99.58
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.57
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.57
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.57
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.57
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.56
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.56
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.56
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.56
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.56
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.56
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.33
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.55
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.55
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.55
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.55
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.55
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.55
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.54
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.54
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.54
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.54
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.54
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.54
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.54
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.53
1x5p_A	97	Negative elongation factor E; structure genomics,	99.53
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.53
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.53
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.53
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.52
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.52
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.52
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.5
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.5
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.5
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.5
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.49
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.49
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.48
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.47
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.46
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.46
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.46
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.45
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.44
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.44
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.44
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.42
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.4
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.38
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.37
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.37
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.36
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.35
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.27
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.23
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.22
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.19
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.16
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.01
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.0
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.93
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.93
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.81
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.8
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.74
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.69
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.49
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.99
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.78
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.69
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.59
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.45
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.14
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.07
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.85
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.7
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.56
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.51
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.38
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.33
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.18
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.88
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.27
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.81
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.53
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.45
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	85.64
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	80.32

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=3.3e-43  Score=359.90  Aligned_cols=256  Identities=21%  Similarity=0.312  Sum_probs=231.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ++++|||+|||+++|+++|+++|+.|| |.++++      ++++|||||.|.+.++|.+|++.||+..|.|++|+|.|+.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            468999999999999999999999999 999888      4567899999999999999999999999999999999965


Q ss_pred             CCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCe
Q 006282          108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDK  186 (652)
Q Consensus       108 ~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~  186 (652)
                      .        ..+|||+|||.++++++|+++|+.||.|.+|++..+ .+|.++|||||+|.+.++|.+|++.+++..+.|+
T Consensus        94 ~--------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~  165 (284)
T 3smz_A           94 T--------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR  165 (284)
T ss_dssp             C--------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             C--------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            4        358999999999999999999999999999999988 5899999999999999999999999999999999


Q ss_pred             eeeecccccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHH
Q 006282          187 QVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV  266 (652)
Q Consensus       187 ~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai  266 (652)
                      .+.|.+..+.....                                                                  
T Consensus       166 ~i~v~~a~~~~~~~------------------------------------------------------------------  179 (284)
T 3smz_A          166 TLYVHWTDAGQLTP------------------------------------------------------------------  179 (284)
T ss_dssp             ECEEEECCGGGCCT------------------------------------------------------------------
T ss_pred             EEEEEECCCCCCCc------------------------------------------------------------------
Confidence            99998764321100                                                                  


Q ss_pred             HHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCC-CHHHHHHHhhhcCCeeEEEEec
Q 006282          267 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSI-DDEKLKELFSEFGTITSCKVMR  345 (652)
Q Consensus       267 ~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~-te~~L~~~F~~fG~I~~v~i~~  345 (652)
                                                              .....++|||+|||.++ ++++|+++|+.||.|.+++|+.
T Consensus       180 ----------------------------------------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~  219 (284)
T 3smz_A          180 ----------------------------------------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC  219 (284)
T ss_dssp             ----------------------------------------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEE
T ss_pred             ----------------------------------------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEE
Confidence                                                    00235689999999996 9999999999999999999999


Q ss_pred             CCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHHHHHHHHhhhcC
Q 006282          346 DPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQM  404 (652)
Q Consensus       346 ~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r~~~~~~~~~~~  404 (652)
                      +.+|+++|||||+|.+.++|.+|+..|||..++|+.|.|.|+.++..++..+.++....
T Consensus       220 ~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~aaq  278 (284)
T 3smz_A          220 GQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQ  278 (284)
T ss_dssp             CSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCHHHHHHHHHHHT
T ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCcccchhhhhhHHH
Confidence            99999999999999999999999999999999999999999999988887777665543

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=1.3e-41  Score=349.53  Aligned_cols=251  Identities=20%  Similarity=0.343  Sum_probs=217.3

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      .....+++|||+|||+++|+++|+++|+.||+|.+|++++|..+  ++|||||+|.+.++|.+|++ +|+..|.|+.|+|
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v  112 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIV  112 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEE
Confidence            34567899999999999999999999999999999999998754  57999999999999999996 9999999999999


Q ss_pred             ecccCCcccccCCCcceeecCCCccccHHHHHhhhccCC-CeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCce
Q 006282          104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG-NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGML  182 (652)
Q Consensus       104 ~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG-~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~  182 (652)
                      .|+.         ..+|||+|||.++++++|+++|+.|| .|.+|.+..+..|.++|||||+|.+.++|..|++.+++..
T Consensus       113 ~~~~---------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~  183 (292)
T 2ghp_A          113 SHLT---------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK  183 (292)
T ss_dssp             EECC---------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             EECC---------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            9864         56899999999999999999999999 9999999999888899999999999999999999999999


Q ss_pred             ecCeeeeecccccchhhHHH-hhccCcceEEecCCCCC-CCHHHHHHHhccCCCeeEEEEeeCCC--CCcceeEEEeeCC
Q 006282          183 INDKQVFVGHFLRKQERETV-AIKTKFNNVFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGD--GKSKCFGFVNFEN  258 (652)
Q Consensus       183 l~g~~~~v~~~~~~~~~~~~-~~~~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~v~~~~i~~~~~--g~~~g~~fV~f~~  258 (652)
                      +.|+.+.|.+..+....... ......++|||+|||.+ +++++|+++|+.||.|.++.+..+.+  |.++|||||+|.+
T Consensus       184 ~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~  263 (292)
T 2ghp_A          184 IEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN  263 (292)
T ss_dssp             ETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESS
T ss_pred             eCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCC
Confidence            99999999988766544333 33456788999999999 99999999999999999999999876  9999999999999


Q ss_pred             HHHHHHHHHHHCCCccCCceEEEEccccc
Q 006282          259 ADDAAKAVEALNGKKFDDREWYVGKAQKK  287 (652)
Q Consensus       259 ~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~  287 (652)
                      .++|.+|+ .|++..+.|+.|.|.++.++
T Consensus       264 ~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          264 KDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999999 99999999999999999765

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=4e-41  Score=345.80  Aligned_cols=251  Identities=21%  Similarity=0.380  Sum_probs=217.2

Q ss_pred             ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecc
Q 006282          113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGH  192 (652)
Q Consensus       113 ~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~  192 (652)
                      +....++|||+|||.++++++|+++|+.||.|.+|++..+..+ ++|||||+|.+.++|.+|+ .+++..+.|+.+.+.+
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~  114 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSH  114 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHH-HhCCcEeCCcEEEEEE
Confidence            3445678999999999999999999999999999999998766 5899999999999999999 5899999999999976


Q ss_pred             cccchhhHHHhhccCcceEEecCCCCCCCHHHHHHHhccCC-CeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCC
Q 006282          193 FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG  271 (652)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~  271 (652)
                      .             ..++|||+|||.++++++|+++|+.|| .|.++.+..+..|.++|||||+|.+.++|..|+..|++
T Consensus       115 ~-------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g  181 (292)
T 2ghp_A          115 L-------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG  181 (292)
T ss_dssp             C-------------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTT
T ss_pred             C-------------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            4             468899999999999999999999999 99999999988899999999999999999999999999


Q ss_pred             CccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCC--
Q 006282          272 KKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPS--  348 (652)
Q Consensus       272 ~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~te~~L~~~F~~fG~I~~v~i~~~~~--  348 (652)
                      ..+.|+.|.|.++.........           .......++|||+|||.. +++++|+++|+.||.|.+|+|+.+..  
T Consensus       182 ~~~~g~~l~v~~a~~~~~~~~~-----------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~t  250 (292)
T 2ghp_A          182 LKIEGYTLVTKVSNPLEKSKRT-----------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEH  250 (292)
T ss_dssp             CEETTEECEEEECCCC--------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC--
T ss_pred             CEeCCcEEEEEECCCCcccccc-----------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcC
Confidence            9999999999998765433211           122345689999999999 99999999999999999999999887  


Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          349 GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       349 g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      |.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.|+.++
T Consensus       251 g~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          251 SFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             -CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            999999999999999999999 99999999999999999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=1e-33  Score=276.45  Aligned_cols=193  Identities=58%  Similarity=0.989  Sum_probs=163.8

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ..+..++++|||+|||+++||++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.+|+..+.|+.|+
T Consensus         9 ~~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~   88 (213)
T 4f02_A            9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVR   88 (213)
T ss_dssp             ------CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccc
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCce
Q 006282          103 IMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGML  182 (652)
Q Consensus       103 i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~  182 (652)
                      +.|+............+|||+||+.++++++|+++|+.||.|.+|+|..|..+ ++|||||+|.+.++|.+|++.|||..
T Consensus        89 ~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~-~~g~~fV~f~~~~~a~~Ai~~lng~~  167 (213)
T 4f02_A           89 IMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGML  167 (213)
T ss_dssp             EEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTE-EEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             cccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCC-CceEEEEEeCCHHHHHHHHHHhCCCE
Confidence            99998887777777889999999999999999999999999999999998544 89999999999999999999999999


Q ss_pred             ecCeeeeecccccchhhHHHhhccCcceEEecCCC
Q 006282          183 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLD  217 (652)
Q Consensus       183 l~g~~~~v~~~~~~~~~~~~~~~~~~~~l~V~nlp  217 (652)
                      ++|+.|.|.++.++.++.... .......+..++|
T Consensus       168 ~~g~~i~V~~a~~~~~~~~~~-~~~~~~~~p~~~P  201 (213)
T 4f02_A          168 LNDRKVFVGRFKSRKEREAEL-GARAKEFYPYDVP  201 (213)
T ss_dssp             ETTEECEEEECCCHHHHHHHH-C------------
T ss_pred             ECCEEEEEEEcCCCcccchhh-hcccCCCCCCCCC
Confidence            999999999988776554432 2233334444444

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.98  E-value=3e-31  Score=258.93  Aligned_cols=175  Identities=34%  Similarity=0.512  Sum_probs=157.5

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...++|||+|||+++++++|+++|++||.|.+|.++++ .+|+++|||||+|.+.++|.+|++.+++..+.|+.+.+.++
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            34578999999999999999999999999999999988 46999999999999999999999999999999999999988


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE  364 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~  364 (652)
                      .........                ..++|||+|||.++++++|+++|+.||.|++|+|++|. +.++|||||+|.+.++
T Consensus        93 ~~~~~~~~~----------------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~  155 (213)
T 4f02_A           93 QRDPSLRKS----------------GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEA  155 (213)
T ss_dssp             CCCTHHHHH----------------CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHH
T ss_pred             ccccccccc----------------ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHH
Confidence            765443221                23579999999999999999999999999999999885 4479999999999999


Q ss_pred             HHHHHHHhcCcEecCeeEEEEecccHHHHHHHH
Q 006282          365 ASRALAEMNGKMIVSKPLYVAVAQRKEERRARL  397 (652)
Q Consensus       365 A~~A~~~lng~~~~g~~l~v~~~~~~~~r~~~~  397 (652)
                      |.+|++.|||..|+|++|.|.++.++.++....
T Consensus       156 a~~Ai~~lng~~~~g~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          156 AERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECCCHHHHHHHH
T ss_pred             HHHHHHHhCCCEECCEEEEEEEcCCCcccchhh
Confidence            999999999999999999999999987776543

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum}

Probab=99.97  E-value=4.7e-33  Score=217.53  Aligned_cols=78  Identities=79%  Similarity=1.074  Sum_probs=74.6

Q ss_pred             cccchhhhhcCChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHHHHh
Q 006282          555 ITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQ  632 (652)
Q Consensus       555 ~~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~~~~  632 (652)
                      .++++++|++++|++||++|||+|||+|++++|++||||||||||||++|||+||+|+++|+.||+||++||++|+++
T Consensus         7 ~~~~as~La~~~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~Ell~Lles~e~L~~kv~EA~~vL~~~~~~   84 (85)
T 2dyd_A            7 IGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAKVAEAMEVLRSAQQH   84 (85)
T ss_dssp             TTTSCHHHHCCCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHCHHHHHHHTTCSHHHHHHHHHHHHHHTSCSSC
T ss_pred             hhhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHhhc
Confidence            356999999999999999999999999999999999999999999999999999999999999999999999988653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=1.3e-30  Score=243.73  Aligned_cols=164  Identities=29%  Similarity=0.544  Sum_probs=155.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      ++|||+|||.++|+++|+++|+.||+|.+|++++++. ++++|||||+|.+.++|.+|++.+|+..+.|+.|+|.|+...
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 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            5899999999999999999999999999999999975 679999999999999999999999999999999999999888


Q ss_pred             cccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeee
Q 006282          110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV  188 (652)
Q Consensus       110 ~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~  188 (652)
                      .........+|||+|||.++++++|+++|+.||.|.++.+..+ .+|.++|||||+|.+.++|.+|++.+|+..++|+.|
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  159 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL  159 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Confidence            7777778889999999999999999999999999999999998 688999999999999999999999999999999999


Q ss_pred             eecccc
Q 006282          189 FVGHFL  194 (652)
Q Consensus       189 ~v~~~~  194 (652)
                      .|.++.
T Consensus       160 ~v~~a~  165 (166)
T 3md3_A          160 RINWAA  165 (166)
T ss_dssp             EEEESC
T ss_pred             EEEecC
Confidence            998764

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1

Probab=99.97  E-value=6e-33  Score=216.92  Aligned_cols=78  Identities=54%  Similarity=0.721  Sum_probs=74.9

Q ss_pred             CccccchhhhhcCChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 006282          553 MPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVA  630 (652)
Q Consensus       553 ~~~~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~~  630 (652)
                      .+.++++++|++++|++||++|||+|||+|++++|++||||||||||||++|||+||+|+++|+.||+||++||++|+
T Consensus         6 ~~~~l~~s~La~a~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~ElL~Lle~~e~L~~kV~EA~~vL~~~~   83 (85)
T 1nmr_A            6 SQGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRHM   83 (85)
T ss_dssp             CCCCTTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTTCCC
T ss_pred             CCCccCHHHHHcCChHHHHHHHHHHHHHHHHHhCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHhh
Confidence            346899999999999999999999999999999999999999999999999999999999999999999999998775

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1

Probab=99.97  E-value=2.5e-32  Score=216.77  Aligned_cols=78  Identities=33%  Similarity=0.445  Sum_probs=75.4

Q ss_pred             ccchhhhhcCChHHHHHHhhhhchhhhhh--ccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHHHHhh
Q 006282          556 TALSTALANASPEQQRTLLGESLYPLVEQ--LERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQ  633 (652)
Q Consensus       556 ~~~~~~l~~~~~~~~~~~~g~~~~~~~~~--~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~~~~~  633 (652)
                      |.++++|+++++++||++|||+|||+|++  ++|++||||||||||||++|||+||+|+++|+.||+||++||++|++.+
T Consensus         6 p~~a~~la~~~p~~Qkq~LGE~LyplV~~~~~~pelAgKITGMLLEmd~~ElL~LLes~e~L~~kV~EA~~vL~~~~~~~   85 (92)
T 1ifw_A            6 PRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQ   85 (92)
T ss_dssp             SSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             ccchHHHhcCChHHHHHHHHHHHHHHHHHhhcCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHhh
Confidence            57999999999999999999999999999  9999999999999999999999999999999999999999999999754

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A

Probab=99.97  E-value=1.6e-31  Score=230.59  Aligned_cols=82  Identities=44%  Similarity=0.738  Sum_probs=77.6

Q ss_pred             CccccchhhhhcCChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHHHHh
Q 006282          553 MPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQ  632 (652)
Q Consensus       553 ~~~~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~~~~  632 (652)
                      .+.++++++|+++++++||++|||+|||+|+.++|++|+||||||||||++|||+||+|+++|++||+||++||++|+++
T Consensus        49 ~~~pl~as~La~a~p~eQkq~LGE~LyplV~~~~p~~A~KITGMLLEmd~~ElL~LLes~e~L~~kV~EA~~vL~~~~~~  128 (144)
T 1g9l_A           49 GQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAK  128 (144)
T ss_dssp             SCCCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTTTSSSHHHHHHHHCTTHHHHHHHHHHHHHHTTSSS
T ss_pred             CcchhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhccCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHhc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             hc
Q 006282          633 QA  634 (652)
Q Consensus       633 ~~  634 (652)
                      +.
T Consensus       129 ~~  130 (144)
T 1g9l_A          129 EA  130 (144)
T ss_dssp             TT
T ss_pred             cc
Confidence            53

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.97  E-value=3.4e-30  Score=248.04  Aligned_cols=176  Identities=27%  Similarity=0.455  Sum_probs=152.8

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ...+..+++|||+|||+++||++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|.+|++. ++..+.|+.|+
T Consensus         7 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~   85 (196)
T 1l3k_A            7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVE   85 (196)
T ss_dssp             -CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEee
Confidence            34556789999999999999999999999999999999999999999999999999999999999985 88899999999


Q ss_pred             eecccCCcccc----cCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHH
Q 006282          103 IMYSHRDPSIR----KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK  177 (652)
Q Consensus       103 i~~s~~~~~~~----~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~  177 (652)
                      |.|+.......    .....+|||+|||.++++++|+++|+.||.|.+|.+..+ .+|.++|||||+|.+.++|.+|+..
T Consensus        86 v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  165 (196)
T 1l3k_A           86 PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ  165 (196)
T ss_dssp             EEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC
T ss_pred             eecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh
Confidence            99987654322    224578999999999999999999999999999999998 4889999999999999999999976


Q ss_pred             hcCceecCeeeeecccccchhhH
Q 006282          178 LNGMLINDKQVFVGHFLRKQERE  200 (652)
Q Consensus       178 lng~~l~g~~~~v~~~~~~~~~~  200 (652)
                       ++..++|+.|.|.+..++....
T Consensus       166 -~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          166 -KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             -SCCEETTEECEEEECC------
T ss_pred             -CCcEECCEEEEEEecCChhHhc
Confidence             8999999999999988776553

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.97  E-value=3.4e-30  Score=241.47  Aligned_cols=163  Identities=31%  Similarity=0.567  Sum_probs=152.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ++++|||+|||+++|+++|+++|+.||+|.+|++.+++.+++++|||||+|.+.++|++|++.+++..+.|++|+|.|+.
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            47899999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCC-CCCcccEEEEEEcCHHHHHHHHHHhcCceecC-
Q 006282          108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLIND-  185 (652)
Q Consensus       108 ~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~-~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g-  185 (652)
                      ....  .....+|||+|||.++++++|+++|+.||.|..+.+..+. +|.++|||||+|.+.++|.+|++.+|+..+.| 
T Consensus        82 ~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  159 (168)
T 1b7f_A           82 PGGE--SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG  159 (168)
T ss_dssp             CCSS--TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCcc--cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCC
Confidence            6543  3456789999999999999999999999999999999985 88999999999999999999999999999977 


Q ss_pred             -eeeeecc
Q 006282          186 -KQVFVGH  192 (652)
Q Consensus       186 -~~~~v~~  192 (652)
                       +.|.|.+
T Consensus       160 ~~~l~V~~  167 (168)
T 1b7f_A          160 SQPLSVRL  167 (168)
T ss_dssp             SSCCEEEE
T ss_pred             CeEEEEEe
Confidence             8888765

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A

Probab=99.97  E-value=1.2e-31  Score=211.96  Aligned_cols=79  Identities=46%  Similarity=0.793  Sum_probs=75.7

Q ss_pred             ccchhhhhcCChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHHHHhhc
Q 006282          556 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA  634 (652)
Q Consensus       556 ~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~~~~~~  634 (652)
                      ++++++|++++|++||++|||+|||+|++++|++||||||||||||++|||+||+|+++|+.||+||++||++|++++.
T Consensus         6 ~l~~s~la~a~p~~Qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~Ell~lle~~e~L~~kV~EA~~vL~~~~~~~~   84 (88)
T 3kuj_A            6 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA   84 (88)
T ss_dssp             CCCHHHHHTSCHHHHHHHHHHHHHHHHHHHCTTTHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             cchHHHHHcCCHHHHHHHHHHHhHHHHHhhCCCccchhhhHhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999999998773

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.97  E-value=5.5e-30  Score=239.66  Aligned_cols=163  Identities=34%  Similarity=0.614  Sum_probs=150.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ++++|||+|||+++|+++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|++.||+..+.|++|+|.|+.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCC-CCCcccEEEEEEcCHHHHHHHHHHhcCceecCe
Q 006282          108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDK  186 (652)
Q Consensus       108 ~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~-~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~  186 (652)
                      ....  .....+|||+|||.++++++|+++|+.||.|.++++..+. +|.++|||||+|.+.++|.+|++.+||..+.|+
T Consensus        81 ~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A           81 PSSA--SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             CCCG--GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCcc--cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            6543  3345689999999999999999999999999999999984 888999999999999999999999999999997


Q ss_pred             e--eeecc
Q 006282          187 Q--VFVGH  192 (652)
Q Consensus       187 ~--~~v~~  192 (652)
                      .  |.|.+
T Consensus       159 ~~~i~v~~  166 (167)
T 1fxl_A          159 TEPITVKF  166 (167)
T ss_dssp             SSCCEEEE
T ss_pred             ccceEEEe
Confidence            6  55544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=9.2e-30  Score=237.89  Aligned_cols=165  Identities=30%  Similarity=0.532  Sum_probs=152.5

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccch
Q 006282          209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  288 (652)
Q Consensus       209 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~  288 (652)
                      ++|||+|||.++++++|+++|+.||.|.++.+..+.+++++|||||+|.+.++|..|++.+++..+.|+.+.+.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            47999999999999999999999999999999999889999999999999999999999999999999999999986543


Q ss_pred             HHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHH
Q 006282          289 EREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASR  367 (652)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~  367 (652)
                      .                ......++|||+|||..+++++|+++|+.||.|.+++++.+ .+|.++|||||+|.+.++|.+
T Consensus        81 ~----------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~  144 (166)
T 3md3_A           81 Q----------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN  144 (166)
T ss_dssp             C----------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHH
T ss_pred             C----------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHH
Confidence            2                12335678999999999999999999999999999999988 578999999999999999999


Q ss_pred             HHHHhcCcEecCeeEEEEeccc
Q 006282          368 ALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       368 A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      |+..|||..++|+.|.|.|+++
T Consensus       145 A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          145 AMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHHTTCEETTEECEEEESCC
T ss_pred             HHHHhCCCccCCcEEEEEecCC
Confidence            9999999999999999999864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.97  E-value=7.6e-30  Score=249.56  Aligned_cols=171  Identities=22%  Similarity=0.477  Sum_probs=154.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ..+++|||+|||+++|+++|+++|+.||+|.+|++++|..+++++|||||+|.+.++|.+|++.||+..|.|+.|+|.++
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            35789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCCccc---------ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHH
Q 006282          107 HRDPSI---------RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID  176 (652)
Q Consensus       107 ~~~~~~---------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~  176 (652)
                      ......         ......+|||+|||.++++++|+++|+.||.|..|++..+ .+|.++|||||+|.+.++|.+|++
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  185 (216)
T 2qfj_A          106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS  185 (216)
T ss_dssp             SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHH
Confidence            755321         2245678999999999999999999999999999999998 588999999999999999999999


Q ss_pred             HhcCceecCeeeeecccccch
Q 006282          177 KLNGMLINDKQVFVGHFLRKQ  197 (652)
Q Consensus       177 ~lng~~l~g~~~~v~~~~~~~  197 (652)
                      .+|+..+.|+.|.|.+.....
T Consensus       186 ~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          186 SMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHTTCBCSSSBCEEEECSSCS
T ss_pred             HccCCEeCCcEEEEEEecCCC
Confidence            999999999999999877653

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.97  E-value=2.6e-29  Score=237.07  Aligned_cols=165  Identities=25%  Similarity=0.394  Sum_probs=148.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCC--CcccEEEEEeCCHHHHHHHHhhcCCcccC---CceeE
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR--RSLGYGYVNYANPADAARALDVLNFTPLN---NKSIR  102 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~--~s~g~AfV~F~~~e~A~~Al~~ln~~~i~---G~~i~  102 (652)
                      .+++|||+|||+++||++|+++|+.||+|.+|+++++..++  +++|||||+|.+.++|++|++.||+..+.   ++.++
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            47899999999999999999999999999999999999887  89999999999999999999999987775   67888


Q ss_pred             eecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCce
Q 006282          103 IMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGML  182 (652)
Q Consensus       103 i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~  182 (652)
                      +.++..... ......+|||+|||.++++++|+++|+.||.|.+|.+..+.+|.++|||||+|.+.++|.+|++.+||..
T Consensus        82 ~~~~~~~~~-~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (175)
T 3nmr_A           82 MKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ  160 (175)
T ss_dssp             EEECGGGCC-SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSC
T ss_pred             Ecccccccc-ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCc
Confidence            887765432 2335668999999999999999999999999999999999889999999999999999999999999987


Q ss_pred             ec---Ceeeeeccc
Q 006282          183 IN---DKQVFVGHF  193 (652)
Q Consensus       183 l~---g~~~~v~~~  193 (652)
                      +.   ++.+.|.++
T Consensus       161 ~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          161 TMEGCSSPMVVKFA  174 (175)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             ccCCCCCCeEEEec
Confidence            65   388888764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.96  E-value=7.1e-29  Score=242.64  Aligned_cols=178  Identities=24%  Similarity=0.403  Sum_probs=155.6

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...++|||+|||.++++++|+++|+.||.|.++.++++. +|.++|||||+|.+.++|.+|++.+++..+.|+.|.|.++
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            456789999999999999999999999999999999884 7899999999999999999999999999999999999998


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  363 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~  363 (652)
                      ..............       ......++|||+|||.++++++|+++|+.||.|++|+|+.+. +|+++|||||+|.+.+
T Consensus       106 ~~~~~~~~~~~~~~-------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~  178 (216)
T 2qfj_A          106 SNIGQAQPIIDQLA-------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ  178 (216)
T ss_dssp             SCCGGGHHHHHHHH-------HHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             CCccccchhhhhhh-------cccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHH
Confidence            77655433222111       122346789999999999999999999999999999999884 7899999999999999


Q ss_pred             HHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          364 EASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       364 ~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +|.+|+..|||..|+|+.|.|.++..+
T Consensus       179 ~A~~A~~~l~g~~~~g~~i~V~~a~~~  205 (216)
T 2qfj_A          179 SSQDAVSSMNLFDLGGQYLRVGKAVTP  205 (216)
T ss_dssp             HHHHHHHHHTTCBCSSSBCEEEECSSC
T ss_pred             HHHHHHHHccCCEeCCcEEEEEEecCC
Confidence            999999999999999999999998743

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.96  E-value=1.3e-28  Score=230.28  Aligned_cols=162  Identities=32%  Similarity=0.603  Sum_probs=149.6

Q ss_pred             cceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCC-CCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       208 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      .++|||+|||.++++++|+++|+.||.|.++.++++. +|.++|||||+|.+.++|..|++.+++..+.|+.+.+.++..
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            5789999999999999999999999999999999986 899999999999999999999999999999999999999875


Q ss_pred             chHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHH
Q 006282          287 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA  365 (652)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A  365 (652)
                      ...                  ....++|||+|||..+++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|
T Consensus        82 ~~~------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A  143 (167)
T 1fxl_A           82 SSA------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA  143 (167)
T ss_dssp             CCG------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             Ccc------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHH
Confidence            532                  1245689999999999999999999999999999999886 788999999999999999


Q ss_pred             HHHHHHhcCcEecCee--EEEEec
Q 006282          366 SRALAEMNGKMIVSKP--LYVAVA  387 (652)
Q Consensus       366 ~~A~~~lng~~~~g~~--l~v~~~  387 (652)
                      .+|++.|||..+.|+.  |.|.||
T Consensus       144 ~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          144 EEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999964  888875

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.96  E-value=6.3e-29  Score=232.85  Aligned_cols=163  Identities=31%  Similarity=0.566  Sum_probs=151.2

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ..++|||+|||.++++++|+++|+.||.|.++.++++ .+|.++|||||+|.+.++|..|++.+++..+.|+.|.+.++.
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            3578999999999999999999999999999999987 578999999999999999999999999999999999999987


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHH
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  364 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~  364 (652)
                      .+..                  ....++|||+|||..+++++|+++|++||.|.+++++.+. +|.++|||||+|.+.++
T Consensus        82 ~~~~------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~  143 (168)
T 1b7f_A           82 PGGE------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE  143 (168)
T ss_dssp             CCSS------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHH
T ss_pred             CCcc------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHH
Confidence            6532                  2245789999999999999999999999999999999886 88999999999999999


Q ss_pred             HHHHHHHhcCcEecC--eeEEEEec
Q 006282          365 ASRALAEMNGKMIVS--KPLYVAVA  387 (652)
Q Consensus       365 A~~A~~~lng~~~~g--~~l~v~~~  387 (652)
                      |.+|++.|||..+.|  ++|.|.||
T Consensus       144 A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          144 AQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHhcCCEecCCCeEEEEEeC
Confidence            999999999999987  99999986

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.96  E-value=9.6e-29  Score=237.85  Aligned_cols=176  Identities=24%  Similarity=0.465  Sum_probs=148.7

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...++|||+|||.++++++|+++|+.||.|.++.++.+ .+|.++|||||+|.+.++|.+|++. ++..+.|+.|.+.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            45688999999999999999999999999999999988 4689999999999999999999975 899999999999998


Q ss_pred             ccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHH
Q 006282          285 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  363 (652)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~  363 (652)
                      .........            ......++|||+|||.++++++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.+
T Consensus        90 ~~~~~~~~~------------~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~  157 (196)
T 1l3k_A           90 VSREDSQRP------------GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD  157 (196)
T ss_dssp             CC-----------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             cCccccccc------------ccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHH
Confidence            765432211            122345789999999999999999999999999999999885 7899999999999999


Q ss_pred             HHHHHHHHhcCcEecCeeEEEEecccHHHHHH
Q 006282          364 EASRALAEMNGKMIVSKPLYVAVAQRKEERRA  395 (652)
Q Consensus       364 ~A~~A~~~lng~~~~g~~l~v~~~~~~~~r~~  395 (652)
                      +|.+|+.. +|..++|+.|.|.++.+++....
T Consensus       158 ~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          158 SVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HHHHHHHC-SCCEETTEECEEEECC-------
T ss_pred             HHHHHHHh-CCcEECCEEEEEEecCChhHhcc
Confidence            99999985 89999999999999998876643

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.96  E-value=8.9e-30  Score=238.45  Aligned_cols=164  Identities=22%  Similarity=0.503  Sum_probs=150.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ++++|||+|||+++||++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.  ...+.|+.|++.++.
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            578999999999999999999999999999999999999999999999999999999999994  468899999999886


Q ss_pred             CCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCe
Q 006282          108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDK  186 (652)
Q Consensus       108 ~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~  186 (652)
                      ....  .....+|||+|||.++++++|+++|+.||.|.+|++..+ .+|.++|||||+|.+.++|.+|++ +++..+.|+
T Consensus        80 ~~~~--~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~  156 (167)
T 2cjk_A           80 PRDE--QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDR  156 (167)
T ss_dssp             CHHH--HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSS
T ss_pred             chhh--ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCe
Confidence            5432  223568999999999999999999999999999999998 579999999999999999999997 899999999


Q ss_pred             eeeecccccc
Q 006282          187 QVFVGHFLRK  196 (652)
Q Consensus       187 ~~~v~~~~~~  196 (652)
                      .|.|.++.++
T Consensus       157 ~i~V~~a~pk  166 (167)
T 2cjk_A          157 KIEIKRAEPR  166 (167)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEeecCCC
Confidence            9999987654

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.96  E-value=1.1e-28  Score=232.69  Aligned_cols=165  Identities=27%  Similarity=0.503  Sum_probs=147.7

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCC---CcceeEEEeeCCHHHHHHHHHHHCCCccC---CceEE
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVEALNGKKFD---DREWY  280 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g---~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~---g~~l~  280 (652)
                      ..++|||+|||.++++++|+++|++||.|.++.++++..+   +++|||||+|.+.++|..|++.+++..+.   ++.+.
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            4578999999999999999999999999999999988655   89999999999999999999999998775   56777


Q ss_pred             EEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeC
Q 006282          281 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS  360 (652)
Q Consensus       281 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~  360 (652)
                      +.++.....                 .....++|||+|||.++++++|+++|++||.|.+++++.+.+|.++|||||+|.
T Consensus        82 ~~~~~~~~~-----------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~  144 (175)
T 3nmr_A           82 MKPADSEKN-----------------NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFT  144 (175)
T ss_dssp             EEECGGGCC-----------------SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEES
T ss_pred             Ecccccccc-----------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEEC
Confidence            777654322                 123466899999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHhcCcEec---CeeEEEEecc
Q 006282          361 TPEEASRALAEMNGKMIV---SKPLYVAVAQ  388 (652)
Q Consensus       361 s~~~A~~A~~~lng~~~~---g~~l~v~~~~  388 (652)
                      +.++|.+|++.|||..+.   +++|.|.|+.
T Consensus       145 ~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999998776   4999999974

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.96  E-value=3.3e-29  Score=236.61  Aligned_cols=167  Identities=20%  Similarity=0.310  Sum_probs=151.2

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ..+.+.++|||+|||.++|+++|+++|+.||.|.. .++++..+++++|||||+|.+.++|.+|++ ||+..|.|++|+|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v   85 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEE
Confidence            34567899999999999999999999999998877 445566778899999999999999999995 9999999999999


Q ss_pred             ecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCcee
Q 006282          104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLI  183 (652)
Q Consensus       104 ~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l  183 (652)
                      .|+............+|||+|||.++++++|+++|+.||.|..+    ..++.++|||||+|.+.++|.+|++.+|+..+
T Consensus        86 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 1fje_B           86 EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI  161 (175)
T ss_dssp             ECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEE
T ss_pred             ecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            99988776666778899999999999999999999999988766    66788999999999999999999999999999


Q ss_pred             cCeeeeecccccc
Q 006282          184 NDKQVFVGHFLRK  196 (652)
Q Consensus       184 ~g~~~~v~~~~~~  196 (652)
                      .|+.|.|.++.++
T Consensus       162 ~g~~i~v~~a~~k  174 (175)
T 1fje_B          162 DGRSVSLYYTGEK  174 (175)
T ss_dssp             TTEEEEEEECSSC
T ss_pred             CCeEEEEEecCCC
Confidence            9999999987654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.96  E-value=1.2e-28  Score=230.68  Aligned_cols=163  Identities=25%  Similarity=0.526  Sum_probs=148.3

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ..++|||+|||.++++++|+++|+.||.|.++.++++ .+|.++|||||+|.+.++|..|++  ++..+.|+.+.+.++.
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 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            3578999999999999999999999999999999988 579999999999999999999998  4678899999998886


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHH
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  364 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~  364 (652)
                      .+....                  ..++|||+|||.++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++
T Consensus        80 ~~~~~~------------------~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~  141 (167)
T 2cjk_A           80 PRDEQD------------------KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA  141 (167)
T ss_dssp             CHHHHH------------------HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHH
T ss_pred             chhhcc------------------CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHH
Confidence            643221                  24589999999999999999999999999999999885 79999999999999999


Q ss_pred             HHHHHHHhcCcEecCeeEEEEecccH
Q 006282          365 ASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       365 A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      |.+|++ +||..++|+.|.|.|+.++
T Consensus       142 a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          142 VDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            999998 8999999999999999875

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.96  E-value=9.4e-28  Score=245.08  Aligned_cols=174  Identities=22%  Similarity=0.323  Sum_probs=161.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++|+++|+++|+.||.|.++++++|..+++++|||||+|.+.++|.+|++.||+..|.|+.|+|.|+.
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            46899999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCccc-ccCCCcceeecCCCccc-cHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecC
Q 006282          108 RDPSI-RKSGTGNIFIKNLDKSI-DHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIND  185 (652)
Q Consensus       108 ~~~~~-~~~~~~~lfV~nLp~~~-t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g  185 (652)
                      ..... ......+|||+|||.++ ++++|+++|+.||.|.+|++..+.+|.++|+|||+|.+.++|.+|++.+||..+.|
T Consensus       174 ~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  253 (284)
T 3smz_A          174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGG  253 (284)
T ss_dssp             GGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC
Confidence            65432 33456789999999995 99999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeecccccchhhHH
Q 006282          186 KQVFVGHFLRKQERET  201 (652)
Q Consensus       186 ~~~~v~~~~~~~~~~~  201 (652)
                      +.|.|.+..++..+..
T Consensus       254 ~~l~v~~a~~~~~~~~  269 (284)
T 3smz_A          254 SHLRVSFCAPGPPGRS  269 (284)
T ss_dssp             EECEEEECCSSSCHHH
T ss_pred             eEEEEEEecCCCcccc
Confidence            9999999987765443

>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=99.95  E-value=3.9e-28  Score=234.44  Aligned_cols=154  Identities=17%  Similarity=0.263  Sum_probs=136.4

Q ss_pred             CccEEEEcCCC-CCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           28 LTTSLYVGDLD-FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        28 ~~~sL~V~nLp-~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ++++|||+||| +++|+++|+++|+.||.|.+|+|.+++     +|||||+|.+.++|++|++.||+..+.|++|+|.|+
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 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            57899999999 899999999999999999999998763     589999999999999999999999999999999998


Q ss_pred             cCCccc-----------------------c------------cCCCcceeecCCCccccHHHHHhhhccCCCe--eEEEE
Q 006282          107 HRDPSI-----------------------R------------KSGTGNIFIKNLDKSIDHKALHDTFSSFGNI--LSCKI  149 (652)
Q Consensus       107 ~~~~~~-----------------------~------------~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I--~~~~v  149 (652)
                      +.....                       +            .....+|||+|||.++++++|+++|+.||.|  .++++
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            643210                       0            0123469999999999999999999999999  89999


Q ss_pred             eeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCee
Q 006282          150 ATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQ  187 (652)
Q Consensus       150 ~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~  187 (652)
                      ..+. +.++|+|||+|.+.++|.+|+..||+..+.++.
T Consensus       158 ~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~  194 (205)
T 3tyt_A          158 FSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPN  194 (205)
T ss_dssp             CSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS
T ss_pred             EcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC
Confidence            8876 556799999999999999999999999998763

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.95  E-value=1.2e-27  Score=225.07  Aligned_cols=157  Identities=24%  Similarity=0.535  Sum_probs=143.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQV----G-------QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL   96 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~----G-------~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i   96 (652)
                      ++++|||+|||+++|+++|+++|+.|    |       .|.++++.+      ++|||||+|.+.++|.+|+ .+|+..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            57899999999999999999999999    6       777777754      4689999999999999999 7999999


Q ss_pred             CCceeEeecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHH
Q 006282           97 NNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI  175 (652)
Q Consensus        97 ~G~~i~i~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai  175 (652)
                      .|+.|+|.|+.....  .....+|||+|||.++++++|+++|+.||.|.+|.+..+ .+|.++|||||+|.+.++|.+|+
T Consensus        76 ~g~~i~v~~~~~~~~--~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~  153 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQP--LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI  153 (172)
T ss_dssp             TTEECEEECCSSCCC--CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHH
T ss_pred             cCceeeecCCcccCC--CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Confidence            999999999875432  344678999999999999999999999999999999999 58999999999999999999999


Q ss_pred             HHhcCceecCeeeeeccc
Q 006282          176 DKLNGMLINDKQVFVGHF  193 (652)
Q Consensus       176 ~~lng~~l~g~~~~v~~~  193 (652)
                      +.+|+..++|+.+.|.++
T Consensus       154 ~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          154 AGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHTTCEETTEECEEEEC
T ss_pred             HHcCCCEECCeEEEEEeC
Confidence            999999999999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=1.4e-27  Score=230.13  Aligned_cols=163  Identities=23%  Similarity=0.511  Sum_probs=144.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQV----G-------QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL   96 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~----G-------~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i   96 (652)
                      .+++|||+|||+++||++|+++|+.|    |       .|.++++      ++++|||||+|.+.++|++|+ .||+..|
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            57899999999999999999999999    5       5666655      456799999999999999999 7999999


Q ss_pred             CCceeEeecccCCccc------------------ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCc
Q 006282           97 NNKSIRIMYSHRDPSI------------------RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQS  157 (652)
Q Consensus        97 ~G~~i~i~~s~~~~~~------------------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~s  157 (652)
                      .|++|+|.|+......                  ......+|||+|||.++++++|+++|+.||.|.+|.+..+ .+|.+
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence            9999999998754211                  1245678999999999999999999999999999999999 48999


Q ss_pred             ccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccch
Q 006282          158 KGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQ  197 (652)
Q Consensus       158 kG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~  197 (652)
                      +|||||+|.+.++|.+|++.+|+..++|+.+.|.+..++.
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9999999999999999999999999999999999876653

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A

Probab=99.95  E-value=3.9e-29  Score=183.43  Aligned_cols=60  Identities=45%  Similarity=0.720  Sum_probs=59.0

Q ss_pred             HHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHH
Q 006282          570 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV  629 (652)
Q Consensus       570 ~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~  629 (652)
                      ||++|||+|||+|++++|++||||||||||||++|||+||+|+++|++||+||++||++|
T Consensus         1 qkq~LGe~Lyp~V~~~~p~~A~KITGMLLE~d~~ell~ll~~~e~L~~kv~EA~~vl~~~   60 (61)
T 1i2t_A            1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH   60 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhCcccccchhhhhccCCHHHHHHHHcCHHHHHHHHHHHHHHHHHc
Confidence            799999999999999999999999999999999999999999999999999999999987

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.95  E-value=2.3e-27  Score=241.93  Aligned_cols=163  Identities=24%  Similarity=0.431  Sum_probs=145.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLY----DLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~----~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ...++++|||+|||+++|+++|+    ++|+.||.|.+|++++   +++++|||||+|.+.++|.+|++.||+..|.|+.
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            44668999999999999999965    9999999999999987   6789999999999999999999999999999999


Q ss_pred             eEeecccCCccc--------------------------------------------------------------------
Q 006282          101 IRIMYSHRDPSI--------------------------------------------------------------------  112 (652)
Q Consensus       101 i~i~~s~~~~~~--------------------------------------------------------------------  112 (652)
                      |+|.|+..+...                                                                    
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence            999998754420                                                                    


Q ss_pred             -----------------------------------------ccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEee
Q 006282          113 -----------------------------------------RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIAT  151 (652)
Q Consensus       113 -----------------------------------------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~  151 (652)
                                                               ......+|||+||+.++++++|+++|+.||.|.+|++..
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec
Confidence                                                     111346699999999999999999999999999999997


Q ss_pred             CCCCCcccEEEEEEcCHHHHHHHHHHhcCceec-Ceeeeecccc
Q 006282          152 DGSGQSKGFGFVQFENKESAQNAIDKLNGMLIN-DKQVFVGHFL  194 (652)
Q Consensus       152 ~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~-g~~~~v~~~~  194 (652)
                      +    .+|||||+|.+.++|.+|++.+||..+. |+.|.|.+..
T Consensus       242 ~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          242 G----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             C----CCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            5    3689999999999999999999999999 9999998764

>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=99.95  E-value=1.1e-27  Score=231.30  Aligned_cols=176  Identities=17%  Similarity=0.234  Sum_probs=142.8

Q ss_pred             CcceEEecCCC-CCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          207 KFNNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       207 ~~~~l~V~nlp-~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ..++|||+||+ .++++++|+++|+.||.|.++.++++    ++|||||+|.+.++|..|++.|++..+.|+.|.|.++.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            45789999999 89999999999999999999999875    36899999999999999999999999999999999886


Q ss_pred             cchHHHHH---Hh------HHHHHh----------hhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCe--eEEEEe
Q 006282          286 KKSEREQE---LK------GQFEQA----------MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTI--TSCKVM  344 (652)
Q Consensus       286 ~~~~~~~~---~~------~~~~~~----------~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I--~~v~i~  344 (652)
                      .+......   ..      ..+...          ........++++|||+|||+++|+++|+++|++||.|  .+++++
T Consensus        79 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~  158 (205)
T 3tyt_A           79 QPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVF  158 (205)
T ss_dssp             CSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEEC
T ss_pred             CCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEE
Confidence            43210000   00      000000          0000012346789999999999999999999999999  899999


Q ss_pred             cCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCe----eEEEEec
Q 006282          345 RDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK----PLYVAVA  387 (652)
Q Consensus       345 ~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~----~l~v~~~  387 (652)
                      .+. |.++|||||+|.+.++|.+|+..|||..+.|+    ++.|+|+
T Consensus       159 ~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          159 SGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             cCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            886 56679999999999999999999999999876    6777765

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.95  E-value=3e-27  Score=233.23  Aligned_cols=164  Identities=23%  Similarity=0.245  Sum_probs=145.6

Q ss_pred             CCCCCCccEEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           23 SGNQFLTTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~-~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      +.+..++++|||+|||+ ++|+++|+++|+.||.|.+|++++|+     +|||||+|.+.++|++|++.||+..|.|+.|
T Consensus        28 ~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l  102 (229)
T 2adc_A           28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPI  102 (229)
T ss_dssp             GGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBC
T ss_pred             CCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            34456789999999999 99999999999999999999999875     5799999999999999999999999999999


Q ss_pred             EeecccCCccc---------------------------------ccCCCcceeecCCCccccHHHHHhhhccCC-CeeEE
Q 006282          102 RIMYSHRDPSI---------------------------------RKSGTGNIFIKNLDKSIDHKALHDTFSSFG-NILSC  147 (652)
Q Consensus       102 ~i~~s~~~~~~---------------------------------~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG-~I~~~  147 (652)
                      +|.|+......                                 ......+|||+|||.++++++|+++|+.|| .|.+|
T Consensus       103 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v  182 (229)
T 2adc_A          103 RITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF  182 (229)
T ss_dssp             EEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEE
T ss_pred             EEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEE
Confidence            99998743110                                 012256799999999999999999999999 99999


Q ss_pred             EEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceec-Ceeeeeccccc
Q 006282          148 KIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLIN-DKQVFVGHFLR  195 (652)
Q Consensus       148 ~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~-g~~~~v~~~~~  195 (652)
                      ++..+    ++|||||+|.+.++|.+|++.+|+..+. |+.|.|.+..+
T Consensus       183 ~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          183 KFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             EECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             EEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            99764    5789999999999999999999999999 99999988754

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.95  E-value=7.7e-27  Score=238.04  Aligned_cols=178  Identities=22%  Similarity=0.402  Sum_probs=148.1

Q ss_pred             cCcceEEecCCCCCCCHHHHH----HHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEE
Q 006282          206 TKFNNVFVKNLDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  281 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~----~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v  281 (652)
                      ...++|||+|||.++++++|+    ++|+.||.|.+|.+++  +|+++|||||+|.+.++|.+|++.|++..+.|+.|.|
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            456889999999999999976    8999999999998886  6789999999999999999999999999999999999


Q ss_pred             EccccchHHHHHHhHHHH------------------Hhh-----------------------------------------
Q 006282          282 GKAQKKSEREQELKGQFE------------------QAM-----------------------------------------  302 (652)
Q Consensus       282 ~~a~~~~~~~~~~~~~~~------------------~~~-----------------------------------------  302 (652)
                      .++..+............                  ...                                         
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            998665421111000000                  000                                         


Q ss_pred             ----------------------------------hhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q 006282          303 ----------------------------------KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS  348 (652)
Q Consensus       303 ----------------------------------~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~  348 (652)
                                                        ........+++|||+|||.++++++|+++|+.||.|++|+++.+. 
T Consensus       165 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-  243 (282)
T 3pgw_A          165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-  243 (282)
T ss_pred             CCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-
Confidence                                              000122346789999999999999999999999999999999763 


Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHhcCcEec-CeeEEEEeccc
Q 006282          349 GISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQR  389 (652)
Q Consensus       349 g~s~g~afV~F~s~~~A~~A~~~lng~~~~-g~~l~v~~~~~  389 (652)
                         +|||||+|.+.++|.+|+..|||..|+ |+.|.|.|+++
T Consensus       244 ---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          244 ---HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             ---CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence               589999999999999999999999999 99999999864

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.95  E-value=3.8e-27  Score=221.65  Aligned_cols=158  Identities=24%  Similarity=0.476  Sum_probs=142.4

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccC----C-------CeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccC
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEY----G-------TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD  275 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G-------~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~  275 (652)
                      ..++|||+|||.++++++|+++|+.|    |       .|.++.+.+     ++|||||+|.+.++|.+|+ .+++..+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----DKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET-----TTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC-----CCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            35789999999999999999999999    6       677776653     4789999999999999999 89999999


Q ss_pred             CceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccE
Q 006282          276 DREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGS  354 (652)
Q Consensus       276 g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~  354 (652)
                      |+.+.+.++.....                  ....++|||+|||.++++++|+++|++||.|.+++++.+. +|.++||
T Consensus        77 g~~i~v~~~~~~~~------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~  138 (172)
T 2g4b_A           77 GQSLKIRRPHDYQP------------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY  138 (172)
T ss_dssp             TEECEEECCSSCCC------------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEE
T ss_pred             CceeeecCCcccCC------------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceE
Confidence            99999998754421                  1235789999999999999999999999999999999985 8999999


Q ss_pred             EEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          355 GFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       355 afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      |||+|.+.++|.+|++.|||..++|+.|.|.||.
T Consensus       139 afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          139 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999999999999999999999999999999974

>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=99.95  E-value=9.5e-28  Score=226.54  Aligned_cols=164  Identities=27%  Similarity=0.397  Sum_probs=145.4

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ...++|||+|||.++++++|+++|+.||.+..+.+....+|.++|||||+|.+.++|.+|+ .+++..+.|+.|.|.++.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~   89 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPK   89 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCC
Confidence            4668899999999999999999999999877644444467889999999999999999999 599999999999999987


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHH
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA  365 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A  365 (652)
                      .+...                .....++|||+|||.++++++|+++|+.||.|..+    +.+|.++|||||+|.+.++|
T Consensus        90 ~~~~~----------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A  149 (175)
T 1fje_B           90 GRDSK----------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADA  149 (175)
T ss_dssp             CSSCS----------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHH
T ss_pred             Ccccc----------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHH
Confidence            65321                12245789999999999999999999999988766    66789999999999999999


Q ss_pred             HHHHHHhcCcEecCeeEEEEecccH
Q 006282          366 SRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       366 ~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .+|+..|||..++|+.|.|.|+.++
T Consensus       150 ~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          150 EKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999999999999999999999764

>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=99.94  E-value=2.3e-26  Score=231.52  Aligned_cols=160  Identities=25%  Similarity=0.455  Sum_probs=145.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ......++|||+|||+++|+++|+++|+.||.|.+|++.+      ++|||||.|.+.++|.+|++.+|+..|.|+.|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            3445678999999999999999999999999999999964      3589999999999999999999999999999999


Q ss_pred             ecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHh-cCce
Q 006282          104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL-NGML  182 (652)
Q Consensus       104 ~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~l-ng~~  182 (652)
                      .|+..        ..+|||+|||.++++++|+++|+.||.|.+|.+..+.+|.++|||||+|.+.++|.+|+..+ ++..
T Consensus        91 ~~a~~--------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~  162 (261)
T 3sde_A           91 RFATH--------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAF  162 (261)
T ss_dssp             EECCC--------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCE
T ss_pred             eeccc--------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeE
Confidence            99874        45899999999999999999999999999999999999999999999999999999999999 5555


Q ss_pred             ec---Ceeeeecccccch
Q 006282          183 IN---DKQVFVGHFLRKQ  197 (652)
Q Consensus       183 l~---g~~~~v~~~~~~~  197 (652)
                      +.   ++.+.|.+.....
T Consensus       163 ~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          163 LLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             ESSSSCCBCEEEECCCEE
T ss_pred             EecCCCceEEEeeccccC
Confidence            54   8889988876543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.94  E-value=9e-27  Score=224.54  Aligned_cols=158  Identities=23%  Similarity=0.280  Sum_probs=142.1

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           29 TTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        29 ~~sL~V~nLp~-~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      +++|||+|||+ ++|+++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++.||+..|.|+.|+|.|+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            58999999999 99999999999999999999999875     5799999999999999999999999999999999987


Q ss_pred             CCcccc---------------------------------cCCCcceeecCCCccccHHHHHhhhccCC-CeeEEEEeeCC
Q 006282          108 RDPSIR---------------------------------KSGTGNIFIKNLDKSIDHKALHDTFSSFG-NILSCKIATDG  153 (652)
Q Consensus       108 ~~~~~~---------------------------------~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG-~I~~~~v~~~~  153 (652)
                      ......                                 .....+|||+|||.++++++|+++|+.|| .|.+|++..+ 
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-  156 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  156 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-
Confidence            542110                                 12266799999999999999999999999 9999999764 


Q ss_pred             CCCcccEEEEEEcCHHHHHHHHHHhcCceec-Ceeeeeccccc
Q 006282          154 SGQSKGFGFVQFENKESAQNAIDKLNGMLIN-DKQVFVGHFLR  195 (652)
Q Consensus       154 ~g~skG~afV~F~t~e~A~~Ai~~lng~~l~-g~~~~v~~~~~  195 (652)
                         ++|+|||+|.+.++|.+|++.+|+..+. |+.+.|.+..+
T Consensus       157 ---~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          157 ---DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             ---TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             ---CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence               4789999999999999999999999999 99999988654

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.94  E-value=2.6e-26  Score=226.47  Aligned_cols=177  Identities=21%  Similarity=0.318  Sum_probs=146.6

Q ss_pred             cCcceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcc
Q 006282          206 TKFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  284 (652)
Q Consensus       206 ~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a  284 (652)
                      ...++|||+|||. ++++++|+++|+.||.|.++.++++.    +|||||+|.+.++|.+|++.+++..+.|+.|.|.++
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  107 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS  107 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            4678899999999 99999999999999999999999875    679999999999999999999999999999999988


Q ss_pred             ccchHHH-------HHHhHHHHHhh----------hhcccccccceeeecCCCCCCCHHHHHHHhhhcC-CeeEEEEecC
Q 006282          285 QKKSERE-------QELKGQFEQAM----------KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRD  346 (652)
Q Consensus       285 ~~~~~~~-------~~~~~~~~~~~----------~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG-~I~~v~i~~~  346 (652)
                      ..+....       ......+....          ........+++|||+|||.++++++|+++|+.|| .|.+|+++.+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~  187 (229)
T 2adc_A          108 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  187 (229)
T ss_dssp             SCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS
T ss_pred             cCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC
Confidence            6542100       00000000000          0001123468899999999999999999999999 9999999765


Q ss_pred             CCCCCccEEEEEeCCHHHHHHHHHHhcCcEec-CeeEEEEecccH
Q 006282          347 PSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQRK  390 (652)
Q Consensus       347 ~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~-g~~l~v~~~~~~  390 (652)
                          ++|||||+|.+.++|.+|+..|||..++ |+.|.|.|++++
T Consensus       188 ----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          188 ----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             ----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             ----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence                3789999999999999999999999999 999999999753

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.93  E-value=9e-26  Score=227.15  Aligned_cols=156  Identities=31%  Similarity=0.547  Sum_probs=143.7

Q ss_pred             cCcceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccc
Q 006282          206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  285 (652)
Q Consensus       206 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~  285 (652)
                      ...++|||+|||.++++++|+++|+.||.|.++.+.++     +|||||+|.+.++|..|+..+++..+.|+.|.|.++.
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~   94 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            45678999999999999999999999999999998643     7899999999999999999999999999999999885


Q ss_pred             cchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHH
Q 006282          286 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA  365 (652)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A  365 (652)
                      .                        +++|||+|||..+|+++|+++|+.||.|.+|+|+.+.+|+++|||||+|.+.++|
T Consensus        95 ~------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A  150 (261)
T 3sde_A           95 H------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA  150 (261)
T ss_dssp             C------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHH
T ss_pred             c------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHH
Confidence            3                        4589999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhc-CcEec---CeeEEEEecccH
Q 006282          366 SRALAEMN-GKMIV---SKPLYVAVAQRK  390 (652)
Q Consensus       366 ~~A~~~ln-g~~~~---g~~l~v~~~~~~  390 (652)
                      .+|+..|| +..+.   +++|.|.++...
T Consensus       151 ~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          151 RKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            99999995 55554   999999998754

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.93  E-value=1.4e-26  Score=223.07  Aligned_cols=178  Identities=22%  Similarity=0.423  Sum_probs=145.8

Q ss_pred             CcceEEecCCCCCCCHHHHHHHhccC----C-------CeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccC
Q 006282          207 KFNNVFVKNLDESTTDEDLKKIFGEY----G-------TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD  275 (652)
Q Consensus       207 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G-------~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~  275 (652)
                      ..++|||+|||.++++++|+++|+.|    |       .|.++.+     ++++|||||+|.+.++|.+|+ .+++..+.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-----~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-----ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-----cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            45789999999999999999999999    4       5555554     355899999999999999999 89999999


Q ss_pred             CceEEEEccccchHHHHHHhHH--HHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCc
Q 006282          276 DREWYVGKAQKKSEREQELKGQ--FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISK  352 (652)
Q Consensus       276 g~~l~v~~a~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~  352 (652)
                      |+.|.|.++.............  ..............++|||+|||.++++++|+++|+.||.|.+++++.+. +|.++
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEE
T ss_pred             CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcc
Confidence            9999999986542211000000  00000111122456899999999999999999999999999999999985 89999


Q ss_pred             cEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          353 GSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       353 g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      |||||+|.+.++|.+|+..|||..++|+.|.|.++.++
T Consensus       157 g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             EEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            99999999999999999999999999999999999865

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.93  E-value=2.5e-26  Score=221.45  Aligned_cols=175  Identities=20%  Similarity=0.302  Sum_probs=144.8

Q ss_pred             cceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          208 FNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       208 ~~~l~V~nlp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      .++|||+|||. ++++++|+++|+.||.|.++.+..+.    +|||||+|.+.++|..|++.|++..+.|+.|.|.++..
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~   78 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   78 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecC
Confidence            57899999999 99999999999999999999998875    67999999999999999999999999999999998865


Q ss_pred             chHHHHHHh-------HHHHHh--------h--hhcccccccceeeecCCCCCCCHHHHHHHhhhcC-CeeEEEEecCCC
Q 006282          287 KSEREQELK-------GQFEQA--------M--KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDPS  348 (652)
Q Consensus       287 ~~~~~~~~~-------~~~~~~--------~--~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG-~I~~v~i~~~~~  348 (652)
                      .........       ..+...        .  .......++++|||+|||..+++++|+++|+.|| .|.+++++.+  
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~--  156 (198)
T 1qm9_A           79 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--  156 (198)
T ss_dssp             CSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST--
T ss_pred             CCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC--
Confidence            421100000       000000        0  0000123478899999999999999999999999 9999999875  


Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHhcCcEec-CeeEEEEecccH
Q 006282          349 GISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQRK  390 (652)
Q Consensus       349 g~s~g~afV~F~s~~~A~~A~~~lng~~~~-g~~l~v~~~~~~  390 (652)
                        ++|||||+|.+.++|.+|+..|||..++ |+.|.|.|++++
T Consensus       157 --~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 --DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             --TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             --CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence              3789999999999999999999999999 999999998753

>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=99.83  E-value=8.7e-21  Score=165.31  Aligned_cols=104  Identities=28%  Similarity=0.471  Sum_probs=74.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .+++|||+|||+++||++|+++|+.||.|.+|+|++|.  ++++|||||+|.+.++|++|++.||+..|.|+.|+|.|+.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999995  4589999999999999999999999999999999999987


Q ss_pred             CCcc------cccCCCcceeecCCCccccHHH
Q 006282          108 RDPS------IRKSGTGNIFIKNLDKSIDHKA  133 (652)
Q Consensus       108 ~~~~------~~~~~~~~lfV~nLp~~~t~~~  133 (652)
                      ....      .+.....+|||+|||+++|++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           82 SRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCCC----------------------------
T ss_pred             CccccccccccccCCCCceEeCCCCCCccccc
Confidence            5432      2233455799999999998764

>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=99.83  E-value=1.8e-20  Score=173.38  Aligned_cols=147  Identities=21%  Similarity=0.274  Sum_probs=112.7

Q ss_pred             EEEeeCCCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeec
Q 006282          238 AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIK  317 (652)
Q Consensus       238 ~~i~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~  317 (652)
                      +.++.+.. +++||+||+|.+.++|.+|++.+++....+..+.+...........     ..............++|||+
T Consensus         3 ~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l~v~   76 (158)
T 2kn4_A            3 YKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE-----GSHHHHHHMDVEGMTSLKVD   76 (158)
T ss_dssp             EEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEEC-----CCCCSSCCCCCCBCCEEEEE
T ss_pred             EEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccc-----cccccccccCCCCCCEEEEe
Confidence            45555543 6899999999999999999988876544444444332221100000     00000111223456899999


Q ss_pred             CCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          318 NLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       318 nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      |||.++++++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|.+|+..|||..|+|+.|.|.++..+
T Consensus        77 nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A           77 NLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  150 (158)
T ss_dssp             SCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCS
T ss_pred             CCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            999999999999999999999999999985 7999999999999999999999999999999999999999854

>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=99.81  E-value=5.7e-20  Score=155.25  Aligned_cols=83  Identities=41%  Similarity=0.631  Sum_probs=79.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      -..+++|||+|||+++||++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      ++.
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            863

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.80  E-value=1.6e-19  Score=152.45  Aligned_cols=82  Identities=38%  Similarity=0.639  Sum_probs=78.2

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      .+++++|||+|||.++|+++|+++|++||.|.+|+|++|. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5678999999999999999999999999999999999885 699999999999999999999999999999999999999


Q ss_pred             ccc
Q 006282          387 AQR  389 (652)
Q Consensus       387 ~~~  389 (652)
                      +++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>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=99.80  E-value=3e-19  Score=165.09  Aligned_cols=138  Identities=17%  Similarity=0.266  Sum_probs=111.6

Q ss_pred             EEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe-------ecccC----CcccccCCCcceeecCCC
Q 006282           58 SVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI-------MYSHR----DPSIRKSGTGNIFIKNLD  126 (652)
Q Consensus        58 ~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i-------~~s~~----~~~~~~~~~~~lfV~nLp  126 (652)
                      +++|.++..  +++|||||+|.+.++|++|++.++.....+..+.+       .+...    ..........+|||+|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            567888755  68999999999999999999887753222222222       11111    111223446789999999


Q ss_pred             ccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccch
Q 006282          127 KSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQ  197 (652)
Q Consensus       127 ~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~~  197 (652)
                      .++++++|+++|+.||.|.+|++..+ .+|.++|||||+|.+.++|..|++.+|+..+.|+.|.|.+..+..
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            99999999999999999999999998 589999999999999999999999999999999999999987654

>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=99.78  E-value=1.2e-19  Score=166.15  Aligned_cols=138  Identities=22%  Similarity=0.323  Sum_probs=113.3

Q ss_pred             CCcceeEEEeeCCHHHHHHHHHHH-CCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCC
Q 006282          246 GKSKCFGFVNFENADDAAKAVEAL-NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID  324 (652)
Q Consensus       246 g~~~g~~fV~f~~~~~A~~Ai~~l-~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t  324 (652)
                      ...+|+++|+|.+.++|.+|++.+ ++..+.| .+.+.++..+........  ..............++|||+|||++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~V~nl~~~~t   86 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSH--HHHHHMHRDSCPLDCKVYVGNLGNNGN   86 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSS--SCCCCSCSSSSTTSCEEEEESCCSCCS
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccc--cccccccccCCCCCCEEEEeCCCCCCC
Confidence            366899999999999999999999 9999999 999998865432100000  000001122234568999999999999


Q ss_pred             HHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          325 DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       325 e~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +++|+++|+.||.|.+|+|+.+    ++|||||+|.+.++|.+|+..|||..++|++|.|.|+.++
T Consensus        87 ~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           87 KTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             CHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            9999999999999999999987    6899999999999999999999999999999999999764

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=150.30  Aligned_cols=83  Identities=20%  Similarity=0.278  Sum_probs=79.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .+.++|||+|||+++||++|+++|++||.|.+|+|++|+.|++++|||||.|.+.++|++|++.||+..|.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 006282          107 HRD  109 (652)
Q Consensus       107 ~~~  109 (652)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>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=99.77  E-value=5.7e-19  Score=153.74  Aligned_cols=108  Identities=58%  Similarity=0.979  Sum_probs=75.6

Q ss_pred             CCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeeccccc
Q 006282          116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLR  195 (652)
Q Consensus       116 ~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~  195 (652)
                      +.++|||+|||.++++++|+++|+.||.|.+|+|..+.. .++|||||+|.+.++|.+|++.+++..+.|+.|.|.+...
T Consensus         4 ~~~~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            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            456899999999999999999999999999999999864 4899999999999999999999999999999999998877


Q ss_pred             chhhHHHh--hccCcceEEecCCCCCCCHHH
Q 006282          196 KQERETVA--IKTKFNNVFVKNLDESTTDED  224 (652)
Q Consensus       196 ~~~~~~~~--~~~~~~~l~V~nlp~~~t~~~  224 (652)
                      +..+....  .....++|||+|||+++|++.
T Consensus        83 ~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           83 RKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCC----------------------------
T ss_pred             ccccccccccccCCCCceEeCCCCCCccccc
Confidence            65543322  235667899999999998764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.77  E-value=2.8e-19  Score=148.59  Aligned_cols=83  Identities=20%  Similarity=0.360  Sum_probs=77.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC-CcccCCceeEeecc
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVG-QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN-FTPLNNKSIRIMYS  106 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G-~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln-~~~i~G~~i~i~~s  106 (652)
                      +.+|||+|||+++||++|+++|+.|| +|.+|+|++|+.|++++|||||+|.+.++|++|++.++ +..|.|++|+|.|+
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            57999999999999999999999999 89999999999999999999999999999999999774 56799999999999


Q ss_pred             cCCcc
Q 006282          107 HRDPS  111 (652)
Q Consensus       107 ~~~~~  111 (652)
                      ...+.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            86543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.77  E-value=3.5e-19  Score=148.61  Aligned_cols=84  Identities=15%  Similarity=0.350  Sum_probs=77.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCC--eEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc----ccCC
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ--VLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT----PLNN   98 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~--V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~----~i~G   98 (652)
                      ......||||+|||+++||++|+++|++||.  |.+|++++|+.|++|+|||||+|.+.++|++|++.||+.    .|+|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3456789999999999999999999999994  789999999999999999999999999999999999986    4899


Q ss_pred             ceeEeecccC
Q 006282           99 KSIRIMYSHR  108 (652)
Q Consensus        99 ~~i~i~~s~~  108 (652)
                      |+|+|.|++.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999874

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.77  E-value=3.7e-18  Score=146.93  Aligned_cols=90  Identities=12%  Similarity=0.266  Sum_probs=83.1

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      +.++|||+||++++++++|+++|++||.|++|+|++|. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
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            46789999999999999999999999999999999886 59999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHH
Q 006282          389 RKEERRARLQA  399 (652)
Q Consensus       389 ~~~~r~~~~~~  399 (652)
                      ....+....+.
T Consensus        85 ~~~~~~~~~~~   95 (110)
T 3s8s_A           85 KGQQRMKYYEL   95 (110)
T ss_dssp             TTHHHHHHHHH
T ss_pred             CCcHHHHHHHH
Confidence            88777655444

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.1e-18  Score=144.48  Aligned_cols=87  Identities=25%  Similarity=0.460  Sum_probs=81.7

Q ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        21 ~~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      .+.....+.++|||+|||+++++++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|+.
T Consensus         8 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   87 (94)
T 2e5h_A            8 MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRV   87 (94)
T ss_dssp             CCCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEE
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            35555677899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEeeccc
Q 006282          101 IRIMYSH  107 (652)
Q Consensus       101 i~i~~s~  107 (652)
                      |+|.|++
T Consensus        88 l~v~~ak   94 (94)
T 2e5h_A           88 IKASIAI   94 (94)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999874

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.76  E-value=1.7e-18  Score=142.75  Aligned_cols=84  Identities=29%  Similarity=0.477  Sum_probs=77.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..+.++|||+|||.++|+++|+++|+.||.|.+|++.+|+.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.|
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 006282          106 SHRD  109 (652)
Q Consensus       106 s~~~  109 (652)
                      +...
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            8765

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3e-18  Score=145.88  Aligned_cols=92  Identities=32%  Similarity=0.519  Sum_probs=85.0

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      +.....+.++|||+|||+++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|+|+.|
T Consensus         5 ~~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 1x5s_A            5 SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQI   84 (102)
T ss_dssp             CCCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            44556678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCCcccc
Q 006282          102 RIMYSHRDPSIR  113 (652)
Q Consensus       102 ~i~~s~~~~~~~  113 (652)
                      +|.|+......+
T Consensus        85 ~v~~a~~~~~~~   96 (102)
T 1x5s_A           85 RVDQAGKSSDNR   96 (102)
T ss_dssp             EEEEEECCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999998765443

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=6.3e-18  Score=144.67  Aligned_cols=91  Identities=27%  Similarity=0.495  Sum_probs=84.7

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......+.++|||+|||+++|+++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            44556678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|+......
T Consensus        88 ~v~~a~~~~~~   98 (105)
T 1x5u_A           88 RVNKASAHNKN   98 (105)
T ss_dssp             EEEETTTTSCC
T ss_pred             EEEECCCCCcC
Confidence            99999876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=6e-18  Score=141.96  Aligned_cols=85  Identities=31%  Similarity=0.526  Sum_probs=81.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .++++|||+|||.++|+++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 006282          107 HRDPS  111 (652)
Q Consensus       107 ~~~~~  111 (652)
                      .....
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87654

>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=99.75  E-value=2e-18  Score=157.99  Aligned_cols=125  Identities=18%  Similarity=0.251  Sum_probs=111.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHhhc-CCcccCCceeEeecccCC--------------cccccCCCcceeecCCCccccH
Q 006282           67 TRRSLGYGYVNYANPADAARALDVL-NFTPLNNKSIRIMYSHRD--------------PSIRKSGTGNIFIKNLDKSIDH  131 (652)
Q Consensus        67 t~~s~g~AfV~F~~~e~A~~Al~~l-n~~~i~G~~i~i~~s~~~--------------~~~~~~~~~~lfV~nLp~~~t~  131 (652)
                      ..+.+|+++|+|.+.++|++|++.+ |+..+.| .|++.++...              .........+|||+|||.++++
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~   87 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNK   87 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSC
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCH
Confidence            3467899999999999999999999 9999999 9999987652              1233445678999999999999


Q ss_pred             HHHHhhhccCCCeeEEEEeeCCCCCcccEEEEEEcCHHHHHHHHHHhcCceecCeeeeecccccc
Q 006282          132 KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRK  196 (652)
Q Consensus       132 ~~L~~~Fs~fG~I~~~~v~~~~~g~skG~afV~F~t~e~A~~Ai~~lng~~l~g~~~~v~~~~~~  196 (652)
                      ++|+++|+.||.|.+|++..+    ++|||||+|.+.++|..|++.+|+..+.|+.|.|.+..++
T Consensus        88 ~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           88 TELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            999999999999999999886    7899999999999999999999999999999999887654

>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=99.75  E-value=3.4e-18  Score=140.29  Aligned_cols=83  Identities=28%  Similarity=0.439  Sum_probs=79.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...+.++|||+|||+++++++|+++|++||+|.+|++.+|..+++++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 006282          105 YSH  107 (652)
Q Consensus       105 ~s~  107 (652)
                      |++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            874

>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=99.75  E-value=2.5e-18  Score=149.85  Aligned_cols=105  Identities=23%  Similarity=0.443  Sum_probs=94.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      +.++++|||+|||+++|+++|+++|+.||.|.+|++.++   ++++|||||+|.+.++|.+|++.||+..|.|+.|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999999976   45589999999999999999999999999999999999


Q ss_pred             ccCCcccccCCCcceeecCCCccccHHHHHhhhccCCC
Q 006282          106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGN  143 (652)
Q Consensus       106 s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~  143 (652)
                      +......          ++++...++++|.++|+.||-
T Consensus        82 a~~~~~~----------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           82 YNANRAF----------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CCHHHHT----------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             ecCChhh----------hhhhHhHhHHHHHHHHHHhCC
Confidence            8865432          578888999999999999973

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=7.9e-18  Score=142.40  Aligned_cols=89  Identities=18%  Similarity=0.432  Sum_probs=82.5

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      +....+.++|||+|||.++|+++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|++|++ +|+..|.|+.|+
T Consensus         4 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~   82 (99)
T 2dgs_A            4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVE   82 (99)
T ss_dssp             CCCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999999 999999999999


Q ss_pred             eecccCCccc
Q 006282          103 IMYSHRDPSI  112 (652)
Q Consensus       103 i~~s~~~~~~  112 (652)
                      |.|+......
T Consensus        83 V~~a~~~~~~   92 (99)
T 2dgs_A           83 VKRAEPRDSK   92 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCccc
Confidence            9999876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=4.7e-18  Score=143.79  Aligned_cols=88  Identities=27%  Similarity=0.503  Sum_probs=82.3

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeE-EEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVL-SVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~-~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      +.....++++|||+|||+++||++|+++|+.||+|. +|++++|+.+++++|||||+|.+.++|++|++.||+..|.|+.
T Consensus         2 ss~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (99)
T 2div_A            2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGAT   81 (99)
T ss_dssp             CCCCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCS
T ss_pred             CCCCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCC
Confidence            344566789999999999999999999999999999 9999999999999999999999999999999999999999999


Q ss_pred             ----eEeecccCC
Q 006282          101 ----IRIMYSHRD  109 (652)
Q Consensus       101 ----i~i~~s~~~  109 (652)
                          |+|.|+...
T Consensus        82 ~~~~l~v~~a~~~   94 (99)
T 2div_A           82 PAKRFKLNYATYS   94 (99)
T ss_dssp             SCEECCEEETTCC
T ss_pred             cceeEEEeecCCC
Confidence                999998764

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=6.8e-18  Score=141.63  Aligned_cols=87  Identities=28%  Similarity=0.369  Sum_probs=82.1

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ....+.++++|||+|||+++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A            8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             CCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            44556778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccC
Q 006282          102 RIMYSHR  108 (652)
Q Consensus       102 ~i~~s~~  108 (652)
                      +|.|++.
T Consensus        88 ~v~~a~~   94 (95)
T 2cqc_A           88 RVSGPSS   94 (95)
T ss_dssp             EEECCSC
T ss_pred             EEEecCC
Confidence            9999864

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=5.3e-18  Score=144.61  Aligned_cols=89  Identities=19%  Similarity=0.330  Sum_probs=83.0

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      +.....+.++|||+|||+++|+++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2dnm_A            6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL   85 (103)
T ss_dssp             CSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCC
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            33445668999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCCc
Q 006282          102 RIMYSHRDP  110 (652)
Q Consensus       102 ~i~~s~~~~  110 (652)
                      +|.|+....
T Consensus        86 ~V~~a~~~~   94 (103)
T 2dnm_A           86 RVQVARYGR   94 (103)
T ss_dssp             EEEECSSCC
T ss_pred             EEEECCcCC
Confidence            999998654

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=8.2e-18  Score=142.31  Aligned_cols=87  Identities=18%  Similarity=0.331  Sum_probs=82.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++++|||+|||+++|+++|+++|+.||+|.+|++++|..+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45689999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ccCCccc
Q 006282          106 SHRDPSI  112 (652)
Q Consensus       106 s~~~~~~  112 (652)
                      +......
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9876554

>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=99.75  E-value=8.1e-18  Score=146.56  Aligned_cols=88  Identities=24%  Similarity=0.374  Sum_probs=82.4

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....+.++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCcc
Q 006282          104 MYSHRDPS  111 (652)
Q Consensus       104 ~~s~~~~~  111 (652)
                      .|+.....
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpz_A          100 QLKRSKND  107 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EEcCCCCc
Confidence            99987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=150.84  Aligned_cols=89  Identities=27%  Similarity=0.400  Sum_probs=83.0

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .......++|||+|||.++||++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            34456689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus       116 v~~a~~~~~  124 (139)
T 1u6f_A          116 VALAASGHQ  124 (139)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            999986543

>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=99.74  E-value=6.5e-18  Score=137.88  Aligned_cols=81  Identities=36%  Similarity=0.575  Sum_probs=78.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      +.+|||+|||.++|+++|+++|+.||+|.++++.+|..+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|+..
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q 006282          109 D  109 (652)
Q Consensus       109 ~  109 (652)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=8.3e-18  Score=143.38  Aligned_cols=89  Identities=17%  Similarity=0.334  Sum_probs=83.4

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .....++++|||+|||+++|+++|+++|+.||+|.+|++++++.+++++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            34466789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus        89 v~~a~~~~~   97 (103)
T 2cq0_A           89 VEWAKPSTN   97 (103)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            999987643

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.74  E-value=1.8e-17  Score=144.35  Aligned_cols=92  Identities=27%  Similarity=0.475  Sum_probs=84.7

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......+.++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (115)
T 2dgo_A            8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   87 (115)
T ss_dssp             SCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            33455678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCCcccc
Q 006282          102 RIMYSHRDPSIR  113 (652)
Q Consensus       102 ~i~~s~~~~~~~  113 (652)
                      +|.|+...+...
T Consensus        88 ~V~~a~~~~~~~   99 (115)
T 2dgo_A           88 RTNWATRKPPAP   99 (115)
T ss_dssp             EEEESSCCCCCS
T ss_pred             EEEEccCCCCCC
Confidence            999998765443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.9e-17  Score=140.37  Aligned_cols=86  Identities=21%  Similarity=0.423  Sum_probs=80.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....+.++|||+|||+++|+++|+++|+.||+|.+|++.+|. +++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   90 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            445668999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|+...+
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9987653

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.74  E-value=9.4e-18  Score=143.86  Aligned_cols=90  Identities=19%  Similarity=0.346  Sum_probs=83.2

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc---CC
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL---NN   98 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i---~G   98 (652)
                      ......+.++|||+|||.++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..+   .|
T Consensus         6 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g   85 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN   85 (106)
T ss_dssp             CSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC
Confidence            444566789999999999999999999999999999999999999999999999999999999999999999887   89


Q ss_pred             ceeEeecccCCcc
Q 006282           99 KSIRIMYSHRDPS  111 (652)
Q Consensus        99 ~~i~i~~s~~~~~  111 (652)
                      ++|+|.|+.....
T Consensus        86 ~~l~v~~a~~~~~   98 (106)
T 2dgp_A           86 RPIQVKPADSESR   98 (106)
T ss_dssp             SCCEEEECCCCSC
T ss_pred             ceEEEEECCcccc
Confidence            9999999986543

>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=99.74  E-value=8.1e-18  Score=141.16  Aligned_cols=85  Identities=25%  Similarity=0.510  Sum_probs=78.2

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......+.++|||+|||+++++++|+++|+.||+|.+|++++|.. ++++|||||+|.+.++|++|++.||+..|.|++|
T Consensus         9 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (95)
T 2ywk_A            9 FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI   87 (95)
T ss_dssp             ---CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEE
Confidence            344556789999999999999999999999999999999999986 8999999999999999999999999999999999


Q ss_pred             Eeeccc
Q 006282          102 RIMYSH  107 (652)
Q Consensus       102 ~i~~s~  107 (652)
                      +|.|+.
T Consensus        88 ~V~~a~   93 (95)
T 2ywk_A           88 NVSGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEEEcC
Confidence            999876

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.6e-18  Score=144.16  Aligned_cols=90  Identities=28%  Similarity=0.417  Sum_probs=83.8

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      +.....+.++|||+|||+++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus         5 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 2cqb_A            5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   84 (102)
T ss_dssp             SSCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cCCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            44456678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+.....
T Consensus        85 ~V~~a~~~~~   94 (102)
T 2cqb_A           85 RVNLAKPMRI   94 (102)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987644

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.73  E-value=3.2e-18  Score=142.01  Aligned_cols=82  Identities=21%  Similarity=0.400  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G--~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .+|||+|||+++|+++|+++|+.||  .|.++++.+|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999999999999999999999988


Q ss_pred             CCcc
Q 006282          108 RDPS  111 (652)
Q Consensus       108 ~~~~  111 (652)
                      ..+.
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.73  E-value=2.2e-17  Score=141.79  Aligned_cols=85  Identities=29%  Similarity=0.512  Sum_probs=80.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ....+++|||+|||.++|+++|+++|+.||+|.+|++++++.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 006282          105 YSHRD  109 (652)
Q Consensus       105 ~s~~~  109 (652)
                      |+...
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            98765

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.73  E-value=8.4e-18  Score=141.35  Aligned_cols=83  Identities=28%  Similarity=0.500  Sum_probs=79.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ++++|||+|||.++++++|+++|+.||.|.+|++.+|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|+.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCc
Q 006282          108 RDP  110 (652)
Q Consensus       108 ~~~  110 (652)
                      ...
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.73  E-value=9e-18  Score=149.01  Aligned_cols=88  Identities=28%  Similarity=0.394  Sum_probs=83.0

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ....+.++++|||+|||+++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|+|++|
T Consensus        39 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l  118 (129)
T 2kxn_B           39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI  118 (129)
T ss_dssp             CSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            44556778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccCC
Q 006282          102 RIMYSHRD  109 (652)
Q Consensus       102 ~i~~s~~~  109 (652)
                      +|.|+..+
T Consensus       119 ~V~~a~~~  126 (129)
T 2kxn_B          119 RVDFSITK  126 (129)
T ss_dssp             EESCCSSS
T ss_pred             EEEEecCC
Confidence            99998764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=140.44  Aligned_cols=85  Identities=21%  Similarity=0.366  Sum_probs=80.2

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~--------i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      ..++.+.++|||+|||+++|+++|+++|+.||.|.+        |++.+|+.+++++|||||+|.+.++|++|++.||+.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            345667899999999999999999999999999999        999999999999999999999999999999999999


Q ss_pred             ccCCceeEeeccc
Q 006282           95 PLNNKSIRIMYSH  107 (652)
Q Consensus        95 ~i~G~~i~i~~s~  107 (652)
                      .|.|+.|+|.|++
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999874

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=7.7e-18  Score=141.60  Aligned_cols=85  Identities=29%  Similarity=0.560  Sum_probs=80.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSV-RVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i-~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      .++++|||+|||+++|+++|+++|+.||+|.+| ++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            457899999999999999999999999999999 9999999999999999999999999999999999999999999999


Q ss_pred             ccCCcc
Q 006282          106 SHRDPS  111 (652)
Q Consensus       106 s~~~~~  111 (652)
                      +.....
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            986543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.3e-17  Score=140.75  Aligned_cols=86  Identities=26%  Similarity=0.504  Sum_probs=80.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCC---CCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS---TRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~---t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      .++++|||+|||+++|+++|+++|+.||+|.+|++.+|..   |++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4578999999999999999999999999999999999987   7799999999999999999999999999999999999


Q ss_pred             ecccCCccc
Q 006282          104 MYSHRDPSI  112 (652)
Q Consensus       104 ~~s~~~~~~  112 (652)
                      .|+......
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=2.8e-17  Score=140.11  Aligned_cols=88  Identities=24%  Similarity=0.385  Sum_probs=81.3

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ...+..+.++|||+|||+++|+++|+++|+.|| |.+|++++|+.+++++|||||+|.+.++|++|+ .||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   85 (103)
T 2dng_A            8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSL   85 (103)
T ss_dssp             CCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEE
Confidence            344556789999999999999999999999997 999999999999999999999999999999999 799999999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+.....
T Consensus        86 ~V~~a~~~~~   95 (103)
T 2dng_A           86 RVDIAEGRKQ   95 (103)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEecCCCC
Confidence            9999987654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.5e-17  Score=143.71  Aligned_cols=90  Identities=27%  Similarity=0.372  Sum_probs=82.5

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ........++|||+|||+++||++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|++|++.+|+ .|.|+.|
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l   88 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   88 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEE
Confidence            344556789999999999999999999999999999999999999999999999999999999999999998 8999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|+......
T Consensus        89 ~V~~a~~~~~~   99 (116)
T 2cqd_A           89 NVNLAYLGAKP   99 (116)
T ss_dssp             EEEESTTTCCC
T ss_pred             EEEEcccCCCc
Confidence            99999765443

>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=2e-17  Score=141.54  Aligned_cols=90  Identities=24%  Similarity=0.393  Sum_probs=83.0

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ........++|||+|||+++|+++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|++|++. |+..|.|+.|
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l   87 (105)
T 2dh8_A            9 NNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNI   87 (105)
T ss_dssp             CCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEE
T ss_pred             CcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEE
Confidence            344566789999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|+......
T Consensus        88 ~V~~a~~~~~~   98 (105)
T 2dh8_A           88 DPKPCTPRGMQ   98 (105)
T ss_dssp             BCCCSCCSSCC
T ss_pred             EEEEccCCCCC
Confidence            99999866543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.8e-17  Score=142.15  Aligned_cols=87  Identities=21%  Similarity=0.271  Sum_probs=81.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....++++|||+|||+++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|+...+
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9987643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.73  E-value=9.8e-18  Score=146.76  Aligned_cols=84  Identities=25%  Similarity=0.358  Sum_probs=79.1

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....+.++|||+|||+++|+++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccc
Q 006282          104 MYSH  107 (652)
Q Consensus       104 ~~s~  107 (652)
                      .|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9874

>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=99.72  E-value=2.7e-17  Score=142.28  Aligned_cols=88  Identities=16%  Similarity=0.309  Sum_probs=82.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC------CcccC
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN------FTPLN   97 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln------~~~i~   97 (652)
                      ....+.++|||+|||+++|+++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|++|++.+|      +..|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            345678999999999999999999999999999999999999999999999999999999999999999      99999


Q ss_pred             CceeEeecccCCcc
Q 006282           98 NKSIRIMYSHRDPS  111 (652)
Q Consensus        98 G~~i~i~~s~~~~~  111 (652)
                      |+.|+|.|+.....
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            99999999986644

>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=3.7e-17  Score=139.86  Aligned_cols=86  Identities=20%  Similarity=0.313  Sum_probs=80.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC---cee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN---KSI  101 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G---~~i  101 (652)
                      ...++++|||+|||+++|+++|+++|+.||.|.+|+|++|. +++++|||||+|.+.++|++|++.||+..+.|   ++|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34568999999999999999999999999999999999998 79999999999999999999999999999998   999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+...+.
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9999987654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.72  E-value=1.2e-17  Score=133.78  Aligned_cols=75  Identities=21%  Similarity=0.235  Sum_probs=70.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      .-.+..|||+||++.+||++|+++|++||+|.++++..      ++|||||+|.+.++|++|++.||+..+.|++|+|.+
T Consensus         4 ~~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~   77 (89)
T 2wbr_A            4 AWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAES   77 (89)
T ss_dssp             CCCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEE
Confidence            34588999999999999999999999999999999854      679999999999999999999999999999999987


Q ss_pred             c
Q 006282          106 S  106 (652)
Q Consensus       106 s  106 (652)
                      +
T Consensus        78 A   78 (89)
T 2wbr_A           78 P   78 (89)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.7e-17  Score=140.42  Aligned_cols=86  Identities=30%  Similarity=0.424  Sum_probs=80.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhc-cCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcc-cCCceeE
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQ-VGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTP-LNNKSIR  102 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~-~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~-i~G~~i~  102 (652)
                      ...++++|||+|||+++|+++|+++|+. ||.|.+|+|++|. +++++|||||+|.+.++|++|++.||+.. |.|++|+
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            4556899999999999999999999999 9999999999998 89999999999999999999999999999 9999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus        84 v~~a~~~~~   92 (104)
T 2dhg_A           84 LSVAIPKAS   92 (104)
T ss_dssp             CCBCCCCCS
T ss_pred             EEEccCCCc
Confidence            999876543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.5e-17  Score=141.42  Aligned_cols=89  Identities=21%  Similarity=0.473  Sum_probs=82.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEee-CCCCCcccEEEEEeCCHHHHHHHHhhc-CCcccCCcee
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD-LSTRRSLGYGYVNYANPADAARALDVL-NFTPLNNKSI  101 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d-~~t~~s~g~AfV~F~~~e~A~~Al~~l-n~~~i~G~~i  101 (652)
                      ......++|||+|||+++|+++|+++|+.||.|.+|+++++ ..+++++|||||+|.+.++|++|++.| |+..|.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34557899999999999999999999999999999999999 789999999999999999999999999 9999999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|+..+...
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999876544

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.72  E-value=8e-18  Score=150.15  Aligned_cols=87  Identities=17%  Similarity=0.341  Sum_probs=80.4

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEE--EEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc----c
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLS--VRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT----P   95 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~--i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~----~   95 (652)
                      ........++|||+|||+++||++|+++|+.||.|.+  |+|++|+.+++++|||||+|.+. +|.+|++.||+.    .
T Consensus        16 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           16 EPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3344567889999999999999999999999999977  99999999999999999999999 999999999999    9


Q ss_pred             cCCceeEeecccCC
Q 006282           96 LNNKSIRIMYSHRD  109 (652)
Q Consensus        96 i~G~~i~i~~s~~~  109 (652)
                      |.|+.|+|.|+...
T Consensus        95 ~~gr~l~V~~a~~~  108 (131)
T 2m2b_A           95 IDGKTINVEFAKGS  108 (131)
T ss_dssp             GGGCCCCCEECCCS
T ss_pred             CCCEEEEEEECCCC
Confidence            99999999998754

>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=99.72  E-value=4.2e-17  Score=139.00  Aligned_cols=89  Identities=26%  Similarity=0.404  Sum_probs=80.3

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ........++|||+|||+++|+++|+++|+.||+|.+|++++|..+  ++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   85 (103)
T 2cqi_A            8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEV   85 (103)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeE
Confidence            3345567899999999999999999999999999999999998554  68999999999999999999999999999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|+......
T Consensus        86 ~V~~a~~~~~~   96 (103)
T 2cqi_A           86 KVNWATTPSSQ   96 (103)
T ss_dssp             EEEECCCTTCC
T ss_pred             EEEECCCCccc
Confidence            99999876543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.6e-17  Score=139.89  Aligned_cols=82  Identities=13%  Similarity=0.215  Sum_probs=73.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC--cccCCceeE
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF--TPLNNKSIR  102 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~--~~i~G~~i~  102 (652)
                      .+.++++|||+|||+++||++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.+++  ..|.|++|+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            3456899999999999999999999999999999999875      48999999999999999998864  689999999


Q ss_pred             eecccCCccc
Q 006282          103 IMYSHRDPSI  112 (652)
Q Consensus       103 i~~s~~~~~~  112 (652)
                      |.|++.....
T Consensus        86 V~~A~~~~~~   95 (105)
T 1sjq_A           86 IQFSNHKELK   95 (105)
T ss_dssp             BCCCSSSSCC
T ss_pred             EEEcCCCCCC
Confidence            9999876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4e-17  Score=139.12  Aligned_cols=87  Identities=26%  Similarity=0.489  Sum_probs=81.0

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .....+.++|||+|||+++|+++|+++|+.||.|.+|++++|  +++++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            344567899999999999999999999999999999999998  889999999999999999999999999999999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus        87 V~~a~~~~~   95 (103)
T 2d9p_A           87 VALAQRKEE   95 (103)
T ss_dssp             EEECSSCCC
T ss_pred             EEEeccccc
Confidence            999987654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=8.3e-18  Score=142.39  Aligned_cols=82  Identities=18%  Similarity=0.233  Sum_probs=78.5

Q ss_pred             CCccEEEEcCCCC------CCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC-c
Q 006282           27 FLTTSLYVGDLDF------NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN-K   99 (652)
Q Consensus        27 ~~~~sL~V~nLp~------~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G-~   99 (652)
                      ..+++|||+|||.      ++++++|+++|++||+|.+|+|++|+.|++++|||||+|.+.++|++|++.||+..|.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4578999999999      99999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             eeEeecccC
Q 006282          100 SIRIMYSHR  108 (652)
Q Consensus       100 ~i~i~~s~~  108 (652)
                      .|+|.|+..
T Consensus        84 ~l~V~~a~~   92 (100)
T 3ns6_A           84 RLFLYTMKD   92 (100)
T ss_dssp             BCEEEESHH
T ss_pred             EEEEEECch
Confidence            999998864

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.72  E-value=5e-18  Score=140.98  Aligned_cols=79  Identities=20%  Similarity=0.363  Sum_probs=73.2

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcC-CeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhc-CcEecCeeEEEEecc
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN-GKMIVSKPLYVAVAQ  388 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG-~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~ln-g~~~~g~~l~v~~~~  388 (652)
                      .+|||+|||.++|+++|+++|+.|| .|++|+|++|. +|.++|||||+|.+.++|.+|++.++ +..++|++|.|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5799999999999999999999999 89999999885 68999999999999999999999874 567999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        82 ~~   83 (91)
T 2lxi_A           82 PK   83 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.71  E-value=8.9e-18  Score=140.10  Aligned_cols=79  Identities=18%  Similarity=0.304  Sum_probs=73.1

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCC--eeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCc----EecCeeEE
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK----MIVSKPLY  383 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~--I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~----~~~g~~l~  383 (652)
                      -.+|||+|||+++|+++|+++|++||.  |.+|++++|. +|++||||||+|.+.++|.+|++.|||.    .++|++|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            357999999999999999999999995  6799999886 6999999999999999999999999997    58999999


Q ss_pred             EEeccc
Q 006282          384 VAVAQR  389 (652)
Q Consensus       384 v~~~~~  389 (652)
                      |.||+.
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999975

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.71  E-value=3.2e-17  Score=131.39  Aligned_cols=77  Identities=23%  Similarity=0.386  Sum_probs=71.7

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .+..|||+||++.+|+++|+++|.+||.|.++++..     +||||||+|.+.++|.+|++.||+..+.|++|+|++|..
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e   80 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSE   80 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCH
Confidence            356799999999999999999999999999999976     599999999999999999999999999999999999964


Q ss_pred             HH
Q 006282          390 KE  391 (652)
Q Consensus       390 ~~  391 (652)
                      .+
T Consensus        81 ~~   82 (89)
T 2wbr_A           81 NE   82 (89)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=1.8e-17  Score=140.76  Aligned_cols=92  Identities=25%  Similarity=0.420  Sum_probs=81.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      ++|||+|||+++|+++|+++|+.||+|.+|++.++     ++|||||+|.+.++|++|++.||+..|.|+.|+|.|+...
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            58999999999999999999999999999999987     6789999999999999999999999999999999999765


Q ss_pred             ccc--------ccCCCcceeecCCC
Q 006282          110 PSI--------RKSGTGNIFIKNLD  126 (652)
Q Consensus       110 ~~~--------~~~~~~~lfV~nLp  126 (652)
                      +..        +.....+|||+||+
T Consensus        76 ~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCcccCCCCCccccCCCceecCCCC
Confidence            422        22235679999986

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=8.1e-18  Score=138.00  Aligned_cols=82  Identities=23%  Similarity=0.418  Sum_probs=77.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      +.++++|||+|||+++++++|+++|+.||+|.++++.+|+.+++++|||||+|.+.++|++|++.||+..|.|+.|++.|
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            34688999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 006282          106 SH  107 (652)
Q Consensus       106 s~  107 (652)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.71  E-value=3.6e-17  Score=134.72  Aligned_cols=81  Identities=25%  Similarity=0.468  Sum_probs=75.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|++.+|+.+++++|||||+|.+.++|++|++ +++..|+|+.|+|.
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            44568999999999999999999999999999999999999999999999999999999999997 57788999999998


Q ss_pred             cc
Q 006282          105 YS  106 (652)
Q Consensus       105 ~s  106 (652)
                      |+
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.71  E-value=4.4e-17  Score=141.91  Aligned_cols=84  Identities=25%  Similarity=0.458  Sum_probs=79.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++++|. +++++|||||+|.+.++|++|++.||+..|.|+.|+|.|
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 899999999999999999999999999999999999999


Q ss_pred             ccCCc
Q 006282          106 SHRDP  110 (652)
Q Consensus       106 s~~~~  110 (652)
                      ++...
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            97654

>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=8.9e-17  Score=136.95  Aligned_cols=88  Identities=27%  Similarity=0.433  Sum_probs=80.3

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......+.++|||+|||+++|+++|+++|+.||.|.+|+|++|..  .++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   85 (103)
T 2cq3_A            8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKI   85 (103)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            445566789999999999999999999999999999999999865  388999999999999999999999999999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+...+.
T Consensus        86 ~v~~a~~~~~   95 (103)
T 2cq3_A           86 EVNNATARVM   95 (103)
T ss_dssp             EEEECCSSCC
T ss_pred             EEEEcccCCC
Confidence            9999987654

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1e-16  Score=136.52  Aligned_cols=89  Identities=24%  Similarity=0.358  Sum_probs=80.7

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......+.++|||+|||+++|+++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|++|++  ++..|.|+.|
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l   85 (103)
T 2cqg_A            8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWC   85 (103)
T ss_dssp             CSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEE
T ss_pred             CCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEE
Confidence            33445668999999999999999999999999999999999999999999999999999999999999  4578999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|+......
T Consensus        86 ~v~~a~~~~~~   96 (103)
T 2cqg_A           86 DCKLPNSKQSQ   96 (103)
T ss_dssp             EEECCCTTCCC
T ss_pred             EEEecCCCCcC
Confidence            99999876544

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.71  E-value=5.8e-17  Score=135.03  Aligned_cols=84  Identities=25%  Similarity=0.383  Sum_probs=78.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..+.++|||+|||+++|+++|+++|+.||+|.+|++.++  +++++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456789999999999999999999999999999999985  788999999999999999999999999999999999999


Q ss_pred             ccCCcc
Q 006282          106 SHRDPS  111 (652)
Q Consensus       106 s~~~~~  111 (652)
                      ++....
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            887543

>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=99.71  E-value=3.1e-17  Score=133.82  Aligned_cols=79  Identities=34%  Similarity=0.650  Sum_probs=75.7

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ++|||+|||.++++++|+++|+.||.|.+++++.+ .+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.++
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            58999999999999999999999999999999988 57899999999999999999999999999999999999999875

>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=99.70  E-value=4.6e-17  Score=134.06  Aligned_cols=81  Identities=28%  Similarity=0.539  Sum_probs=75.3

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.|+.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            46789999999999999999999999999999999884 88999999999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            65

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.70  E-value=5e-17  Score=146.88  Aligned_cols=87  Identities=29%  Similarity=0.487  Sum_probs=80.9

Q ss_pred             CCCCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCc
Q 006282           20 AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK   99 (652)
Q Consensus        20 ~~~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~   99 (652)
                      .+......+.++|||+|||.++|+++|+++|+.||+|.+|++.+|+.+++++|||||+|.+.++|++|++.||+..|.|+
T Consensus        54 ~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  133 (140)
T 2ku7_A           54 GGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR  133 (140)
T ss_dssp             CSSCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTE
T ss_pred             CCCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            33555667889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEeecc
Q 006282          100 SIRIMYS  106 (652)
Q Consensus       100 ~i~i~~s  106 (652)
                      .|+|.|+
T Consensus       134 ~l~v~~A  140 (140)
T 2ku7_A          134 TIRVNLA  140 (140)
T ss_dssp             EEEEEC-
T ss_pred             EEEEEeC
Confidence            9999875

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.70  E-value=3.1e-17  Score=141.22  Aligned_cols=87  Identities=26%  Similarity=0.415  Sum_probs=76.2

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .......++|||+|||.++|+++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|++|++.++ ..|.|+.|+
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~   97 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTID   97 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999999765 899999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.|+....
T Consensus        98 V~~a~~~~  105 (109)
T 2rs2_A           98 PKVAFPRR  105 (109)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99987654

>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=99.70  E-value=4.2e-17  Score=134.93  Aligned_cols=80  Identities=21%  Similarity=0.438  Sum_probs=76.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++|+++|+++|+.||.|.+|++.+|..+++++|||||+|.+.++|++|+ .+|+..|.|+.|+|.|++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3689999999999999999999999999999999999999999999999999999999999 899999999999999987


Q ss_pred             C
Q 006282          108 R  108 (652)
Q Consensus       108 ~  108 (652)
                      .
T Consensus        84 ~   84 (89)
T 3ucg_A           84 T   84 (89)
T ss_dssp             T
T ss_pred             C
Confidence            5

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.3e-17  Score=139.06  Aligned_cols=80  Identities=16%  Similarity=0.289  Sum_probs=75.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++|+++|+++|+.||+|.+|++++|.. ++++|||||+|.+.++|++|++ +|+..|.|+.|+|.|.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3568999999999999999999999999999999999987 9999999999999999999999 8999999999999987


Q ss_pred             cC
Q 006282          107 HR  108 (652)
Q Consensus       107 ~~  108 (652)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            64

>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=3.5e-17  Score=141.27  Aligned_cols=87  Identities=18%  Similarity=0.279  Sum_probs=81.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....++++|||+|||+++|+++|+++|+.||.|.+|++.+|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34556899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|+...+
T Consensus       101 ~~a~~~~  107 (110)
T 1oo0_B          101 DWCFVKG  107 (110)
T ss_dssp             EESEESS
T ss_pred             EEcccCC
Confidence            9987653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1e-16  Score=139.27  Aligned_cols=87  Identities=24%  Similarity=0.408  Sum_probs=80.5

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......++++|||+|||+++|+++|+++|+.||.|.+|+|++|+ +++++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (114)
T 2do0_A            8 ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM   86 (114)
T ss_dssp             CCCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEE
Confidence            44455678999999999999999999999999999999999997 58999999999999999999999999999999999


Q ss_pred             EeecccCC
Q 006282          102 RIMYSHRD  109 (652)
Q Consensus       102 ~i~~s~~~  109 (652)
                      +|.|+...
T Consensus        87 ~v~~a~~~   94 (114)
T 2do0_A           87 HVKMDERA   94 (114)
T ss_dssp             EEEECSCC
T ss_pred             EEEEcccC
Confidence            99998753

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.8e-17  Score=138.39  Aligned_cols=88  Identities=25%  Similarity=0.436  Sum_probs=81.0

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCC-CCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLST-RRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t-~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ..+..+.++|||+|||+++|+++|+++|+.|| |.+|+|++|+.+ ++++|||||+|.+.++|++|+ .||+..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            34455679999999999999999999999999 999999999988 999999999999999999999 899999999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|+......
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999876543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.70  E-value=4.1e-17  Score=149.60  Aligned_cols=81  Identities=23%  Similarity=0.411  Sum_probs=77.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G--~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++|||+|||+++||++|+++|+.||  .|.+|+|++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            865

>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=99.70  E-value=5.3e-17  Score=136.35  Aligned_cols=85  Identities=21%  Similarity=0.270  Sum_probs=77.9

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLY----DLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN   98 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~----~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G   98 (652)
                      ..+....++|||+|||+++++++|+    ++|++||+|.+|+|.+|+.+   +|||||+|.+.++|++|++.||+..|.|
T Consensus         3 s~~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~g   79 (96)
T 2dgx_A            3 SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGS   79 (96)
T ss_dssp             CCCCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3445567899999999999999999    99999999999999999776   6899999999999999999999999999


Q ss_pred             ceeEeecccCCc
Q 006282           99 KSIRIMYSHRDP  110 (652)
Q Consensus        99 ~~i~i~~s~~~~  110 (652)
                      ++|+|.|++..+
T Consensus        80 r~l~V~~a~~~~   91 (96)
T 2dgx_A           80 KKILVSLATGAS   91 (96)
T ss_dssp             EEEEEEECCCSS
T ss_pred             eEEEEEEcCCCC
Confidence            999999987653

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.70  E-value=5.8e-17  Score=139.15  Aligned_cols=83  Identities=30%  Similarity=0.463  Sum_probs=78.7

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....++++|||+|||+++|+++|+++|+.||+|.+|+++++. +++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            445678999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             eccc
Q 006282          104 MYSH  107 (652)
Q Consensus       104 ~~s~  107 (652)
                      .|+.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9875

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=6.1e-17  Score=140.48  Aligned_cols=88  Identities=23%  Similarity=0.388  Sum_probs=82.2

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcc
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVL--------SVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTP   95 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~--------~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~   95 (652)
                      ......++|||+|||+++|+++|+++|+.||.|.        .|+|++|+.+++++|||||+|.+.++|++|++.||+..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3455789999999999999999999999999999        69999999999999999999999999999999999999


Q ss_pred             cCCceeEeecccCCcc
Q 006282           96 LNNKSIRIMYSHRDPS  111 (652)
Q Consensus        96 i~G~~i~i~~s~~~~~  111 (652)
                      |.|+.|+|.|+.....
T Consensus        90 ~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPP  105 (113)
T ss_dssp             ETTEECEEECSSCCCC
T ss_pred             cCCCEEEEEECCCCCC
Confidence            9999999999987654

>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=99.70  E-value=6.9e-17  Score=137.06  Aligned_cols=85  Identities=16%  Similarity=0.276  Sum_probs=77.6

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ...+...++|||+|||+++||++|+++|+.||.| +|+|++|+ +++++|||||+|.+.++|++||+ +|+..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (102)
T 1wez_A            9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVE   85 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            4456678999999999999999999999999955 99999998 89999999999999999999996 799999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.++....
T Consensus        86 V~~~~~~~   93 (102)
T 1wez_A           86 LFLNSTAG   93 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEECCCCC
Confidence            99887654

>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=3.6e-17  Score=138.02  Aligned_cols=85  Identities=15%  Similarity=0.214  Sum_probs=79.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      .....++|||+|||+++|+++|+++|+.||.|.++++++++.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 006282          105 YSHRD  109 (652)
Q Consensus       105 ~s~~~  109 (652)
                      |+...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98754

>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=99.69  E-value=3.7e-17  Score=152.05  Aligned_cols=139  Identities=19%  Similarity=0.337  Sum_probs=79.0

Q ss_pred             EeeCCHHHHHHHHHHHCCCccC--CceEEEEccccchHHHHHHhHH----HHHhhhhcccccccceeeecCCCCCCCHHH
Q 006282          254 VNFENADDAAKAVEALNGKKFD--DREWYVGKAQKKSEREQELKGQ----FEQAMKETVDKFQGLNLYIKNLGDSIDDEK  327 (652)
Q Consensus       254 V~f~~~~~A~~Ai~~l~~~~~~--g~~l~v~~a~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~l~V~nlp~~~te~~  327 (652)
                      ..|++.+++..++..+++....  |+.....+....  +.......    .............+++|||+|||..+++++
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~--~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~   88 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTRE--AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDE   88 (165)
T ss_dssp             ---------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccc--cccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHH
Confidence            6788999999999888876654  444443332111  10000000    000011112234567899999999999999


Q ss_pred             HHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHHHH
Q 006282          328 LKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR  394 (652)
Q Consensus       328 L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~r~  394 (652)
                      |+++|+.||.|.+|+|+.+ .+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+..+..+.
T Consensus        89 L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             HHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            9999999999999999988 488999999999999999999999999999999999999998765443

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.69  E-value=4.6e-17  Score=135.67  Aligned_cols=79  Identities=24%  Similarity=0.316  Sum_probs=72.5

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcE--ecCeeEEE
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKM--IVSKPLYV  384 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~--~~g~~l~v  384 (652)
                      ...++++|||+|||+++|+++|+++|++||.|++|+++++     ||||||+|.+.++|.+|++.||+..  +.|++|+|
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            3456789999999999999999999999999999999864     8999999999999999999999875  78999999


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .|++.+
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            999875

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.69  E-value=2.7e-17  Score=131.34  Aligned_cols=75  Identities=25%  Similarity=0.471  Sum_probs=72.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      +|||+|||+++|+++|+++|+.||+|.+|++.+++.+++++|||||+|.+.++|++|++ +|+..|.|++|+|.|+
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            58999999999999999999999999999999999999999999999999999999998 9999999999999875

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.9e-17  Score=137.59  Aligned_cols=79  Identities=19%  Similarity=0.360  Sum_probs=72.4

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhc--CcEecCeeEEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN--GKMIVSKPLYVA  385 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~ln--g~~~~g~~l~v~  385 (652)
                      ....++|||+|||+++++++|+++|++||.|++|+|+++     ||||||+|.+.++|.+|++.++  +..+.|++|+|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            345789999999999999999999999999999999986     7999999999999999999886  478999999999


Q ss_pred             ecccHH
Q 006282          386 VAQRKE  391 (652)
Q Consensus       386 ~~~~~~  391 (652)
                      |++.+.
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            998653

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=6.4e-17  Score=137.05  Aligned_cols=83  Identities=25%  Similarity=0.448  Sum_probs=78.7

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+.+|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34567899999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      .++
T Consensus        94 ~~~   96 (100)
T 2do4_A           94 NSG   96 (100)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=5.1e-17  Score=138.72  Aligned_cols=84  Identities=30%  Similarity=0.540  Sum_probs=79.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCc
Q 006282          107 HRDP  110 (652)
Q Consensus       107 ~~~~  110 (652)
                      ....
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            8654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.69  E-value=7.5e-17  Score=134.38  Aligned_cols=80  Identities=14%  Similarity=0.154  Sum_probs=72.0

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcc--cCCcee
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTP--LNNKSI  101 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~--i~G~~i  101 (652)
                      ....++++|||+|||.++||++|+++|++||.|.+|++.+      ++|||||+|.+.++|.+|++.||+..  |.|++|
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            3445789999999999999999999999999999999975      35899999999999999999999775  789999


Q ss_pred             EeecccCC
Q 006282          102 RIMYSHRD  109 (652)
Q Consensus       102 ~i~~s~~~  109 (652)
                      +|.||+..
T Consensus        90 ~V~~S~~k   97 (100)
T 3r27_A           90 FVNYSTSQ   97 (100)
T ss_dssp             EEEECSCS
T ss_pred             EEEecccc
Confidence            99999864

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.69  E-value=1.9e-17  Score=140.21  Aligned_cols=83  Identities=19%  Similarity=0.303  Sum_probs=77.7

Q ss_pred             ccceeeecCCCC------CCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecC-ee
Q 006282          310 QGLNLYIKNLGD------SIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVS-KP  381 (652)
Q Consensus       310 ~~~~l~V~nlp~------~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g-~~  381 (652)
                      .+++|||+|||.      ++++++|+++|++||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..+.| +.
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            457899999999      99999999999999999999999887 49999999999999999999999999999999 99


Q ss_pred             EEEEecccHHH
Q 006282          382 LYVAVAQRKEE  392 (652)
Q Consensus       382 l~v~~~~~~~~  392 (652)
                      |.|.++.+++.
T Consensus        85 l~V~~a~~~~~   95 (100)
T 3ns6_A           85 LFLYTMKDVER   95 (100)
T ss_dssp             CEEEESHHHHH
T ss_pred             EEEEECchhhh
Confidence            99999987643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.1e-16  Score=133.00  Aligned_cols=84  Identities=18%  Similarity=0.412  Sum_probs=78.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ......++|||+|||+++|+++|+++|+.| .|.+|++++| .+++++|||||+|.+.++|++|++ +|+..|.|+.|+|
T Consensus         5 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v   81 (91)
T 2dgw_A            5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEV   81 (91)
T ss_dssp             CCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEE
T ss_pred             CCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEE
Confidence            345568999999999999999999999999 9999999999 789999999999999999999999 9999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|++..+
T Consensus        82 ~~a~~~~   88 (91)
T 2dgw_A           82 FREKSGP   88 (91)
T ss_dssp             EEESSCC
T ss_pred             EECCcCC
Confidence            9988754

>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=99.69  E-value=2.1e-16  Score=136.15  Aligned_cols=86  Identities=16%  Similarity=0.319  Sum_probs=77.6

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .....+.++|||+|||+++|+++|+++|+.||.|.+|+|..+   ++++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR   92 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            344557899999999999999999999999999999999654   56889999999999999999999999999999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|++....
T Consensus        93 V~~a~~~~~  101 (109)
T 1x4a_A           93 VEFPRSGRG  101 (109)
T ss_dssp             EECCCCCCC
T ss_pred             EEEcccCCC
Confidence            999987644

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.69  E-value=5.5e-17  Score=133.93  Aligned_cols=82  Identities=24%  Similarity=0.414  Sum_probs=77.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCC-cccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR-SLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~-s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ..++|||+|||+++|+++|+++|+.||.|.+|++.+|..++. ++|||||+|.+.++|++|++.||+..|.|+.|+|.|+
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            468999999999999999999999999999999999988766 9999999999999999999999999999999999998


Q ss_pred             cCC
Q 006282          107 HRD  109 (652)
Q Consensus       107 ~~~  109 (652)
                      ...
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=2.4e-17  Score=132.35  Aligned_cols=76  Identities=29%  Similarity=0.521  Sum_probs=73.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ++|||+|||+++|+++|+++|++||+|.++++.+|+.+++++|||||+|.+.++|++|++.++ ..+.|+.|+|.|+
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            579999999999999999999999999999999999999999999999999999999999999 9999999999886

>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=99.69  E-value=7e-17  Score=132.34  Aligned_cols=80  Identities=29%  Similarity=0.484  Sum_probs=75.5

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|++||.|.+++++.+ .+|+++|||||+|.+.++|.+|++.|||..++|+.|.|.|+
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            35678999999999999999999999999999999887 57889999999999999999999999999999999999997


Q ss_pred             c
Q 006282          388 Q  388 (652)
Q Consensus       388 ~  388 (652)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=5.9e-17  Score=137.52  Aligned_cols=84  Identities=20%  Similarity=0.291  Sum_probs=77.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|+++..|+++|||||+|.+.++|.+|+. +|+..++|+.|.|.++.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            34578999999999999999999999999999999999889999999999999999999999 99999999999999988


Q ss_pred             cHHHH
Q 006282          389 RKEER  393 (652)
Q Consensus       389 ~~~~r  393 (652)
                      .-..+
T Consensus        88 ~~~~~   92 (103)
T 1s79_A           88 DYFAK   92 (103)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65433

>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=99.69  E-value=7.8e-17  Score=142.77  Aligned_cols=88  Identities=20%  Similarity=0.269  Sum_probs=82.2

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .....++++|||+|||+++|+++|+++|+.||.|.+|+|.+|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            34455688999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.|+....
T Consensus        96 v~~a~~~~  103 (126)
T 3ex7_B           96 VDWCFVRG  103 (126)
T ss_dssp             EEESEESS
T ss_pred             EEEecCCC
Confidence            99997654

>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=99.69  E-value=2.1e-17  Score=137.10  Aligned_cols=80  Identities=24%  Similarity=0.337  Sum_probs=71.1

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcC--CeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG--~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .+|||+|||.++++++|+++|+.||  .|.+++++.+. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999885 89999999999999999999999999999999999999988


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      ++.
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            653

>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=1e-16  Score=141.52  Aligned_cols=86  Identities=28%  Similarity=0.417  Sum_probs=81.1

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....++++|||+|||+++++++|+++|+.||+|.+|++++|. +++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        30 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            455678999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|+....
T Consensus       109 ~~a~~~~  115 (124)
T 2kt5_A          109 QLVASQI  115 (124)
T ss_dssp             EEECCTT
T ss_pred             EEeCCCC
Confidence            9988654

>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=99.69  E-value=8.8e-17  Score=134.78  Aligned_cols=81  Identities=31%  Similarity=0.507  Sum_probs=77.0

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+.+.+|+++|||||+|.+.++|.+|++.|||..++|+.|.|.+++
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            35678999999999999999999999999999999999889999999999999999999999999999999999999986


Q ss_pred             c
Q 006282          389 R  389 (652)
Q Consensus       389 ~  389 (652)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.69  E-value=1.3e-16  Score=135.99  Aligned_cols=85  Identities=21%  Similarity=0.275  Sum_probs=77.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLS-VRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~-i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ......++|||+|||+++||++|+++|+.||.|.+ |+|++| .+++++|||||+|.+.++|++|++. |+..|.|+.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~   87 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIE   87 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEE
Confidence            34456799999999999999999999999999998 999998 7899999999999999999999997 99999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.++....
T Consensus        88 v~~~~~~~   95 (104)
T 1wg5_A           88 IFKSSRAE   95 (104)
T ss_dssp             EEEECTTT
T ss_pred             EEECCHHH
Confidence            99887643

>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=99.68  E-value=9.9e-17  Score=134.75  Aligned_cols=83  Identities=25%  Similarity=0.420  Sum_probs=77.9

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .++|||+|||.++++++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++..
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            5689999999999999999999999999999999885 689999999999999999999999999999999999999987


Q ss_pred             HHHH
Q 006282          390 KEER  393 (652)
Q Consensus       390 ~~~r  393 (652)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            6543

>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=99.68  E-value=9.1e-17  Score=135.83  Aligned_cols=83  Identities=30%  Similarity=0.474  Sum_probs=78.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|+..|||..+.|+.|.|.++
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            356789999999999999999999999999999999887 8999999999999999999999999999999999999999


Q ss_pred             ccHH
Q 006282          388 QRKE  391 (652)
Q Consensus       388 ~~~~  391 (652)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T 1whw_A           86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            8763

>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=99.68  E-value=2.9e-17  Score=137.77  Aligned_cols=82  Identities=16%  Similarity=0.201  Sum_probs=76.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....++|||+|||+++|+++|+++|+.||.|.++++++++.+++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 006282          106 SH  107 (652)
Q Consensus       106 s~  107 (652)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>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=99.68  E-value=2.9e-17  Score=139.12  Aligned_cols=86  Identities=23%  Similarity=0.449  Sum_probs=75.0

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeC-CCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDL-STRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~-~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ........++|||+|||.++|+++|+++|+.|| |.+|++.+|+ .+++++|||||+|.+.++|++|+ .||+..|.|+.
T Consensus        12 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~   89 (100)
T 2j76_E           12 SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRR   89 (100)
T ss_dssp             --------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBC
T ss_pred             CcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeE
Confidence            334556789999999999999999999999999 9999999998 68999999999999999999999 79999999999


Q ss_pred             eEeecccCC
Q 006282          101 IRIMYSHRD  109 (652)
Q Consensus       101 i~i~~s~~~  109 (652)
                      |+|.|+...
T Consensus        90 l~V~~a~~~   98 (100)
T 2j76_E           90 IRVDVADQA   98 (100)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEeccCC
Confidence            999998764

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=6.3e-17  Score=136.31  Aligned_cols=83  Identities=19%  Similarity=0.238  Sum_probs=73.9

Q ss_pred             CCCCCccEEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc--ccCCce
Q 006282           24 GNQFLTTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT--PLNNKS  100 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~-~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~--~i~G~~  100 (652)
                      ....++++|||+|||+ ++||++|+++|++||.|.+|+|.+++      |||||+|.+.++|++|++.||+.  .|.|++
T Consensus        10 ~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   83 (102)
T 1x4d_A           10 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKP   83 (102)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcE
Confidence            3455789999999999 99999999999999999999998753      79999999999999999998864  499999


Q ss_pred             eEeecccCCccc
Q 006282          101 IRIMYSHRDPSI  112 (652)
Q Consensus       101 i~i~~s~~~~~~  112 (652)
                      |+|.|++....+
T Consensus        84 l~V~~a~~~~~~   95 (102)
T 1x4d_A           84 VRVHLSQKYKRI   95 (102)
T ss_dssp             CEEEEECCCTTS
T ss_pred             EEEEECCCCCCC
Confidence            999999865543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.68  E-value=8.1e-17  Score=140.66  Aligned_cols=84  Identities=17%  Similarity=0.196  Sum_probs=77.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ---VLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~---V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ......++|||+|||+++||++|+++|+.||.   |.+|+|++|+. ++++|||||+|.+.++|++|++ +|+..|.|+.
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~   89 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRY   89 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeE
Confidence            34556899999999999999999999999999   89999999987 9999999999999999999999 9999999999


Q ss_pred             eEeecccCC
Q 006282          101 IRIMYSHRD  109 (652)
Q Consensus       101 i~i~~s~~~  109 (652)
                      |+|.++..+
T Consensus        90 i~V~~a~~~   98 (118)
T 2db1_A           90 IEVFKSHRT   98 (118)
T ss_dssp             EEEEEECHH
T ss_pred             EEEEECCHH
Confidence            999987643

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=7.3e-17  Score=140.13  Aligned_cols=87  Identities=17%  Similarity=0.236  Sum_probs=81.2

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCe-eEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I-~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||+++++++|+++|+.||.| .+|+|+.|.+|+++|||||+|.+.++|.+|+.. |+..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            456789999999999999999999999999 899999999999999999999999999999996 999999999999999


Q ss_pred             ccHHHHHHH
Q 006282          388 QRKEERRAR  396 (652)
Q Consensus       388 ~~~~~r~~~  396 (652)
                      ..++.+...
T Consensus        92 ~~~~~~~~~  100 (114)
T 2cpy_A           92 TLEDMREIE  100 (114)
T ss_dssp             CHHHHHHHH
T ss_pred             CHHHHHHHH
Confidence            988777544

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=6.5e-17  Score=137.79  Aligned_cols=85  Identities=62%  Similarity=1.028  Sum_probs=79.6

Q ss_pred             ccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       306 ~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ......++|||+|||.++++++|+++|+.||.|.+|+|+.+ +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.
T Consensus        10 ~~~~~~~~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           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34457889999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             ecccHH
Q 006282          386 VAQRKE  391 (652)
Q Consensus       386 ~~~~~~  391 (652)
                      |+.++.
T Consensus        89 ~a~~~~   94 (103)
T 2d9p_A           89 LAQRKE   94 (103)
T ss_dssp             ECSSCC
T ss_pred             Eecccc
Confidence            998653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=7.7e-17  Score=138.76  Aligned_cols=88  Identities=28%  Similarity=0.455  Sum_probs=79.2

Q ss_pred             CCCCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCc
Q 006282           20 AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK   99 (652)
Q Consensus        20 ~~~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~   99 (652)
                      +.........++|||+|||.++|+++|+++|+.||+|.+|++++|.  ++++|||||+|.+.++|++|++.||+..|+|+
T Consensus        20 S~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   97 (109)
T 2err_A           20 HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGR   97 (109)
T ss_dssp             --CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTE
T ss_pred             CCCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3345556678999999999999999999999999999999999985  35889999999999999999999999999999


Q ss_pred             eeEeecccCC
Q 006282          100 SIRIMYSHRD  109 (652)
Q Consensus       100 ~i~i~~s~~~  109 (652)
                      .|+|.|+...
T Consensus        98 ~l~V~~a~~~  107 (109)
T 2err_A           98 KIEVNNATAR  107 (109)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998764

>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=99.68  E-value=1.4e-16  Score=137.27  Aligned_cols=86  Identities=19%  Similarity=0.261  Sum_probs=79.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEE-eeCCCCCcccEEEEEeCCHHHHHHHHhhcC--CcccCCcee
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ-VLSVRVC-RDLSTRRSLGYGYVNYANPADAARALDVLN--FTPLNNKSI  101 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~-V~~i~v~-~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln--~~~i~G~~i  101 (652)
                      +.+.++|||+|||+++|+++|+++|+.||. |.+|++. +|+.+++++|||||+|.+.++|++|++.||  +..|.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            345789999999999999999999999998 9999999 888899999999999999999999999996  589999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+.....
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.6e-16  Score=137.99  Aligned_cols=82  Identities=30%  Similarity=0.552  Sum_probs=77.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|++|+|+.+.+|+++|||||+|.+.++|.+|+..|||..|+|+.|.|.++.
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   92 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE   92 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcc
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ..
T Consensus        93 ~~   94 (114)
T 2do0_A           93 RA   94 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            53

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=2.4e-16  Score=133.75  Aligned_cols=81  Identities=14%  Similarity=0.114  Sum_probs=72.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc--ccCCceeE
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT--PLNNKSIR  102 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~--~i~G~~i~  102 (652)
                      ...++++|||+|||+++||++|+++|++||.|.+|++.++      +|||||+|.+.++|++|++.|++.  .|.|++|+
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4567899999999999999999999999999999999764      589999999999999999988754  48999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus        85 V~~a~~~~~   93 (104)
T 1wex_A           85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCccc
Confidence            999987543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.3e-16  Score=133.68  Aligned_cols=81  Identities=35%  Similarity=0.619  Sum_probs=76.8

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
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            46789999999999999999999999999999999885 68999999999999999999999999999999999999997


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        84 ~~   85 (95)
T 2dnz_A           84 ER   85 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.67  E-value=1.9e-16  Score=145.15  Aligned_cols=86  Identities=19%  Similarity=0.293  Sum_probs=79.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcC--CeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG--~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ..++|||+|||+++++++|+++|+.||  .|.+|+|+.|. +|+++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            357899999999999999999999999  99999999884 899999999999999999999999999999999999999


Q ss_pred             cccHHHHHH
Q 006282          387 AQRKEERRA  395 (652)
Q Consensus       387 ~~~~~~r~~  395 (652)
                      +.++..+..
T Consensus       134 a~~~~~~~~  142 (156)
T 3n9u_C          134 ATRQNLSQF  142 (156)
T ss_dssp             CCHHHHHHH
T ss_pred             cCCCcchhh
Confidence            998765544

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.67  E-value=9.8e-17  Score=139.66  Aligned_cols=82  Identities=28%  Similarity=0.508  Sum_probs=77.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|++|+|+.+.+|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.+++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            34678999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        85 ~~   86 (116)
T 2fy1_A           85 KP   86 (116)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=99.67  E-value=9.8e-17  Score=137.20  Aligned_cols=83  Identities=33%  Similarity=0.575  Sum_probs=78.7

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC---eeEEEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS---KPLYVA  385 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g---~~l~v~  385 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+.+.+|.++|||||+|.+.++|.+|++.|||..+.|   +.|.|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            45789999999999999999999999999999999999899999999999999999999999999999998   999999


Q ss_pred             ecccHH
Q 006282          386 VAQRKE  391 (652)
Q Consensus       386 ~~~~~~  391 (652)
                      |+..+.
T Consensus        93 ~a~~~~   98 (105)
T 2dnh_A           93 FADTDK   98 (105)
T ss_dssp             ESCSSC
T ss_pred             ECccCc
Confidence            998654

>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=99.67  E-value=1.1e-16  Score=139.39  Aligned_cols=83  Identities=36%  Similarity=0.549  Sum_probs=78.2

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.||+..|+|+.|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999886 789999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +.++
T Consensus       102 a~~~  105 (115)
T 2cpz_A          102 KRSK  105 (115)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9865

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.8e-16  Score=132.80  Aligned_cols=82  Identities=24%  Similarity=0.336  Sum_probs=76.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|.+|+..|||..++|+.|.|.|
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            4456889999999999999999999999999999999885 588999999999999999999999999999999999999


Q ss_pred             ccc
Q 006282          387 AQR  389 (652)
Q Consensus       387 ~~~  389 (652)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            874

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.67  E-value=2.3e-17  Score=147.75  Aligned_cols=121  Identities=19%  Similarity=0.270  Sum_probs=78.7

Q ss_pred             eEEEeeCCHHHHHHHHHHHCCCccCCceEEEEccccchHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHH
Q 006282          251 FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE  330 (652)
Q Consensus       251 ~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~  330 (652)
                      +.|++|++...+..|+..+++....++.-. .+..                  ........++|||+|||.++++++|++
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~~-~~~~------------------~~~~~~~~~~l~V~nLp~~~te~~L~~   66 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGSM-SYGR------------------PPPDVEGMTSLKVDNLTYRTSPDTLRR   66 (135)
T ss_dssp             -----------------------------C-CSCC------------------SCSSGGGCCCEEEECCCSSCHHHHHHH
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCCC-CcCC------------------CCCCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            568888888888899988887665544211 1111                  111233467899999999999999999


Q ss_pred             HhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          331 LFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       331 ~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      +|+.||.|++|+|+.+. +|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.|++.+
T Consensus        67 ~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             HHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCC
T ss_pred             HHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            99999999999999875 7899999999999999999999999999999999999999854

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=1.3e-16  Score=140.55  Aligned_cols=84  Identities=18%  Similarity=0.296  Sum_probs=75.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLY----DLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~----~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ...++++|||+|||+++++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|.+|++.||+..|.|++
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34568899999999999999865    7999999999988754   5789999999999999999999999999999999


Q ss_pred             eEeecccCCcc
Q 006282          101 IRIMYSHRDPS  111 (652)
Q Consensus       101 i~i~~s~~~~~  111 (652)
                      |+|.|+.....
T Consensus       102 l~V~~a~~~~~  112 (127)
T 2a3j_A          102 LVITFSETPQS  112 (127)
T ss_dssp             CEEEECCCCCH
T ss_pred             EEEEEccCcch
Confidence            99999987654

>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=7e-17  Score=140.36  Aligned_cols=82  Identities=27%  Similarity=0.353  Sum_probs=78.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+++++|||||+|.+.++|++|+ .||+..|.|+.|+|.|+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            45689999999999999999999999999999999999999999999999999999999999 89999999999999998


Q ss_pred             cCC
Q 006282          107 HRD  109 (652)
Q Consensus       107 ~~~  109 (652)
                      ...
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            754

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=9.6e-17  Score=134.83  Aligned_cols=82  Identities=35%  Similarity=0.640  Sum_probs=77.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEE-EEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v-~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      .+++|||+|||.++++++|+++|+.||.|.++ +|+.+ .+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.++
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            46789999999999999999999999999999 99988 58999999999999999999999999999999999999999


Q ss_pred             ccHH
Q 006282          388 QRKE  391 (652)
Q Consensus       388 ~~~~  391 (652)
                      .++.
T Consensus        84 ~~~~   87 (96)
T 1x5t_A           84 FKKD   87 (96)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            8653

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.2e-16  Score=132.10  Aligned_cols=81  Identities=23%  Similarity=0.443  Sum_probs=75.9

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.|
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            3456789999999999999999999999999999999886 588999999999999999999999999999999999999


Q ss_pred             cc
Q 006282          387 AQ  388 (652)
Q Consensus       387 ~~  388 (652)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.67  E-value=9.6e-17  Score=139.39  Aligned_cols=85  Identities=15%  Similarity=0.215  Sum_probs=78.7

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCe-EEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQV-LSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V-~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      .....+.++|||+|||+++|+++|+++|+.||.| .+|+|++|+ +++++|||||+|.+.++|++|++. |+..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i   86 (114)
T 2cpy_A            9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREA   86 (114)
T ss_dssp             CSCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEE
T ss_pred             CCCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEE
Confidence            3455678999999999999999999999999999 899999998 899999999999999999999996 9999999999


Q ss_pred             EeecccCC
Q 006282          102 RIMYSHRD  109 (652)
Q Consensus       102 ~i~~s~~~  109 (652)
                      +|.|+...
T Consensus        87 ~v~~a~~~   94 (114)
T 2cpy_A           87 FVHVVTLE   94 (114)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99998754

>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=99.67  E-value=2.6e-16  Score=134.01  Aligned_cols=82  Identities=28%  Similarity=0.508  Sum_probs=76.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+..+ ++|||||+|.+.++|.+|+..|||..|+|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            445789999999999999999999999999999999998755 8999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus        91 ~~~   93 (103)
T 2cq3_A           91 TAR   93 (103)
T ss_dssp             CSS
T ss_pred             ccC
Confidence            865

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.3e-16  Score=135.96  Aligned_cols=84  Identities=30%  Similarity=0.446  Sum_probs=78.7

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      +....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.
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            34567899999999999999999999999999999999885 78999999999999999999999999999999999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      |+.++
T Consensus        91 ~a~~~   95 (103)
T 2cq0_A           91 WAKPS   95 (103)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            99865

>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=2.1e-16  Score=132.73  Aligned_cols=80  Identities=19%  Similarity=0.276  Sum_probs=74.9

Q ss_pred             cccceeeecCCCCCCCHHHHH----HHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~----~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ..+++|||+|||+++++++|+    ++|++||.|.+|+|+.+..+  +|||||+|.+.++|.+|++.|||..++|+.|.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            356789999999999999999    99999999999999988766  899999999999999999999999999999999


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .+++.+
T Consensus        85 ~~a~~~   90 (96)
T 2dgx_A           85 SLATGA   90 (96)
T ss_dssp             EECCCS
T ss_pred             EEcCCC
Confidence            998754

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.67  E-value=2e-16  Score=135.81  Aligned_cols=81  Identities=31%  Similarity=0.490  Sum_probs=77.5

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||..+++++|+++|+.||.|.+|+|+.+.+|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             c
Q 006282          388 Q  388 (652)
Q Consensus       388 ~  388 (652)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.67  E-value=7.3e-17  Score=144.42  Aligned_cols=87  Identities=25%  Similarity=0.401  Sum_probs=81.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ......++|||+|||+++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  121 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  121 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|+....
T Consensus       122 ~~a~~~~  128 (135)
T 2lea_A          122 QMARYGR  128 (135)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.67  E-value=2e-16  Score=137.68  Aligned_cols=83  Identities=30%  Similarity=0.550  Sum_probs=78.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4467899999999999999999999999999999999885 889999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        92 a~~~   95 (115)
T 2dgo_A           92 ATRK   95 (115)
T ss_dssp             SSCC
T ss_pred             ccCC
Confidence            9865

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.67  E-value=3.2e-17  Score=136.02  Aligned_cols=80  Identities=29%  Similarity=0.567  Sum_probs=74.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      ++|||+|||.++++++|+++|+.||+|.+|++++|+.+++++|||||+|.+.+ |.+|++.||+..+.|+.|+|.|+...
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            68999999999999999999999999999999999999999999999999999 99999999999999999999998865


Q ss_pred             c
Q 006282          110 P  110 (652)
Q Consensus       110 ~  110 (652)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.67  E-value=2.8e-16  Score=144.69  Aligned_cols=87  Identities=30%  Similarity=0.476  Sum_probs=81.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....++++|||+|||+++||++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|+....
T Consensus       114 ~~a~~~~  120 (156)
T 1h2v_Z          114 DWDAGFK  120 (156)
T ss_dssp             EEESCCC
T ss_pred             EECCCCC
Confidence            9997644

>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=99.67  E-value=1.2e-16  Score=137.95  Aligned_cols=84  Identities=24%  Similarity=0.458  Sum_probs=78.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...+++|||+|||.++++++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.|
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4567889999999999999999999999999999999884 789999999999999999999999999999999999999


Q ss_pred             cccHH
Q 006282          387 AQRKE  391 (652)
Q Consensus       387 ~~~~~  391 (652)
                      +..+.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98653

>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=2e-16  Score=139.70  Aligned_cols=82  Identities=22%  Similarity=0.437  Sum_probs=78.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|++|+ .||+..|.|+.|+|.|+.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4689999999999999999999999999999999999999999999999999999999999 699999999999999987


Q ss_pred             CCc
Q 006282          108 RDP  110 (652)
Q Consensus       108 ~~~  110 (652)
                      ...
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.3e-16  Score=137.56  Aligned_cols=85  Identities=21%  Similarity=0.411  Sum_probs=79.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+++++|||||+|.+.++|++|++. |+..|.|+.|+|.|+
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            3469999999999999999999999999999999999999999999999999999999999997 999999999999999


Q ss_pred             cCCccc
Q 006282          107 HRDPSI  112 (652)
Q Consensus       107 ~~~~~~  112 (652)
                      ......
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            876543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=2.7e-16  Score=133.42  Aligned_cols=86  Identities=22%  Similarity=0.378  Sum_probs=77.3

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......+.++|||+|||+++|+++|+++|+.||.|   +++++ .+++++|||||+|.+.++|++|++.||+..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   83 (101)
T 2fc9_A            8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAI   83 (101)
T ss_dssp             CCCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEE
T ss_pred             CccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEE
Confidence            34455678999999999999999999999999977   67777 678999999999999999999999999999999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+.....
T Consensus        84 ~v~~a~~~~~   93 (101)
T 2fc9_A           84 RLELQGPRGS   93 (101)
T ss_dssp             EEEECSSCCC
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>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=99.66  E-value=1.5e-16  Score=135.98  Aligned_cols=83  Identities=28%  Similarity=0.464  Sum_probs=78.4

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4457899999999999999999999999999999999886 789999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        92 a~~~   95 (105)
T 1x5u_A           92 ASAH   95 (105)
T ss_dssp             TTTT
T ss_pred             CCCC
Confidence            9865

>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=99.66  E-value=3e-16  Score=135.64  Aligned_cols=83  Identities=13%  Similarity=0.209  Sum_probs=74.4

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC--cccCCcee
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF--TPLNNKSI  101 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~--~~i~G~~i  101 (652)
                      ....++++|||+|||+++||++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.+++  ..|.|++|
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            34567899999999999999999999999999999999976      48999999999999999998874  57999999


Q ss_pred             EeecccCCccc
Q 006282          102 RIMYSHRDPSI  112 (652)
Q Consensus       102 ~i~~s~~~~~~  112 (652)
                      +|.|++.....
T Consensus       100 ~V~~a~~k~~~  110 (119)
T 2ad9_A          100 YIQFSNHKELK  110 (119)
T ss_dssp             EEEECSSSSCC
T ss_pred             EEEEccCCCCC
Confidence            99999876543

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.1e-16  Score=131.47  Aligned_cols=81  Identities=19%  Similarity=0.239  Sum_probs=72.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC--CcccCCceeE
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN--FTPLNNKSIR  102 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln--~~~i~G~~i~  102 (652)
                      ...++++|||+|||+++||++|+++|++||.|.+|++.++      +|||||+|.+.++|++|++.++  +..|.|++|+
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3456899999999999999999999999999999999875      5899999999999999999774  5679999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus        85 V~~a~~~~~   93 (101)
T 2cq1_A           85 IQYSNHKEL   93 (101)
T ss_dssp             EEECSCSSC
T ss_pred             EEEcCcccC
Confidence            999987644

>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=99.66  E-value=3.5e-16  Score=133.21  Aligned_cols=83  Identities=31%  Similarity=0.478  Sum_probs=76.7

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+..+ ++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            345689999999999999999999999999999999998544 7999999999999999999999999999999999999


Q ss_pred             ccHH
Q 006282          388 QRKE  391 (652)
Q Consensus       388 ~~~~  391 (652)
                      ..+.
T Consensus        91 ~~~~   94 (103)
T 2cqi_A           91 TTPS   94 (103)
T ss_dssp             CCTT
T ss_pred             CCCc
Confidence            8653

>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=141.96  Aligned_cols=83  Identities=16%  Similarity=0.191  Sum_probs=77.6

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ---VLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~---V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ......++|||+|||+++||++|+++|+.||.   |.+|+|++|+. ++++|||||+|.+.++|++|++ +|+..|.|+.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            34566899999999999999999999999999   89999999987 9999999999999999999999 9999999999


Q ss_pred             eEeecccC
Q 006282          101 IRIMYSHR  108 (652)
Q Consensus       101 i~i~~s~~  108 (652)
                      |+|.++..
T Consensus       117 i~V~~a~~  124 (136)
T 2hgl_A          117 IEVFKSHR  124 (136)
T ss_dssp             EEEEECCH
T ss_pred             EEEEECCh
Confidence            99998764

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=5.6e-16  Score=128.44  Aligned_cols=80  Identities=24%  Similarity=0.402  Sum_probs=73.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...+.++|||+|||+++|+++|+++|+.||+|.+|+++        +|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            34568999999999999999999999999999999997        3799999999999999999999999999999999


Q ss_pred             cccCCccc
Q 006282          105 YSHRDPSI  112 (652)
Q Consensus       105 ~s~~~~~~  112 (652)
                      |+...+..
T Consensus        76 ~a~~~~~~   83 (90)
T 2dnq_A           76 ASKNKSKA   83 (90)
T ss_dssp             CSSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=2.4e-16  Score=133.21  Aligned_cols=82  Identities=21%  Similarity=0.420  Sum_probs=76.7

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++ ||+..++|+.|.|.+
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            3456789999999999999999999999999999999885 68899999999999999999999 999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +.++
T Consensus        86 a~~~   89 (99)
T 2dgs_A           86 AEPR   89 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9865

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.66  E-value=2e-16  Score=138.17  Aligned_cols=85  Identities=16%  Similarity=0.240  Sum_probs=79.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCC---eeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGT---ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~---I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|+.+.+|+++|||||+|.+.++|.+|++ +|+..|+|+.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            345678999999999999999999999999   899999999889999999999999999999999 9999999999999


Q ss_pred             EecccHHHH
Q 006282          385 AVAQRKEER  393 (652)
Q Consensus       385 ~~~~~~~~r  393 (652)
                      .++..++..
T Consensus        93 ~~a~~~~~~  101 (118)
T 2db1_A           93 FKSHRTEMD  101 (118)
T ss_dssp             EEECHHHHH
T ss_pred             EECCHHHHH
Confidence            999877654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.6e-16  Score=135.13  Aligned_cols=82  Identities=28%  Similarity=0.463  Sum_probs=77.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|++|+|+.+ .+|+++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+
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            35678999999999999999999999999999999988 47899999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus        90 ~~~   92 (102)
T 2cqb_A           90 KPM   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.66  E-value=2e-16  Score=133.72  Aligned_cols=81  Identities=25%  Similarity=0.493  Sum_probs=76.0

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeE--------EEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~--------v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+        ++++.+ .+|+++|||||+|.+.++|.+|++.|||..+.
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            345789999999999999999999999999999        999988 47899999999999999999999999999999


Q ss_pred             CeeEEEEecc
Q 006282          379 SKPLYVAVAQ  388 (652)
Q Consensus       379 g~~l~v~~~~  388 (652)
                      |+.|.|.+++
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            9999999874

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.2e-16  Score=135.28  Aligned_cols=83  Identities=24%  Similarity=0.479  Sum_probs=77.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...+++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.|
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            3456889999999999999999999999999999999885 589999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus       100 a~~~  103 (106)
T 1p27_B          100 CFVR  103 (106)
T ss_dssp             SEES
T ss_pred             ecCC
Confidence            9865

>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=99.66  E-value=2.6e-16  Score=135.97  Aligned_cols=87  Identities=17%  Similarity=0.314  Sum_probs=79.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHH---HHHhccCCeEEEEEEeeCCCC---CcccEEEEEeCCHHHHHHHHhhcCCcccCC
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLY---DLFSQVGQVLSVRVCRDLSTR---RSLGYGYVNYANPADAARALDVLNFTPLNN   98 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~---~~Fs~~G~V~~i~v~~d~~t~---~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G   98 (652)
                      .....++|||+|||+++++++|+   ++|++||+|.+|+|.+|..++   +++|||||+|.+.++|++|++.||+..|.|
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            44567899999999999999999   999999999999999998754   566999999999999999999999999999


Q ss_pred             ceeEeecccCCcc
Q 006282           99 KSIRIMYSHRDPS  111 (652)
Q Consensus        99 ~~i~i~~s~~~~~  111 (652)
                      ++|+|.|+...+.
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

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=1.1e-16  Score=136.71  Aligned_cols=83  Identities=36%  Similarity=0.561  Sum_probs=78.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhh-cCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcE-ecCeeEEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKM-IVSKPLYVA  385 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~-fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~-~~g~~l~v~  385 (652)
                      ....++|||+|||.++++++|+++|+. ||.|.+|+|+.+.+|.++|||||+|.+.++|.+|++.|||.. ++|+.|.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            345789999999999999999999999 999999999999899999999999999999999999999999 999999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      ++.++
T Consensus        86 ~a~~~   90 (104)
T 2dhg_A           86 VAIPK   90 (104)
T ss_dssp             BCCCC
T ss_pred             EccCC
Confidence            98765

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.8e-16  Score=136.37  Aligned_cols=83  Identities=28%  Similarity=0.477  Sum_probs=77.0

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      .....++|||+|||.++++++|+++|+.||.|.+|+++.+.. .++|||||+|.+.++|.+|++.|||..++|+.|.|.+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345678999999999999999999999999999999998864 4899999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9864

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=2.2e-16  Score=135.50  Aligned_cols=83  Identities=23%  Similarity=0.479  Sum_probs=78.1

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC--CCCCccEEEEEeCCHHHHHHHHHHh-cCcEecCeeEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYV  384 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~--~g~s~g~afV~F~s~~~A~~A~~~l-ng~~~~g~~l~v  384 (652)
                      ....++|||+|||.++++++|+++|+.||.|++|+|+.+.  +|.++|||||+|.+.++|.+|+..| |+..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            4467899999999999999999999999999999999884  8899999999999999999999999 999999999999


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .|+..+
T Consensus        92 ~~a~~~   97 (107)
T 2cph_A           92 EWADSE   97 (107)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            999865

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=1.9e-16  Score=135.53  Aligned_cols=80  Identities=20%  Similarity=0.289  Sum_probs=73.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      .....+|||+|||+++||++|+++|+.| .|.+|+|++|+. ++++|||||+|.+.++|++|+ .+|+..|.|+.|+|..
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   89 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSP   89 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            4456899999999999999999999999 899999999976 899999999999999999999 5999999999999987


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      +..
T Consensus        90 a~~   92 (109)
T 2dnn_A           90 ATE   92 (109)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.9e-16  Score=133.62  Aligned_cols=81  Identities=19%  Similarity=0.402  Sum_probs=75.7

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .++|||+|||+++++++|+++|+.| .|.+|+|+.|.+|+++|||||+|.+.++|.+|+ .+|+..|+|+.|.|..+..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            4689999999999999999999999 899999999988999999999999999999999 69999999999999999876


Q ss_pred             HHH
Q 006282          391 EER  393 (652)
Q Consensus       391 ~~r  393 (652)
                      +..
T Consensus        94 ~~~   96 (109)
T 2dnn_A           94 QWV   96 (109)
T ss_dssp             HHH
T ss_pred             chh
Confidence            543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=5.1e-16  Score=125.51  Aligned_cols=79  Identities=23%  Similarity=0.270  Sum_probs=69.3

Q ss_pred             CCCCccEEEEcCCCCCCCHHH----HHHHHhcc-CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCc
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQ----LYDLFSQV-GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK   99 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~----L~~~Fs~~-G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~   99 (652)
                      .++..++|||+|||.++++++    |+++|++| |+|.+|       |+   |+|||.|.+.++|.+|++.||+..|.||
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr   74 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            333445599999999999998    66899999 599998       33   9999999999999999999999999999


Q ss_pred             eeEeecccCCcccc
Q 006282          100 SIRIMYSHRDPSIR  113 (652)
Q Consensus       100 ~i~i~~s~~~~~~~  113 (652)
                      +|+|.|++..++..
T Consensus        75 ~i~v~~A~~~sd~~   88 (96)
T 2diu_A           75 RIIVSFTPKNRELC   88 (96)
T ss_dssp             CCEEESSCCSCCCC
T ss_pred             eEEEEecCCCccee
Confidence            99999999876643

>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=99.66  E-value=1.1e-16  Score=134.92  Aligned_cols=77  Identities=19%  Similarity=0.294  Sum_probs=70.9

Q ss_pred             cccceeeecCCCC-CCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCc--EecCeeEEEE
Q 006282          309 FQGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK--MIVSKPLYVA  385 (652)
Q Consensus       309 ~~~~~l~V~nlp~-~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~--~~~g~~l~v~  385 (652)
                      .++++|||+|||+ ++++++|+++|++||.|++|+|+++     +|||||+|.+.++|.+|++.||+.  .|.|++|+|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            3578999999999 9999999999999999999999876     689999999999999999999864  5999999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      +++.+
T Consensus        88 ~a~~~   92 (102)
T 1x4d_A           88 LSQKY   92 (102)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            99854

>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=99.65  E-value=1.5e-16  Score=135.79  Aligned_cols=87  Identities=26%  Similarity=0.485  Sum_probs=80.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            34689999999999999999999999999999999884 78899999999999999999999999999999999999999


Q ss_pred             cHHHHHHH
Q 006282          389 RKEERRAR  396 (652)
Q Consensus       389 ~~~~r~~~  396 (652)
                      .+..+...
T Consensus        87 ~~~~~~~~   94 (104)
T 1p1t_A           87 SEKNKEEL   94 (104)
T ss_dssp             CTTHHHHH
T ss_pred             Cccchhhh
Confidence            88766543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=1.9e-16  Score=133.50  Aligned_cols=81  Identities=37%  Similarity=0.667  Sum_probs=75.4

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC--C--CCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS--G--ISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~--g--~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.+..  |  .++|||||+|.+.++|.+|+..|||..|+|+.|.|.
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            467899999999999999999999999999999998753  3  889999999999999999999999999999999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      ++..+
T Consensus        84 ~a~~~   88 (98)
T 2cpf_A           84 ISERA   88 (98)
T ss_dssp             CSSCS
T ss_pred             EccCC
Confidence            99765

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.65  E-value=4e-16  Score=133.27  Aligned_cols=83  Identities=17%  Similarity=0.245  Sum_probs=76.0

Q ss_pred             CCCCccEEEEcCCCCCC------CHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC
Q 006282           25 NQFLTTSLYVGDLDFNV------TDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN   98 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~v------te~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G   98 (652)
                      ....+++|||+|||+++      |+++|+++|+.||+|.+|++.+  .+++++|||||+|.+.++|.+|++.||+..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            34457899999999999      7899999999999999999983  678999999999999999999999999999999


Q ss_pred             c-eeEeecccCC
Q 006282           99 K-SIRIMYSHRD  109 (652)
Q Consensus        99 ~-~i~i~~s~~~  109 (652)
                      + +|+|.|+...
T Consensus        89 ~~~l~V~~a~~~  100 (105)
T 2nlw_A           89 QHTFRVNLFTDF  100 (105)
T ss_dssp             TCEEEEECSCCC
T ss_pred             CceEEEEEcchH
Confidence            9 9999998753

>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=99.65  E-value=3.3e-16  Score=129.50  Aligned_cols=79  Identities=20%  Similarity=0.418  Sum_probs=74.7

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .++|||+|||.++++++|+++|+.||.|.+++++.+. +|+++|||||+|.+.++|.+|+ .|||..++|+.|.|.+++.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            4689999999999999999999999999999999885 8899999999999999999999 8999999999999999875


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=8.2e-16  Score=132.10  Aligned_cols=80  Identities=23%  Similarity=0.261  Sum_probs=74.3

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC-----c
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN-----K   99 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G-----~   99 (652)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+|++|       |||||+|.+.++|++|++.||+..|.|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3456899999999999999999999999999999999887       799999999999999999999999999     9


Q ss_pred             eeEeecccCCcc
Q 006282          100 SIRIMYSHRDPS  111 (652)
Q Consensus       100 ~i~i~~s~~~~~  111 (652)
                      .|+|.|+...+.
T Consensus        84 ~i~V~~a~~~~~   95 (108)
T 1x4c_A           84 YIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEESSCCSC
T ss_pred             EEEEEeCCCCCC
Confidence            999999887543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.65  E-value=1.5e-16  Score=136.38  Aligned_cols=84  Identities=18%  Similarity=0.143  Sum_probs=72.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVG-QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G-~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      .+...++|||+|||+++|+++|+++|+.|| .|..++|..    ++++|||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            345678999999999999999999999999 899998853    357899999999999999999999999999999999


Q ss_pred             ecccCCccc
Q 006282          104 MYSHRDPSI  112 (652)
Q Consensus       104 ~~s~~~~~~  112 (652)
                      .++...+..
T Consensus       100 ~~a~~~p~~  108 (111)
T 2jvr_A          100 ERDDNPPPI  108 (111)
T ss_dssp             EESCC----
T ss_pred             EECCCCCCC
Confidence            998866543

>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=99.65  E-value=1.6e-16  Score=141.60  Aligned_cols=84  Identities=17%  Similarity=0.246  Sum_probs=78.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCC---eeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGT---ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~---I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ...++|||+|||+++|+++|+++|+.||.   |.+|+|++|..|+++|||||+|.+.++|.+|++ +|+..|+|+.|.|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            35678999999999999999999999999   899999999889999999999999999999999 99999999999999


Q ss_pred             ecccHHHH
Q 006282          386 VAQRKEER  393 (652)
Q Consensus       386 ~~~~~~~r  393 (652)
                      ++..++..
T Consensus       121 ~a~~~e~~  128 (136)
T 2hgl_A          121 KSHRTEMD  128 (136)
T ss_dssp             ECCHHHHH
T ss_pred             ECChHHHH
Confidence            99877654

>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=99.65  E-value=3.8e-16  Score=131.70  Aligned_cols=80  Identities=21%  Similarity=0.349  Sum_probs=72.5

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh--cCcEecCeeEEE
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYV  384 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l--ng~~~~g~~l~v  384 (652)
                      ...++++|||+|||+++++++|+++|++||.|++|+++++     ||||||+|.+.++|.+|++.|  ++..+.|++|+|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            3456789999999999999999999999999999999875     899999999999999999987  467899999999


Q ss_pred             EecccHH
Q 006282          385 AVAQRKE  391 (652)
Q Consensus       385 ~~~~~~~  391 (652)
                      .|++.+.
T Consensus        86 ~~a~~~~   92 (101)
T 2cq1_A           86 QYSNHKE   92 (101)
T ss_dssp             EECSCSS
T ss_pred             EEcCccc
Confidence            9998653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.65  E-value=2.2e-16  Score=138.16  Aligned_cols=81  Identities=36%  Similarity=0.548  Sum_probs=75.7

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|++||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..++|+.|+|.|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4457899999999999999999999999999999999884 689999999999999999999999999999999999999


Q ss_pred             cc
Q 006282          387 AQ  388 (652)
Q Consensus       387 ~~  388 (652)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.2e-16  Score=134.18  Aligned_cols=82  Identities=28%  Similarity=0.513  Sum_probs=77.2

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.||+..|+|+.|.|.++
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            356789999999999999999999999999999999875 7889999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      .++
T Consensus        90 ~~~   92 (102)
T 1x5s_A           90 GKS   92 (102)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            865

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.65  E-value=2.4e-16  Score=131.26  Aligned_cols=81  Identities=28%  Similarity=0.453  Sum_probs=76.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+++|+.+ +|+++|||||+|.+.++|.+|+..|||..++|+.|.|.+++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            45679999999999999999999999999999999985 78899999999999999999999999999999999999987


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ..
T Consensus        85 ~~   86 (92)
T 2dgv_A           85 NA   86 (92)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.65  E-value=3.4e-16  Score=135.95  Aligned_cols=83  Identities=23%  Similarity=0.475  Sum_probs=77.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            35689999999999999999999999999999999886 4899999999999999999999 899999999999999998


Q ss_pred             cHHHH
Q 006282          389 RKEER  393 (652)
Q Consensus       389 ~~~~r  393 (652)
                      .+..+
T Consensus       103 ~~~~~  107 (114)
T 2cq4_A          103 AEKNR  107 (114)
T ss_dssp             HHHHH
T ss_pred             CCccC
Confidence            77655

>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=99.65  E-value=1.6e-16  Score=155.38  Aligned_cols=86  Identities=21%  Similarity=0.282  Sum_probs=79.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcC--CeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG--~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ..++|||+||++++|+++|+++|+.||  .|++|+|++|. +|+++|||||+|.+.++|.+||+.||+..|+|+.|.|.+
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            457899999999999999999999999  99999999985 899999999999999999999999999999999999999


Q ss_pred             cccHHHHHH
Q 006282          387 AQRKEERRA  395 (652)
Q Consensus       387 ~~~~~~r~~  395 (652)
                      +.+......
T Consensus       147 a~~~~~~~~  155 (229)
T 3q2s_C          147 VNKQFLSQF  155 (229)
T ss_dssp             CCHHHHHHH
T ss_pred             CCCCccchh
Confidence            998765543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=2.2e-16  Score=128.09  Aligned_cols=73  Identities=19%  Similarity=0.332  Sum_probs=68.4

Q ss_pred             ccEEEEcCCCCCC------CHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCc-ee
Q 006282           29 TTSLYVGDLDFNV------TDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK-SI  101 (652)
Q Consensus        29 ~~sL~V~nLp~~v------te~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~-~i  101 (652)
                      +++|||+|||.++      |+++|+++|++||+|.+|++.+  .+++++|||||+|.+.++|++|++.||+..|.|+ +|
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 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4799999999999      7899999999999999999883  5789999999999999999999999999999999 88


Q ss_pred             Ee
Q 006282          102 RI  103 (652)
Q Consensus       102 ~i  103 (652)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            77

>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=99.65  E-value=1e-15  Score=132.95  Aligned_cols=83  Identities=20%  Similarity=0.374  Sum_probs=76.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc--------
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL--------   96 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i--------   96 (652)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+|++|. +++++|||||+|.+.++|++|++.||+..|        
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            34567999999999999999999999999999999999998 899999999999999999999999999999        


Q ss_pred             CCceeEeecccC
Q 006282           97 NNKSIRIMYSHR  108 (652)
Q Consensus        97 ~G~~i~i~~s~~  108 (652)
                      .+++|+|.|+..
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            577788888763

>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=5.9e-16  Score=131.59  Aligned_cols=87  Identities=18%  Similarity=0.329  Sum_probs=78.9

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .....++++|||+|||+++|+++|+++|+.|+   +|++++++.+++++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34556789999999999999999999999773   788999999999999999999999999999999999999999999


Q ss_pred             eecccCCccc
Q 006282          103 IMYSHRDPSI  112 (652)
Q Consensus       103 i~~s~~~~~~  112 (652)
                      |.|++.....
T Consensus        86 V~~a~~~~~~   95 (102)
T 2fc8_A           86 LDWAKPKGEG   95 (102)
T ss_dssp             EEECCCCCSS
T ss_pred             EEEecCCCCC
Confidence            9999876543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.64  E-value=4.4e-16  Score=137.44  Aligned_cols=82  Identities=29%  Similarity=0.482  Sum_probs=77.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..+++|||+|||.++++++|+++|+.||.|.+|+|+.+.+|+++|||||+|.+.++|.+|+..|||..++|+.|.|.++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            45689999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ..
T Consensus       113 ~~  114 (124)
T 2kt5_A          113 SQ  114 (124)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.64  E-value=7.8e-16  Score=129.50  Aligned_cols=81  Identities=23%  Similarity=0.421  Sum_probs=74.3

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC--Ccee
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN--NKSI  101 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~--G~~i  101 (652)
                      ....++++|||+|||+++|+++|+++|+.||.|.+|++.++      +|||||+|.+.++|++|++.||+..|.  |+.|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l   85 (97)
T 1why_A           12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRL   85 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEE
Confidence            34567899999999999999999999999999999999764      579999999999999999999999999  9999


Q ss_pred             EeecccCCc
Q 006282          102 RIMYSHRDP  110 (652)
Q Consensus       102 ~i~~s~~~~  110 (652)
                      +|.|++..+
T Consensus        86 ~V~~a~~~~   94 (97)
T 1why_A           86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCC
Confidence            999998754

>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=99.64  E-value=2.4e-16  Score=135.34  Aligned_cols=83  Identities=34%  Similarity=0.598  Sum_probs=77.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||..+++++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.+
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            3456889999999999999999999999999999999874 788999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +.++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9865

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=2.2e-16  Score=139.39  Aligned_cols=85  Identities=19%  Similarity=0.251  Sum_probs=78.1

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ......++|||+|||+++|+++|+++|+.||.|.++.++.+..+++++|||||+|.+.++|++||+ +|+..|.|+.|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   98 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   98 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            345567999999999999999999999999999997777888899999999999999999999999 9999999999999


Q ss_pred             ecccCC
Q 006282          104 MYSHRD  109 (652)
Q Consensus       104 ~~s~~~  109 (652)
                      .|+...
T Consensus        99 ~~a~~~  104 (124)
T 1wel_A           99 HPITKK  104 (124)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            987653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.1e-16  Score=135.97  Aligned_cols=83  Identities=25%  Similarity=0.469  Sum_probs=77.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCee--------EEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTIT--------SCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~--------~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      ....++|||+|||.++++++|+++|+.||.|.        .|+|+.+ .+|+++|||||+|.+.++|.+|++.|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            44678999999999999999999999999999        6999988 57999999999999999999999999999999


Q ss_pred             CeeEEEEecccH
Q 006282          379 SKPLYVAVAQRK  390 (652)
Q Consensus       379 g~~l~v~~~~~~  390 (652)
                      |+.|.|.++..+
T Consensus        92 g~~l~V~~a~~~  103 (113)
T 2cpe_A           92 GSKLKVSLARKK  103 (113)
T ss_dssp             TEECEEECSSCC
T ss_pred             CCEEEEEECCCC
Confidence            999999999865

>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=99.64  E-value=4.9e-16  Score=144.40  Aligned_cols=87  Identities=18%  Similarity=0.284  Sum_probs=80.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...++++|||+|||+++|+++|+++|+.||.|.+|+|++++.+++++|||||+|.+.++|++|++.||+..|.|++|+|.
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            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCcc
Q 006282          105 YSHRDPS  111 (652)
Q Consensus       105 ~s~~~~~  111 (652)
                      |+...+.
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9976543

>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=99.64  E-value=3e-16  Score=135.60  Aligned_cols=79  Identities=19%  Similarity=0.367  Sum_probs=72.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcC--cEecCeeEEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYVA  385 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng--~~~~g~~l~v~  385 (652)
                      ..++++|||+|||+++++++|+++|++||.|++|+|+++     ||||||+|.+.++|.+|++.+++  ..+.|++|+|.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            446788999999999999999999999999999999986     89999999999999999999874  68999999999


Q ss_pred             ecccHH
Q 006282          386 VAQRKE  391 (652)
Q Consensus       386 ~~~~~~  391 (652)
                      |++.++
T Consensus       103 ~a~~k~  108 (119)
T 2ad9_A          103 FSNHKE  108 (119)
T ss_dssp             ECSSSS
T ss_pred             EccCCC
Confidence            998653

>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=99.64  E-value=4.6e-16  Score=134.44  Aligned_cols=83  Identities=30%  Similarity=0.506  Sum_probs=77.7

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhc------CcEecCe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN------GKMIVSK  380 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~ln------g~~~~g~  380 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|+..||      +..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            3457889999999999999999999999999999999885 68899999999999999999999999      9999999


Q ss_pred             eEEEEecccH
Q 006282          381 PLYVAVAQRK  390 (652)
Q Consensus       381 ~l~v~~~~~~  390 (652)
                      .|.|.|+.++
T Consensus        92 ~l~v~~a~~~  101 (111)
T 1x4h_A           92 QLKVDLAVTR  101 (111)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999999865

>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=99.64  E-value=1.2e-16  Score=127.54  Aligned_cols=75  Identities=15%  Similarity=0.385  Sum_probs=71.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      +|||+|||+++|+++|+++|+.||+|.+|++.+|+.+++++|||||+|.+.++|++|++. ++..+.|+.|+|.++
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            599999999999999999999999999999999999999999999999999999999994 888999999999874

>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=99.64  E-value=3e-16  Score=139.15  Aligned_cols=83  Identities=25%  Similarity=0.348  Sum_probs=77.9

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..|+|+.|.|.|
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            4467899999999999999999999999999999999885 689999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            9865

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.2e-16  Score=134.47  Aligned_cols=82  Identities=26%  Similarity=0.422  Sum_probs=77.1

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            456899999999999999999999999999999999886 5889999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      +.+
T Consensus        91 ~~~   93 (103)
T 2dnm_A           91 RYG   93 (103)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            854

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=4.8e-16  Score=129.14  Aligned_cols=80  Identities=18%  Similarity=0.267  Sum_probs=76.1

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.| .|.+|+|+.+.+|+++|||||+|.+.++|.+|+. |||..|+|+.|.|.++.
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEES
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECC
Confidence            356789999999999999999999999 9999999999899999999999999999999999 99999999999999987


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        86 ~~   87 (91)
T 2dgw_A           86 SG   87 (91)
T ss_dssp             SC
T ss_pred             cC
Confidence            65

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=6.3e-16  Score=128.13  Aligned_cols=81  Identities=30%  Similarity=0.462  Sum_probs=74.1

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .......++|||+|||+++|+++|+++|+.||.|.+|++.++        ||||+|.+.++|++|++.||+..|.|+.|+
T Consensus         3 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   74 (90)
T 2dnp_A            3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRIN   74 (90)
T ss_dssp             CCSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            344567899999999999999999999999999999999854        999999999999999999999999999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|++....
T Consensus        75 v~~a~~~~~   83 (90)
T 2dnp_A           75 VELSTKGQK   83 (90)
T ss_dssp             EEESCCCCC
T ss_pred             EEECCCCCC
Confidence            999987643

>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=99.64  E-value=4.4e-16  Score=132.87  Aligned_cols=82  Identities=27%  Similarity=0.449  Sum_probs=76.2

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC--CCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS--GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~--g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ....++|||+|||.++++++|+++|+.|| |.+|+|+.+..  |+++|||||+|.+.++|.+|+ .||+..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            44568999999999999999999999999 99999998864  899999999999999999999 899999999999999


Q ss_pred             ecccHH
Q 006282          386 VAQRKE  391 (652)
Q Consensus       386 ~~~~~~  391 (652)
                      ++..+.
T Consensus        90 ~a~~~~   95 (104)
T 1wi8_A           90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            998653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=3.6e-16  Score=132.14  Aligned_cols=82  Identities=24%  Similarity=0.429  Sum_probs=76.7

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCee-EEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee----E
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTIT-SCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP----L  382 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~-~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~----l  382 (652)
                      ...++|||+|||.++++++|+++|+.||.|. +|+|+++. +|+++|||||+|.+.++|.+|++.|||..+.|+.    |
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            4568999999999999999999999999999 99999885 7899999999999999999999999999999999    9


Q ss_pred             EEEecccH
Q 006282          383 YVAVAQRK  390 (652)
Q Consensus       383 ~v~~~~~~  390 (652)
                      .|.|+...
T Consensus        87 ~v~~a~~~   94 (99)
T 2div_A           87 KLNYATYS   94 (99)
T ss_dssp             CEEETTCC
T ss_pred             EEeecCCC
Confidence            99998743

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.8e-16  Score=126.04  Aligned_cols=78  Identities=23%  Similarity=0.415  Sum_probs=71.8

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc-CCcccCCceeE
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL-NFTPLNNKSIR  102 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l-n~~~i~G~~i~  102 (652)
                      ......++|||+|||.++|+++|+++|++||.|.+|++.++      +|||||+|.+.++|++|++.| |+..+.|++|+
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            34456899999999999999999999999999999999874      589999999999999999999 99999999999


Q ss_pred             eeccc
Q 006282          103 IMYSH  107 (652)
Q Consensus       103 i~~s~  107 (652)
                      |.|++
T Consensus        81 v~~ak   85 (85)
T 2ytc_A           81 VKWGR   85 (85)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99874

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.64  E-value=1.8e-16  Score=135.98  Aligned_cols=84  Identities=10%  Similarity=0.114  Sum_probs=77.7

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCc
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ---VLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNK   99 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~---V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~   99 (652)
                      .......++|||+|||+++|+++|+++|+.||.   |.+|+|++|+. ++++|||||+|.+.++|++|++ +|+..+.|+
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr   82 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQR   82 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSS
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCe
Confidence            344567899999999999999999999999988   99999999988 9999999999999999999999 999999999


Q ss_pred             eeEeecccC
Q 006282          100 SIRIMYSHR  108 (652)
Q Consensus       100 ~i~i~~s~~  108 (652)
                      .|+|.++..
T Consensus        83 ~i~V~~a~~   91 (107)
T 2lmi_A           83 YVEVYEINN   91 (107)
T ss_dssp             CCCCEECCH
T ss_pred             EEEEEECCH
Confidence            999998764

>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=99.64  E-value=1.6e-16  Score=131.02  Aligned_cols=81  Identities=25%  Similarity=0.443  Sum_probs=74.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC--CCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS--GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~--g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+++++.+..  ++++|||||+|.+.++|.+|+..|||..++|+.|.|.++
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            357899999999999999999999999999999988763  338999999999999999999999999999999999998


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.64  E-value=7.4e-16  Score=132.66  Aligned_cols=83  Identities=23%  Similarity=0.479  Sum_probs=76.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+++++      +|||||+|.+.++|++|++.||+..|.|+.|+|.|
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            446789999999999999999999999999999999886      58999999999999999999999999999999999


Q ss_pred             ccCCccccc
Q 006282          106 SHRDPSIRK  114 (652)
Q Consensus       106 s~~~~~~~~  114 (652)
                      +...+....
T Consensus        96 a~~~~~~~~  104 (109)
T 1x4g_A           96 GKESPDMTS  104 (109)
T ss_dssp             CCCCCSSCC
T ss_pred             cCCCCCCCC
Confidence            988765543

>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=99.64  E-value=7.1e-16  Score=126.92  Aligned_cols=79  Identities=22%  Similarity=0.464  Sum_probs=73.1

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|++||.|.+|+++.+. +|+++|||||+|.+.++|.+|++ +++..++|+.|.|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            3456799999999999999999999999999999999885 69999999999999999999996 688899999999987


Q ss_pred             c
Q 006282          387 A  387 (652)
Q Consensus       387 ~  387 (652)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.64  E-value=9.2e-16  Score=129.57  Aligned_cols=82  Identities=24%  Similarity=0.431  Sum_probs=75.0

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....+.++|||+|||+++|+++|+++|+.||+|.+|++.++      +|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   83 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEE
Confidence            34556789999999999999999999999999999999854      589999999999999999999999999999999


Q ss_pred             ecccCCcc
Q 006282          104 MYSHRDPS  111 (652)
Q Consensus       104 ~~s~~~~~  111 (652)
                      .|+.....
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpj_A           84 RFACHSAS   91 (99)
T ss_dssp             EESSCCSC
T ss_pred             EEcCCCCC
Confidence            99987654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=1.2e-16  Score=135.68  Aligned_cols=84  Identities=19%  Similarity=0.271  Sum_probs=77.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      .....++|||+|||+++|+++|+++|+.||.|.+ ++++|..+++++|||||+|.+.++|++|++ ||+..|.|+.|+|.
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            3446789999999999999999999999999988 778888889999999999999999999999 99999999999999


Q ss_pred             cccCCc
Q 006282          105 YSHRDP  110 (652)
Q Consensus       105 ~s~~~~  110 (652)
                      |+....
T Consensus        91 ~a~~~~   96 (101)
T 1fj7_A           91 KPKGRD   96 (101)
T ss_dssp             CCSCCC
T ss_pred             EcCCCC
Confidence            987654

>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=99.64  E-value=3.7e-16  Score=133.86  Aligned_cols=83  Identities=28%  Similarity=0.586  Sum_probs=77.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEe---cCeeEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI---VSKPLY  383 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~---~g~~l~  383 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..+   .|+.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            3456789999999999999999999999999999999886 589999999999999999999999999988   899999


Q ss_pred             EEecccH
Q 006282          384 VAVAQRK  390 (652)
Q Consensus       384 v~~~~~~  390 (652)
                      |.++..+
T Consensus        90 v~~a~~~   96 (106)
T 2dgp_A           90 VKPADSE   96 (106)
T ss_dssp             EEECCCC
T ss_pred             EEECCcc
Confidence            9999865

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.64  E-value=1.2e-16  Score=135.59  Aligned_cols=78  Identities=21%  Similarity=0.393  Sum_probs=72.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ....+++|||+|||.++|+++|+++|+.||.|.+|++.      +++|||||+|.+.++|++|++.||+..|+|+.|+|.
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34457899999999999999999999999999999997      456899999999999999999999999999999999


Q ss_pred             cccC
Q 006282          105 YSHR  108 (652)
Q Consensus       105 ~s~~  108 (652)
                      |++.
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            9864

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.63  E-value=2.4e-16  Score=125.84  Aligned_cols=74  Identities=22%  Similarity=0.384  Sum_probs=70.6

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      +|||+|||.++++++|+++|+.||.|.+++++.+. +|+++|||||+|.+.++|.+|++ +||..++|+.|.|.+|
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            48999999999999999999999999999999886 78999999999999999999998 9999999999999875

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=4.7e-16  Score=134.31  Aligned_cols=83  Identities=22%  Similarity=0.359  Sum_probs=76.0

Q ss_pred             ccccceeeecCCCCCCCHHHHH---HHhhhcCCeeEEEEecCCC----CCCccEEEEEeCCHHHHHHHHHHhcCcEecCe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLK---ELFSEFGTITSCKVMRDPS----GISKGSGFVAFSTPEEASRALAEMNGKMIVSK  380 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~---~~F~~fG~I~~v~i~~~~~----g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~  380 (652)
                      ....++|||+|||+++++++|+   ++|++||.|.+|+|+.+..    ++++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456789999999999999999   9999999999999998752    35679999999999999999999999999999


Q ss_pred             eEEEEecccH
Q 006282          381 PLYVAVAQRK  390 (652)
Q Consensus       381 ~l~v~~~~~~  390 (652)
                      .|.|.|+..+
T Consensus        92 ~l~V~~a~~k  101 (111)
T 2cpi_A           92 TLKASLGTTK  101 (111)
T ss_dssp             EEEEESCCCC
T ss_pred             EEEEEecccc
Confidence            9999999865

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.63  E-value=4.7e-16  Score=136.93  Aligned_cols=85  Identities=22%  Similarity=0.317  Sum_probs=76.4

Q ss_pred             ccccceeeecCCCCCCCHHHHH----HHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  383 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~----~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~  383 (652)
                      ..++++|||+||++.+++++|+    ++|++||.|.+|.+..  +|+++|||||+|.+.++|.+|+..|||..|.|++|.
T Consensus        26 ~~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           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            3457889999999999999876    6999999999998864  578999999999999999999999999999999999


Q ss_pred             EEecccHHHHH
Q 006282          384 VAVAQRKEERR  394 (652)
Q Consensus       384 v~~~~~~~~r~  394 (652)
                      |.|+..+....
T Consensus       104 V~~a~~~~~~~  114 (127)
T 2a3j_A          104 ITFSETPQSQV  114 (127)
T ss_dssp             EEECCCCCHHH
T ss_pred             EEEccCcchhc
Confidence            99999876554

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.63  E-value=1.9e-16  Score=134.07  Aligned_cols=81  Identities=25%  Similarity=0.438  Sum_probs=73.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC--CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~--~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ....++|||+|||.++++++|+++|+.|| |.+|+|+.+.  +|+++|||||+|.+.++|.+|+ .|||..|+|+.|.|.
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            34568999999999999999999999999 9999999885  7999999999999999999999 899999999999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      ++..+
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            99864

>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=99.63  E-value=2.5e-16  Score=137.03  Aligned_cols=87  Identities=22%  Similarity=0.265  Sum_probs=75.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...++++|||+|||+++|+++|+++|+.||.|.++.+..+..+++++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34568999999999999999999999999999544443333478999999999999999999999999999999999999


Q ss_pred             cccCCcc
Q 006282          105 YSHRDPS  111 (652)
Q Consensus       105 ~s~~~~~  111 (652)
                      |+.....
T Consensus       101 ~a~~~~~  107 (115)
T 2cpx_A          101 FGKNKKQ  107 (115)
T ss_dssp             ECCCCSC
T ss_pred             EccCCCC
Confidence            9987643

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=3.2e-16  Score=133.88  Aligned_cols=81  Identities=15%  Similarity=0.191  Sum_probs=72.3

Q ss_pred             CCCCccEEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC--cccCCcee
Q 006282           25 NQFLTTSLYVGDLDFN-VTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF--TPLNNKSI  101 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~-vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~--~~i~G~~i  101 (652)
                      ...++++|||+|||++ +||++|+++|++||.|.+|+|.+      ++|||||+|.+.++|++|++.||+  ..|.|++|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3567899999999998 99999999999999999999974      458999999999999999998864  46999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|++....
T Consensus        95 ~V~~a~~~~~  104 (112)
T 1x4f_A           95 KVDLSEKYKK  104 (112)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEECccccc
Confidence            9999986543

>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=99.63  E-value=5.7e-16  Score=151.55  Aligned_cols=81  Identities=20%  Similarity=0.401  Sum_probs=77.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G--~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++|||+||++++||++|+++|+.||  .|.+|+|++|+.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.|
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            567899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.3e-15  Score=128.05  Aligned_cols=82  Identities=21%  Similarity=0.363  Sum_probs=73.6

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ......+++|||+|||+++|+++|+++|+.||.|. +++..+    +++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus        13 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (97)
T 2e5j_A           13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR   87 (97)
T ss_dssp             CSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            34455689999999999999999999999999996 677654    6779999999999999999999999999999999


Q ss_pred             eecccCC
Q 006282          103 IMYSHRD  109 (652)
Q Consensus       103 i~~s~~~  109 (652)
                      |.|+...
T Consensus        88 V~~a~~~   94 (97)
T 2e5j_A           88 VALARQQ   94 (97)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9998764

>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=99.63  E-value=4.8e-16  Score=136.17  Aligned_cols=82  Identities=17%  Similarity=0.298  Sum_probs=74.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeE--EEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVL--SVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~--~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ......++|||+|||+++||++|+++|+.| .|.  +|+|++|+. ++++|||||+|.+.++|++|++. ++..|.|+.|
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I  113 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYI  113 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEE
Confidence            445567899999999999999999999999 677  999999987 99999999999999999999995 6799999999


Q ss_pred             EeecccC
Q 006282          102 RIMYSHR  108 (652)
Q Consensus       102 ~i~~s~~  108 (652)
                      +|.++.+
T Consensus       114 ~V~~a~~  120 (126)
T 2hgm_A          114 EVFKSSQ  120 (126)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9988754

>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=99.63  E-value=9.9e-16  Score=131.87  Aligned_cols=81  Identities=20%  Similarity=0.309  Sum_probs=74.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|++|+|..+  +.++|||||+|.+.++|.+|++.||+..|+|+.|.|.|+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            345678999999999999999999999999999999765  568999999999999999999999999999999999998


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      +.+
T Consensus        97 ~~~   99 (109)
T 1x4a_A           97 RSG   99 (109)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.63  E-value=7.8e-16  Score=131.07  Aligned_cols=81  Identities=22%  Similarity=0.392  Sum_probs=75.4

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.|| |.+|+|+.+. +|+++|||||+|.+.++|.+|+ .|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34568999999999999999999999996 9999999886 6899999999999999999999 8999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        90 a~~~   93 (103)
T 2dng_A           90 AEGR   93 (103)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9864

>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=99.63  E-value=3.3e-16  Score=131.82  Aligned_cols=84  Identities=25%  Similarity=0.485  Sum_probs=75.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLY----DLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~----~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ...++++|||+|||+++++++|+    ++|+.||.|.+|++.+   +++++|||||+|.+.++|++|++.||+..|.|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            34568999999999999999999    9999999999999874   4778899999999999999999999999999999


Q ss_pred             eEeecccCCcc
Q 006282          101 IRIMYSHRDPS  111 (652)
Q Consensus       101 i~i~~s~~~~~  111 (652)
                      |+|.|+..++.
T Consensus        81 l~v~~a~~~~~   91 (97)
T 1nu4_A           81 MRIQYAKTDSD   91 (97)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEccCCCc
Confidence            99999987643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=126.32  Aligned_cols=81  Identities=23%  Similarity=0.390  Sum_probs=74.1

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .....+.++|||+|||+++|+++|+++|+.||.|.+|++.++        ||||+|.+.++|++|++.||+..|.|+.|+
T Consensus         4 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   75 (92)
T 2dgt_A            4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMH   75 (92)
T ss_dssp             SCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            345667899999999999999999999999999999999753        999999999999999999999999999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus        76 V~~a~~~~~   84 (92)
T 2dgt_A           76 VQLSTSRLR   84 (92)
T ss_dssp             EEESSCCCS
T ss_pred             EEEccCCCC
Confidence            999986543

>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=99.62  E-value=6.3e-16  Score=136.89  Aligned_cols=83  Identities=24%  Similarity=0.479  Sum_probs=78.1

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...+++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            4457899999999999999999999999999999999885 889999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        99 a~~~  102 (126)
T 3ex7_B           99 CFVR  102 (126)
T ss_dssp             SEES
T ss_pred             ecCC
Confidence            9865

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=8.8e-16  Score=133.79  Aligned_cols=82  Identities=27%  Similarity=0.399  Sum_probs=76.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +++++|||||+|.+.++|.+|++.+|+ .|.|+.|.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            4467899999999999999999999999999999999885 689999999999999999999999998 89999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        93 a~~~   96 (116)
T 2cqd_A           93 AYLG   96 (116)
T ss_dssp             STTT
T ss_pred             cccC
Confidence            8744

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.62  E-value=9.4e-16  Score=131.55  Aligned_cols=80  Identities=21%  Similarity=0.502  Sum_probs=72.5

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ......+++|||+|||+++|+++|+++|+.||.|.+|+++        +|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3445678999999999999999999999999999999998        48999999999999999999999999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.|+...+
T Consensus        97 V~~a~~~~  104 (108)
T 2jvo_A           97 VVYSKLPA  104 (108)
T ss_dssp             EESCSCCC
T ss_pred             EEEecCCC
Confidence            99988654

>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=99.62  E-value=7e-16  Score=133.98  Aligned_cols=82  Identities=33%  Similarity=0.631  Sum_probs=76.8

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEe--------cCe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--------VSK  380 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~--------~g~  380 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+.+.+|.++|||||+|.+.++|.+|+..|||..+        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            456789999999999999999999999999999999998999999999999999999999999999999        578


Q ss_pred             eEEEEecccH
Q 006282          381 PLYVAVAQRK  390 (652)
Q Consensus       381 ~l~v~~~~~~  390 (652)
                      +|.|.|+.++
T Consensus       103 ~l~v~~a~p~  112 (114)
T 1x5o_A          103 PLLCKFSGPS  112 (114)
T ss_dssp             CBEEEECCCS
T ss_pred             ceeEEccCCC
Confidence            8999998753

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.62  E-value=2.4e-16  Score=135.17  Aligned_cols=85  Identities=12%  Similarity=0.147  Sum_probs=79.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCC---eeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGT---ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~---I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|+.+..|+++|||||+|.+.++|.+|+. +|+..++|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            345788999999999999999999999998   999999999889999999999999999999999 9999999999999


Q ss_pred             EecccHHHH
Q 006282          385 AVAQRKEER  393 (652)
Q Consensus       385 ~~~~~~~~r  393 (652)
                      .++.+++..
T Consensus        87 ~~a~~~~~~   95 (107)
T 2lmi_A           87 YEINNEDVD   95 (107)
T ss_dssp             EECCHHHHH
T ss_pred             EECCHHHHH
Confidence            999887654

>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=99.62  E-value=6.5e-16  Score=131.10  Aligned_cols=77  Identities=19%  Similarity=0.264  Sum_probs=70.6

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCc--EecCeeEEEEe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK--MIVSKPLYVAV  386 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~--~~~g~~l~v~~  386 (652)
                      .+.++|||+|||+++++++|+++|++||.|++|+++++     ||||||+|.+.++|.+|++.|++.  .+.|++|+|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~   87 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            45678999999999999999999999999999999875     899999999999999999998765  58999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ++.+
T Consensus        88 a~~~   91 (104)
T 1wex_A           88 STSK   91 (104)
T ss_dssp             CSSS
T ss_pred             ccCc
Confidence            9865

>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=99.62  E-value=1.4e-15  Score=127.89  Aligned_cols=80  Identities=19%  Similarity=0.478  Sum_probs=71.1

Q ss_pred             CCCCCCCccEEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           22 ASGNQFLTTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~-~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ......++++|||+|||+ ++++++|+++|+.||.|.+|++.        +|||||+|.+.++|++|++.||+..+.|+.
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             ----CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEE
T ss_pred             ccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            334556789999999998 99999999999999999999983        589999999999999999999999999999


Q ss_pred             eEeecccCC
Q 006282          101 IRIMYSHRD  109 (652)
Q Consensus       101 i~i~~s~~~  109 (652)
                      |+|.|++..
T Consensus        87 l~V~~a~~~   95 (97)
T 2xnq_A           87 LILEVSSSN   95 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEecCCC
Confidence            999998754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.62  E-value=8.2e-16  Score=131.83  Aligned_cols=78  Identities=22%  Similarity=0.219  Sum_probs=71.8

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcC-CeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG-~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||+++++++|+++|+.|| .|..++|..+   .++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            457899999999999999999999999 9999998643   479999999999999999999999999999999999997


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ..
T Consensus       104 ~~  105 (111)
T 2jvr_A          104 NP  105 (111)
T ss_dssp             C-
T ss_pred             CC
Confidence            55

>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=99.62  E-value=4.9e-16  Score=132.51  Aligned_cols=82  Identities=22%  Similarity=0.288  Sum_probs=76.2

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeE-EEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~-v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||+++++++|+++|+.||.|.+ |+|+.+.+|+++|||||+|.+.++|.+|+.. |+..++|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            45678999999999999999999999999998 8898888999999999999999999999997 999999999999988


Q ss_pred             ccHH
Q 006282          388 QRKE  391 (652)
Q Consensus       388 ~~~~  391 (652)
                      .+++
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.2e-16  Score=129.41  Aligned_cols=79  Identities=27%  Similarity=0.442  Sum_probs=74.1

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .+++|||+|||.++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..+.|+.|++.+.+
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            56789999999999999999999999999999999884 78999999999999999999999999999999999887764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=3.9e-16  Score=136.50  Aligned_cols=87  Identities=17%  Similarity=0.243  Sum_probs=79.1

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCe----eEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTI----TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I----~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ...++|||+|||+++|+++|+++|+.||.|    .+|+|+.+.+|+++|||||+|.+.++|.+|++. |+..++|+.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            356789999999999999999999999875    689999998999999999999999999999995 999999999999


Q ss_pred             EecccHHHHHHH
Q 006282          385 AVAQRKEERRAR  396 (652)
Q Consensus       385 ~~~~~~~~r~~~  396 (652)
                      ..+..++.+...
T Consensus       100 ~~a~~~e~~~~~  111 (123)
T 2dha_A          100 FRSTAAEVQQVL  111 (123)
T ss_dssp             EEECHHHHHHHH
T ss_pred             EECCHHHHHHHH
Confidence            999887766543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.62  E-value=2.2e-16  Score=128.05  Aligned_cols=73  Identities=22%  Similarity=0.352  Sum_probs=67.9

Q ss_pred             ceeeecCCCCCC------CHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCe-eEEE
Q 006282          312 LNLYIKNLGDSI------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK-PLYV  384 (652)
Q Consensus       312 ~~l~V~nlp~~~------te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~-~l~v  384 (652)
                      ++|||+|||..+      ++++|+++|++||.|.+++++ ..+|+++|||||+|.+.++|.+|+..|||..++|+ +|.|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            689999999999      679999999999999999988 46789999999999999999999999999999999 8876


Q ss_pred             E
Q 006282          385 A  385 (652)
Q Consensus       385 ~  385 (652)
                      +
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.62  E-value=4.9e-16  Score=132.73  Aligned_cols=81  Identities=20%  Similarity=0.272  Sum_probs=74.7

Q ss_pred             cccceeeecCCCCCC------CHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCe-e
Q 006282          309 FQGLNLYIKNLGDSI------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK-P  381 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~------te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~-~  381 (652)
                      ...++|||+|||..+      ++++|+++|++||.|.+|+|+ ..+|+++|||||+|.+.++|.+|+..|||..++|+ .
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            346789999999999      789999999999999999998 56789999999999999999999999999999998 9


Q ss_pred             EEEEecccH
Q 006282          382 LYVAVAQRK  390 (652)
Q Consensus       382 l~v~~~~~~  390 (652)
                      |.|.++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999998743

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.62  E-value=7.3e-16  Score=138.98  Aligned_cols=83  Identities=34%  Similarity=0.512  Sum_probs=77.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|++|+|+.+. +|+++|||||+|.+.++|.+|++.|||..|+|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3456789999999999999999999999999999999885 688999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus       119 a~~~  122 (139)
T 1u6f_A          119 AASG  122 (139)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9865

>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=99.62  E-value=4.2e-16  Score=131.41  Aligned_cols=81  Identities=17%  Similarity=0.340  Sum_probs=74.6

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+++++.+ .+|+++|||||+|.+.++|.+|++.|||..|+|+.|.|.++
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            34578999999999999999999999999998877765 57889999999999999999999999999999999999998


Q ss_pred             cc
Q 006282          388 QR  389 (652)
Q Consensus       388 ~~  389 (652)
                      ..
T Consensus        93 ~~   94 (98)
T 2cqp_A           93 SG   94 (98)
T ss_dssp             SC
T ss_pred             CC
Confidence            74

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.62  E-value=2e-16  Score=141.04  Aligned_cols=81  Identities=20%  Similarity=0.343  Sum_probs=76.4

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeE--EEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCc----EecCee
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--CKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK----MIVSKP  381 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~--v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~----~~~g~~  381 (652)
                      ...++|||+|||+++++++|+++|++||.|..  |+|++|. +|+++|||||+|.+. +|.+|+..|||.    .++|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45678999999999999999999999999977  9999987 899999999999999 999999999999    999999


Q ss_pred             EEEEecccH
Q 006282          382 LYVAVAQRK  390 (652)
Q Consensus       382 l~v~~~~~~  390 (652)
                      |.|.++..+
T Consensus       100 l~V~~a~~~  108 (131)
T 2m2b_A          100 INVEFAKGS  108 (131)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEECCCC
Confidence            999999864

>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=99.62  E-value=4.5e-16  Score=130.40  Aligned_cols=80  Identities=18%  Similarity=0.348  Sum_probs=73.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+ .+|+++|||||+|.+.++|.+|++.||+..|+|+.|.|.++.
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            4578999999999999999999999999998887765 478899999999999999999999999999999999999876


Q ss_pred             c
Q 006282          389 R  389 (652)
Q Consensus       389 ~  389 (652)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.62  E-value=4e-16  Score=132.35  Aligned_cols=80  Identities=18%  Similarity=0.245  Sum_probs=73.6

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||+++++++|+++|+.|| +.+|+|+.|.+|+++|||||+|.+.++|.+|++ +|+..|+++.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            4567899999999999999999999999 559999999999999999999999999999995 89999999999999876


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ..
T Consensus        91 ~~   92 (102)
T 1wez_A           91 TA   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.61  E-value=1.3e-15  Score=130.96  Aligned_cols=82  Identities=33%  Similarity=0.539  Sum_probs=73.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+++. +|+++|||||+|.+.++|.+|+..+ +..++|+.|.|.++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            356789999999999999999999999999999999885 6899999999999999999999976 59999999999999


Q ss_pred             ccHH
Q 006282          388 QRKE  391 (652)
Q Consensus       388 ~~~~  391 (652)
                      ..+.
T Consensus       102 ~~~~  105 (109)
T 2rs2_A          102 FPRR  105 (109)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=6.7e-16  Score=131.97  Aligned_cols=82  Identities=24%  Similarity=0.433  Sum_probs=76.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|+.. |+..|+|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            3456899999999999999999999999999999999884 789999999999999999999998 99999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +.++
T Consensus        92 a~~~   95 (105)
T 2dh8_A           92 CTPR   95 (105)
T ss_dssp             SCCS
T ss_pred             ccCC
Confidence            8865

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.1e-15  Score=133.61  Aligned_cols=80  Identities=19%  Similarity=0.203  Sum_probs=73.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCe----EEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQV----LSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V----~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      .....+|||+|||+++||++|+++|+.||+|    .+|+|++| .+++++|||||+|.+.++|++|++. |+..|.|+.|
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 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            3567899999999999999999999999986    69999999 5899999999999999999999996 9999999999


Q ss_pred             Eeeccc
Q 006282          102 RIMYSH  107 (652)
Q Consensus       102 ~i~~s~  107 (652)
                      +|..+.
T Consensus        98 ~V~~a~  103 (123)
T 2dha_A           98 ELFRST  103 (123)
T ss_dssp             CCEEEC
T ss_pred             EEEECC
Confidence            987654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=4.6e-16  Score=124.79  Aligned_cols=75  Identities=35%  Similarity=0.578  Sum_probs=71.5

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ++|||+|||.++++++|+++|++||.|.+++++.+. +|+++|||||+|.+.++|.+|++.++ ..++|+.|.|.++
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            479999999999999999999999999999999885 68999999999999999999999999 9999999999986

>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=99.61  E-value=1.4e-16  Score=170.66  Aligned_cols=82  Identities=20%  Similarity=0.370  Sum_probs=77.2

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+||+..+|+++|+++|+.||.|+.|+|+.+. +|.++|||||+|.+.++|.+||..|||..|+|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            345799999999999999999999999999999999884 8899999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            854

>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=99.61  E-value=4e-16  Score=133.27  Aligned_cols=78  Identities=21%  Similarity=0.283  Sum_probs=70.6

Q ss_pred             ccccceeeecCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcC--cEecCeeEEE
Q 006282          308 KFQGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYV  384 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~-~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng--~~~~g~~l~v  384 (652)
                      ..++++|||+|||++ +++++|+++|++||.|++|+|++     +||||||+|.+.++|.+|++.||+  ..|.|++|+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345789999999998 99999999999999999999975     489999999999999999998864  5699999999


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .|++.+
T Consensus        97 ~~a~~~  102 (112)
T 1x4f_A           97 DLSEKY  102 (112)
T ss_dssp             EEECSC
T ss_pred             EECccc
Confidence            999765

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.2e-15  Score=129.46  Aligned_cols=80  Identities=29%  Similarity=0.419  Sum_probs=73.9

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|   +++.+.+|+++|||||+|.+.++|.+|+..||+..|.|+.|.|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            3457899999999999999999999999977   6777778999999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus        89 ~~~   91 (101)
T 2fc9_A           89 GPR   91 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.61  E-value=1.3e-15  Score=142.76  Aligned_cols=84  Identities=29%  Similarity=0.440  Sum_probs=79.5

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...++++|||+|||+++|+++|+++|+.||+|.+|+|+.|. +++++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567999999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             cccCC
Q 006282          105 YSHRD  109 (652)
Q Consensus       105 ~s~~~  109 (652)
                      |+...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            98764

>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=99.61  E-value=1.6e-15  Score=131.91  Aligned_cols=81  Identities=22%  Similarity=0.368  Sum_probs=75.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..+++|||+|||.++++++|+++|+.||.|.+|+++.+  +.++|||||+|.+.++|.+|+..|||..++|+.|.|.|+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            35678999999999999999999999999999999976  5679999999999999999999999999999999999998


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      .+.
T Consensus        84 ~~~   86 (115)
T 3lqv_A           84 ANR   86 (115)
T ss_dssp             HHH
T ss_pred             CCh
Confidence            643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.40  E-value=4.6e-17  Score=141.97  Aligned_cols=87  Identities=22%  Similarity=0.382  Sum_probs=81.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~--------i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      ..++++|||+|||+++|+++|+++|+.||.|.+        |+|++|+.+++++|||||+|.+.++|++|++.||+..|.
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            346789999999999999999999999999999        999999999999999999999999999999999999999


Q ss_pred             CceeEeecccCCccc
Q 006282           98 NKSIRIMYSHRDPSI  112 (652)
Q Consensus        98 G~~i~i~~s~~~~~~  112 (652)
                      |++|+|.|+...+..
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=1.5e-15  Score=128.70  Aligned_cols=77  Identities=22%  Similarity=0.324  Sum_probs=71.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|.++++..     ++|||||+|.+.++|.+|+..|||..++|+.|.|.|++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            3468999999999999999999999999999999983     58999999999999999999999999999999999987


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.61  E-value=7.9e-16  Score=130.77  Aligned_cols=81  Identities=22%  Similarity=0.524  Sum_probs=75.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ...+++|||+|||+++|+++|+++|+.||.|.+|++.+|. +++++|||||+|.+.++|++|++  ++..++|+.|+|.+
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            3457899999999999999999999999999999999998 89999999999999999999999  88899999999998


Q ss_pred             ccCC
Q 006282          106 SHRD  109 (652)
Q Consensus       106 s~~~  109 (652)
                      +...
T Consensus        83 a~~~   86 (102)
T 2xs2_A           83 AIRK   86 (102)
T ss_dssp             EEEC
T ss_pred             CCcC
Confidence            8754

>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=99.61  E-value=3e-16  Score=130.07  Aligned_cols=79  Identities=33%  Similarity=0.528  Sum_probs=72.1

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ++|||+|||.++++++|+++|+.||.|.+++++.+. +|+++|||||+|.+.+ |.+|+..|||..++|+.|.|.++..+
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            479999999999999999999999999999999886 5899999999999999 99999999999999999999999865


Q ss_pred             H
Q 006282          391 E  391 (652)
Q Consensus       391 ~  391 (652)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.60  E-value=4.3e-15  Score=134.95  Aligned_cols=82  Identities=26%  Similarity=0.293  Sum_probs=72.9

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC--ceeE
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN--KSIR  102 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G--~~i~  102 (652)
                      ++....+|||+||++++||++|+++|++||.|.+|+|..+    +++|||||+|.+.++|++|++.||+..|.|  ++|+
T Consensus        42 ~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             CCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             CCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            3444577999999999999999999999999999999754    356899999999999999999999999965  9999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.|++...
T Consensus       118 V~~Ak~~~  125 (164)
T 1sjr_A          118 IDFSKLTS  125 (164)
T ss_dssp             EEECSSSS
T ss_pred             EEEecCCc
Confidence            99998653

>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=2.9e-15  Score=127.47  Aligned_cols=79  Identities=23%  Similarity=0.412  Sum_probs=72.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...+.++|||+|||+++|+++|+++|+.||.|.+|++.+        |||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            344679999999999999999999999999999999874        499999999999999999999999999999999


Q ss_pred             cccCCcc
Q 006282          105 YSHRDPS  111 (652)
Q Consensus       105 ~s~~~~~  111 (652)
                      |+.....
T Consensus        79 ~a~~~~~   85 (103)
T 2dgu_A           79 FAKPPDQ   85 (103)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCcc
Confidence            9986544

>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=99.60  E-value=3.8e-16  Score=139.57  Aligned_cols=83  Identities=16%  Similarity=0.288  Sum_probs=74.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      .....++|||+|||+++||++|+++|+.|| |.+|+|++|+. ++++|||||+|.+.++|++|| .+|+..|.|+.|+|.
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence            445678999999999999999999999999 66999999976 999999999999999999999 689999999999999


Q ss_pred             cccCCc
Q 006282          105 YSHRDP  110 (652)
Q Consensus       105 ~s~~~~  110 (652)
                      ++....
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            887654

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.60  E-value=1.6e-15  Score=127.33  Aligned_cols=79  Identities=20%  Similarity=0.454  Sum_probs=71.0

Q ss_pred             CCCCccEEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           25 NQFLTTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~-~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ...++++|||+|||+ ++|+++|+++|+.||+|.+|++.        +|||||+|.+.++|++|++.||+..+.|++|+|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345689999999998 99999999999999999999984        489999999999999999999999999999999


Q ss_pred             ecccCCcc
Q 006282          104 MYSHRDPS  111 (652)
Q Consensus       104 ~~s~~~~~  111 (652)
                      .|+.....
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99876543

>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=2.5e-15  Score=122.98  Aligned_cols=76  Identities=26%  Similarity=0.447  Sum_probs=71.2

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh-cCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l-ng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|++||.|.+++++++     +|||||+|.+.++|.+|+..| ||..++|+.|.|.|
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            345678999999999999999999999999999999975     889999999999999999999 99999999999999


Q ss_pred             cc
Q 006282          387 AQ  388 (652)
Q Consensus       387 ~~  388 (652)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.8e-15  Score=131.83  Aligned_cols=80  Identities=34%  Similarity=0.510  Sum_probs=75.3

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|+.. |+..|+|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            35789999999999999999999999999999999885 689999999999999999999997 9999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus       105 ~~  106 (116)
T 1x4b_A          105 AR  106 (116)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.60  E-value=1.6e-15  Score=133.80  Aligned_cols=78  Identities=21%  Similarity=0.378  Sum_probs=74.0

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .++|||+|||.++++++|+++|+.||.|.+|+|+.+ .+|.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.+++.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            468999999999999999999999999999999988 48899999999999999999999 7999999999999999874

>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=99.60  E-value=3.2e-15  Score=128.89  Aligned_cols=79  Identities=24%  Similarity=0.396  Sum_probs=72.1

Q ss_pred             CCCCccEEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           25 NQFLTTSLYVGDLDFN-VTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~-vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      +...+++|||+|||++ +|+++|+++|+.||+|.+|++        ++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   94 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI   94 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            4445689999999999 999999999999999999998        4589999999999999999999999999999999


Q ss_pred             ecccCCcc
Q 006282          104 MYSHRDPS  111 (652)
Q Consensus       104 ~~s~~~~~  111 (652)
                      .|+.....
T Consensus        95 ~~a~~~~~  102 (110)
T 1wf1_A           95 NMAGEPKP  102 (110)
T ss_dssp             EESCCCCS
T ss_pred             EECCCCCC
Confidence            99985443

>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=99.60  E-value=3.1e-15  Score=128.51  Aligned_cols=75  Identities=24%  Similarity=0.325  Sum_probs=71.4

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC-----eeEEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS-----KPLYV  384 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g-----~~l~v  384 (652)
                      ..++|||+|||+++++++|+++|+.||.|++|+|+.+      |||||+|.+.++|.+|++.|||..|.|     +.|.|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEE
Confidence            4678999999999999999999999999999999987      799999999999999999999999999     99999


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .++.++
T Consensus        88 ~~a~~~   93 (108)
T 1x4c_A           88 KVDGPR   93 (108)
T ss_dssp             EESSCC
T ss_pred             EeCCCC
Confidence            999864

>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=99.60  E-value=9.5e-16  Score=128.97  Aligned_cols=83  Identities=33%  Similarity=0.503  Sum_probs=76.2

Q ss_pred             cccceeeecCCCCCCCHHHHH----HHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~----~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ..+++|||+|||.++++++|+    ++|+.||.|.+|+++.  +|.++|||||+|.+.++|.+|+..|||..++|+.|.|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            356799999999999999999    9999999999999885  4678999999999999999999999999999999999


Q ss_pred             EecccHHHH
Q 006282          385 AVAQRKEER  393 (652)
Q Consensus       385 ~~~~~~~~r  393 (652)
                      .|+..+...
T Consensus        84 ~~a~~~~~~   92 (97)
T 1nu4_A           84 QYAKTDSDI   92 (97)
T ss_dssp             EECSSCCTH
T ss_pred             EEccCCCcc
Confidence            999876544

>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=99.60  E-value=1.5e-15  Score=130.72  Aligned_cols=82  Identities=15%  Similarity=0.174  Sum_probs=74.8

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCC-eeEEEEe-cCC-CCCCccEEEEEeCCHHHHHHHHHHhc--CcEecCeeEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGT-ITSCKVM-RDP-SGISKGSGFVAFSTPEEASRALAEMN--GKMIVSKPLY  383 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~-I~~v~i~-~~~-~g~s~g~afV~F~s~~~A~~A~~~ln--g~~~~g~~l~  383 (652)
                      ...++|||+|||.++++++|+++|+.||. |.+|+++ .+. +|.++|||||+|.+.++|.+|+..||  +..++|+.|.
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            35678999999999999999999999998 9999998 554 57899999999999999999999996  5899999999


Q ss_pred             EEecccH
Q 006282          384 VAVAQRK  390 (652)
Q Consensus       384 v~~~~~~  390 (652)
                      |.|+.++
T Consensus        86 V~~a~~~   92 (109)
T 2dis_A           86 VDWAEPE   92 (109)
T ss_dssp             EEESCSS
T ss_pred             EEEcCCC
Confidence            9999865

>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=99.60  E-value=1.1e-15  Score=131.87  Aligned_cols=77  Identities=14%  Similarity=0.223  Sum_probs=71.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++|+++|+++|++||.|.+|++.+      ++|||||+|.+.++|++|++.||+..|.|++|+|.|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3578999999999999999999999999999998864      5589999999999999999999999999999999998


Q ss_pred             cCC
Q 006282          107 HRD  109 (652)
Q Consensus       107 ~~~  109 (652)
                      ..+
T Consensus        82 ~~~   84 (111)
T 1whx_A           82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            764

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.60  E-value=2.1e-15  Score=129.39  Aligned_cols=79  Identities=25%  Similarity=0.567  Sum_probs=72.5

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      .....++|||+|||.++++++|+++|+.||.|.+|+++       +|||||+|.+.++|.+|+..|||..++|+.|.|.|
T Consensus        27 ~~~~~~~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           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34567899999999999999999999999999999998       68999999999999999999999999999999999


Q ss_pred             cccHHH
Q 006282          387 AQRKEE  392 (652)
Q Consensus       387 ~~~~~~  392 (652)
                      ++.+..
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            987643

>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=99.59  E-value=3.6e-15  Score=126.90  Aligned_cols=81  Identities=28%  Similarity=0.395  Sum_probs=74.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|+.  ++..++|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            3456789999999999999999999999999999999885 69999999999999999999998  57899999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        90 a~~~   93 (103)
T 2cqg_A           90 PNSK   93 (103)
T ss_dssp             CCTT
T ss_pred             cCCC
Confidence            9865

>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=99.59  E-value=3e-15  Score=128.79  Aligned_cols=78  Identities=27%  Similarity=0.466  Sum_probs=73.5

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||..+++++|+++|+.||.|.+|+|+.+     +|||||+|.+.++|.+|+..|||..|+|+.|.|.|+
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            345789999999999999999999999999999999987     889999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      +.+
T Consensus        97 ~~~   99 (109)
T 1x4g_A           97 KES   99 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.59  E-value=3e-15  Score=137.76  Aligned_cols=82  Identities=23%  Similarity=0.283  Sum_probs=77.1

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|++|+|+.+. ++.++|||||+|.+.++|.+|++.||+..|+|+.|.|.|+
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            356899999999999999999999999999999999886 6889999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ...
T Consensus       117 ~~~  119 (156)
T 1h2v_Z          117 AGF  119 (156)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            753

>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=99.59  E-value=2.6e-15  Score=126.30  Aligned_cols=77  Identities=21%  Similarity=0.340  Sum_probs=72.2

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec--CeeEEEEe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVAV  386 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~--g~~l~v~~  386 (652)
                      ...++|||+|||.++++++|+++|++||.|++|++..+     +|||||+|.+.++|.+|++.|||..+.  |+.|.|.|
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~   89 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEE
Confidence            35678999999999999999999999999999999865     789999999999999999999999999  99999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ++++
T Consensus        90 a~~~   93 (97)
T 1why_A           90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9865

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.3e-15  Score=134.39  Aligned_cols=85  Identities=19%  Similarity=0.362  Sum_probs=77.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEE-EEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v-~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||+++++++|+++|+.||.|.++ .+..+.+|+++|||||+|.+.++|.+|+. |||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            356899999999999999999999999999984 55566789999999999999999999999 9999999999999999


Q ss_pred             ccHHHHH
Q 006282          388 QRKEERR  394 (652)
Q Consensus       388 ~~~~~r~  394 (652)
                      ..++...
T Consensus       102 ~~~~~~~  108 (124)
T 1wel_A          102 TKKGMLE  108 (124)
T ss_dssp             CHHHHHH
T ss_pred             CHHHHHH
Confidence            9887544

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=3e-15  Score=123.96  Aligned_cols=75  Identities=21%  Similarity=0.459  Sum_probs=70.6

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+++       +|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   78 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK   78 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECC
Confidence            456789999999999999999999999999999997       5799999999999999999999999999999999988


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        79 ~~   80 (90)
T 2dnq_A           79 NK   80 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            55

>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=99.59  E-value=2e-15  Score=125.89  Aligned_cols=79  Identities=27%  Similarity=0.380  Sum_probs=70.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC-cccCCceeEe
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQ-VLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF-TPLNNKSIRI  103 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~-V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~-~~i~G~~i~i  103 (652)
                      ....++|||+|||+++|+++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||+ ..|.|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            346789999999999999999999999999 6666553       468999999999999999999999 9999999999


Q ss_pred             ecccCCcc
Q 006282          104 MYSHRDPS  111 (652)
Q Consensus       104 ~~s~~~~~  111 (652)
                      .|+.....
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99986543

>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=9.4e-15  Score=123.31  Aligned_cols=80  Identities=23%  Similarity=0.363  Sum_probs=72.4

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhcc--CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQV--GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~--G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ....++++|||+|||+++|+++|+++|+.|  |.|.+|++.        +|||||+|.+.++|++|++.||+..|.|+.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPI   81 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            344568999999999999999999999999  999998875        3699999999999999999999999999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+.....
T Consensus        82 ~v~~a~~~~~   91 (99)
T 2cpd_A           82 EVTLAKPVDK   91 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987543

>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=99.59  E-value=2.1e-15  Score=128.92  Aligned_cols=78  Identities=22%  Similarity=0.426  Sum_probs=70.1

Q ss_pred             ccccceeee--cCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEe-----cCe
Q 006282          308 KFQGLNLYI--KNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI-----VSK  380 (652)
Q Consensus       308 ~~~~~~l~V--~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~-----~g~  380 (652)
                      ..+.++|||  +||++++++++|+++|++||.|++|.|+.+     ||||||+|.+.++|.+|++.|||+.+     .|+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            345678999  669999999999999999999999988753     78999999999999999999999998     689


Q ss_pred             eEEEEecccH
Q 006282          381 PLYVAVAQRK  390 (652)
Q Consensus       381 ~l~v~~~~~~  390 (652)
                      +|+|.++...
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999998743

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.59  E-value=3.4e-15  Score=134.71  Aligned_cols=79  Identities=29%  Similarity=0.484  Sum_probs=74.2

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+|||.++++++|+++|+.||.|++++|+.+ .+|+++|||||+|.+.++|.+|++.|||..|+|+.|.|.||
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            35678999999999999999999999999999999988 47899999999999999999999999999999999999985

>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=99.58  E-value=6e-16  Score=165.69  Aligned_cols=151  Identities=17%  Similarity=0.341  Sum_probs=112.5

Q ss_pred             HHHHHhccCCeEEEEEEee----C-CCCCcccEE--EEEeCCHHHHHHHHhhcCCcccCCc---------------eeEe
Q 006282           46 LYDLFSQVGQVLSVRVCRD----L-STRRSLGYG--YVNYANPADAARALDVLNFTPLNNK---------------SIRI  103 (652)
Q Consensus        46 L~~~Fs~~G~V~~i~v~~d----~-~t~~s~g~A--fV~F~~~e~A~~Al~~ln~~~i~G~---------------~i~i  103 (652)
                      |.++|.++|+|..|..+..    + .+....|++  |+.|.+..++..++..++.....++               .+.+
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~~   88 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKM   88 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            7899999999998844432    2 222233444  8888877665554443332222111               1222


Q ss_pred             ecccCCcccccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCce
Q 006282          104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGML  182 (652)
Q Consensus       104 ~~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~~  182 (652)
                      .....++........+|||+||+.++++++|.++|+.||.|..|.|+.+ .+|.++|||||+|.+.++|..||+.||+..
T Consensus        89 ~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  168 (437)
T 3pgw_S           89 WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK  168 (437)
T ss_pred             cCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE
Confidence            2222333334455678999999999999999999999999999999998 588999999999999999999999999999


Q ss_pred             ecCeeeeecccccc
Q 006282          183 INDKQVFVGHFLRK  196 (652)
Q Consensus       183 l~g~~~~v~~~~~~  196 (652)
                      |.|+.|.|.+....
T Consensus       169 i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          169 IDGRRVLVDVERGR  182 (437)
T ss_pred             ECCEEEEEEEeCCC
Confidence            99999999987654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=1.7e-15  Score=128.52  Aligned_cols=75  Identities=27%  Similarity=0.553  Sum_probs=71.8

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ++|||+|||.++++++|+++|++||.|.+|+++.+    ++|||||+|.+.++|.+|++.|||..++|+.|.|.++..+
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            47999999999999999999999999999999987    7899999999999999999999999999999999999865

>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=99.58  E-value=2.4e-15  Score=127.05  Aligned_cols=77  Identities=29%  Similarity=0.439  Sum_probs=72.4

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|++.++     +|||||+|.+.++|.+|++.|||..++|+.|.|.|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   87 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcC
Confidence            45678999999999999999999999999999999865     8899999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        88 ~~   89 (99)
T 2cpj_A           88 HS   89 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.58  E-value=5.7e-15  Score=124.04  Aligned_cols=76  Identities=25%  Similarity=0.441  Sum_probs=70.9

Q ss_pred             ccccceeeecCCCC-CCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~-~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...+++|||+|||. ++++++|+++|+.||.|.++++.       +|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44678999999998 99999999999999999999983       78999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ++.+
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8754

>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=2.2e-15  Score=126.51  Aligned_cols=81  Identities=21%  Similarity=0.406  Sum_probs=73.1

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...+.++|||+|||+++|+++|+++|+.||.|..+     ..+++++|||||+|.+.++|++|++.||+..|.|+.|+|.
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            44568999999999999999999999999987665     3468899999999999999999999999999999999999


Q ss_pred             cccCCc
Q 006282          105 YSHRDP  110 (652)
Q Consensus       105 ~s~~~~  110 (652)
                      |+....
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            987653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.58  E-value=2.6e-15  Score=128.46  Aligned_cols=79  Identities=15%  Similarity=0.179  Sum_probs=71.8

Q ss_pred             ccEEEEcCC----CCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCC----HHH----HHHHHh--hcCCc
Q 006282           29 TTSLYVGDL----DFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN----PAD----AARALD--VLNFT   94 (652)
Q Consensus        29 ~~sL~V~nL----p~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~----~e~----A~~Al~--~ln~~   94 (652)
                      .+.|||+||    |++++|++|+++|+.||+|.++++..|+.|++|+|||||.|.+    +++    |.+|+.  .+|+.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            368999999    9999999999999999999999999999999999999999996    434    899988  78999


Q ss_pred             ccCCceeEeeccc
Q 006282           95 PLNNKSIRIMYSH  107 (652)
Q Consensus        95 ~i~G~~i~i~~s~  107 (652)
                      .|.|+.|+|.+..
T Consensus        82 ~I~Gr~irV~ln~   94 (136)
T 2j8a_A           82 FIMGFKFEVILNK   94 (136)
T ss_dssp             EETTEEEEEEECC
T ss_pred             eecCcEEEEEECc
Confidence            9999999998654

>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=99.58  E-value=2.4e-15  Score=129.67  Aligned_cols=76  Identities=24%  Similarity=0.304  Sum_probs=71.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||.++++++|+++|++||.|.+|+|+.     ++|||||+|.+.++|.+|+..|||..++|+.|.|.|+..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            357899999999999999999999999999999875     588999999999999999999999999999999999975


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      .
T Consensus        84 ~   84 (111)
T 1whx_A           84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=1.1e-14  Score=121.66  Aligned_cols=79  Identities=19%  Similarity=0.238  Sum_probs=71.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....++|||+|||+++|+++|+++|+.||.|.+|  ..|+.+++   ||||+|.+.++|++|++ ||+..|.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456899999999999999999999999999987  66666665   99999999999999999 999999999999998


Q ss_pred             ccCCc
Q 006282          106 SHRDP  110 (652)
Q Consensus       106 s~~~~  110 (652)
                      +....
T Consensus        79 a~~~~   83 (94)
T 2e5g_A           79 REQKE   83 (94)
T ss_dssp             SCCSC
T ss_pred             CCcCC
Confidence            87543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=1.8e-14  Score=121.05  Aligned_cols=81  Identities=20%  Similarity=0.322  Sum_probs=72.7

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....++++|||+||  ++|+++|+++|+.||+|.+|++.      +++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   81 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKV   81 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34557899999996  89999999999999999999983      56789999999999999999999999999999999


Q ss_pred             ecccCCccc
Q 006282          104 MYSHRDPSI  112 (652)
Q Consensus       104 ~~s~~~~~~  112 (652)
                      .|+...+..
T Consensus        82 ~~a~~~~~~   90 (97)
T 1x5p_A           82 NIARKQPML   90 (97)
T ss_dssp             ECCSSCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.58  E-value=4.2e-15  Score=122.51  Aligned_cols=77  Identities=16%  Similarity=0.201  Sum_probs=71.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++|+++|+++|++| .|.++++.      +++|||||+|.+.++|++|++.||+..+.|++|+|.|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            357899999999999999999999999 99999883      67899999999999999999999999999999999999


Q ss_pred             cCCc
Q 006282          107 HRDP  110 (652)
Q Consensus       107 ~~~~  110 (652)
                      ..+.
T Consensus        76 ~~~~   79 (88)
T 1wg1_A           76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            8764

>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=99.57  E-value=1.7e-15  Score=132.71  Aligned_cols=82  Identities=23%  Similarity=0.302  Sum_probs=75.0

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCee--EEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTIT--SCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~--~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...++|||+|||+++|+++|+++|+.| .|+  +|+|+.|.+|+++|||||+|.+.++|.+|++ +++..|+|+.|.|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            346789999999999999999999999 677  9999999889999999999999999999998 578999999999999


Q ss_pred             cccHHH
Q 006282          387 AQRKEE  392 (652)
Q Consensus       387 ~~~~~~  392 (652)
                      +.+++.
T Consensus       118 a~~~e~  123 (126)
T 2hgm_A          118 SSQEEV  123 (126)
T ss_dssp             ECHHHH
T ss_pred             CCHHHh
Confidence            987654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=7.4e-15  Score=122.16  Aligned_cols=76  Identities=20%  Similarity=0.448  Sum_probs=70.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+++++       ||||+|.+.++|.+|+..|||..+.|+.|.|.++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~-------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS-------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC-------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            345689999999999999999999999999999999854       9999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus        80 ~~~   82 (92)
T 2dgt_A           80 TSR   82 (92)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=6.7e-15  Score=121.85  Aligned_cols=76  Identities=24%  Similarity=0.500  Sum_probs=70.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+++++       ||||+|.+.++|.+|+..|||..++|+.|.|.++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~-------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS-------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC-------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            345678999999999999999999999999999999854       9999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      .++
T Consensus        79 ~~~   81 (90)
T 2dnp_A           79 TKG   81 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.57  E-value=1.6e-15  Score=121.00  Aligned_cols=74  Identities=20%  Similarity=0.380  Sum_probs=69.5

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      +|||+|||.++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++ +++..++|+.|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            48999999999999999999999999999998885 68999999999999999999999 5899999999999875

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.56  E-value=2.2e-15  Score=127.95  Aligned_cols=82  Identities=22%  Similarity=0.494  Sum_probs=76.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+|+.+.+|+++|||||+|.+.++|.+|+.  ++..++|+.|.|.++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            34678999999999999999999999999999999999899999999999999999999998  9999999999999998


Q ss_pred             cHHH
Q 006282          389 RKEE  392 (652)
Q Consensus       389 ~~~~  392 (652)
                      ++..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            7643

>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=99.56  E-value=9.1e-16  Score=137.11  Aligned_cols=81  Identities=17%  Similarity=0.243  Sum_probs=74.7

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||+++|+++|+++|+.|| |++|+|+.|.+|+++|||||+|.+.++|.+|+ .+|+..|+|+.|.|.++.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            3467899999999999999999999999 77999999988999999999999999999999 799999999999999887


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      .++
T Consensus       122 ~~~  124 (139)
T 2hgn_A          122 TTG  124 (139)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.56  E-value=1.5e-14  Score=126.46  Aligned_cols=82  Identities=26%  Similarity=0.316  Sum_probs=71.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccE-EEEEeCCHHHHHHHHhhcCCcccCC--ce
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY-GYVNYANPADAARALDVLNFTPLNN--KS  100 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~-AfV~F~~~e~A~~Al~~ln~~~i~G--~~  100 (652)
                      ..+..-..|||+||++.+||++|+++|++||.|.+|++..+.     +|+ |||+|.+.++|++|++.||+..|.|  ++
T Consensus        23 ~~ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~   97 (130)
T 3zzy_A           23 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCT   97 (130)
T ss_dssp             --CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEE
T ss_pred             CCCCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcE
Confidence            344556778899999999999999999999999999998752     466 9999999999999999999999988  89


Q ss_pred             eEeecccCCc
Q 006282          101 IRIMYSHRDP  110 (652)
Q Consensus       101 i~i~~s~~~~  110 (652)
                      |+|.|++...
T Consensus        98 LrI~~ak~~~  107 (130)
T 3zzy_A           98 LRIDFSKLTS  107 (130)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEEecCCCc
Confidence            9999998653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=4.1e-15  Score=125.03  Aligned_cols=78  Identities=19%  Similarity=0.345  Sum_probs=71.4

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|. ++++.+   .++|||||+|.+.++|.+|+..|||..|+|+.|.|.++.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   92 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR   92 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            3467999999999999999999999999997 666654   679999999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        93 ~~   94 (97)
T 2e5j_A           93 QQ   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.56  E-value=5e-15  Score=138.77  Aligned_cols=82  Identities=29%  Similarity=0.482  Sum_probs=78.1

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..+++|||+|||..+++++|+++|+.||.|++|+|+.+.+|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+.
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~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            35689999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ..
T Consensus       166 ~~  167 (177)
T 2f3j_A          166 SQ  167 (177)
T ss_dssp             SG
T ss_pred             CC
Confidence            54

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=7.7e-15  Score=123.11  Aligned_cols=81  Identities=26%  Similarity=0.264  Sum_probs=73.4

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEE-EEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVR-VCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~-v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ....+++|||+|||+++|+++|+++|+.||+|.+++ +.+|+.++    .|||+|.+.++|++|++.||+..|.|++|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   86 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKV   86 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            344578999999999999999999999999999995 88876654    4999999999999999999999999999999


Q ss_pred             ecccCC
Q 006282          104 MYSHRD  109 (652)
Q Consensus       104 ~~s~~~  109 (652)
                      .|+...
T Consensus        87 ~~a~~~   92 (96)
T 2e44_A           87 AYIPDE   92 (96)
T ss_dssp             EECCCC
T ss_pred             EEcCcc
Confidence            998865

>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=4.5e-15  Score=126.93  Aligned_cols=80  Identities=19%  Similarity=0.338  Sum_probs=72.0

Q ss_pred             ceeeecCC----CCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCC----HHH----HHHHHH--HhcCcE
Q 006282          312 LNLYIKNL----GDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFST----PEE----ASRALA--EMNGKM  376 (652)
Q Consensus       312 ~~l~V~nl----p~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s----~~~----A~~A~~--~lng~~  376 (652)
                      +.|||+||    ++.+++++|+++|+.||+|.+|+++.|+ +|+|+|||||+|.+    +++    |.+|+.  .+||..
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            57999999    9999999999999999999999999997 88999999999996    433    899988  789999


Q ss_pred             ecCeeEEEEecccHH
Q 006282          377 IVSKPLYVAVAQRKE  391 (652)
Q Consensus       377 ~~g~~l~v~~~~~~~  391 (652)
                      |+|+.|.|.+.+...
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999987643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.33  E-value=2.8e-16  Score=136.96  Aligned_cols=84  Identities=25%  Similarity=0.512  Sum_probs=78.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeE--------EEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCe
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK  380 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~--------v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~  380 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+        |+|+.+ .+|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4578999999999999999999999999999        889888 4689999999999999999999999999999999


Q ss_pred             eEEEEecccHHHH
Q 006282          381 PLYVAVAQRKEER  393 (652)
Q Consensus       381 ~l~v~~~~~~~~r  393 (652)
                      .|.|.++.++..+
T Consensus        86 ~l~V~~a~~~~~~   98 (116)
T 2lcw_A           86 PIKVSFATRRADF   98 (116)
Confidence            9999999877544

>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=99.55  E-value=4.9e-15  Score=128.82  Aligned_cols=79  Identities=29%  Similarity=0.463  Sum_probs=72.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCe----eEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTI----TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I----~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ...++|||+|||.++++++|+++|+.||.|    ..+++.   +|+++|||||+|.+.++|.+|+..|||..++|+.|.|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   99 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   99 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            456899999999999999999999999999    455554   6889999999999999999999999999999999999


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .|+..+
T Consensus       100 ~~a~~~  105 (115)
T 2cpx_A          100 EFGKNK  105 (115)
T ss_dssp             EECCCC
T ss_pred             EEccCC
Confidence            999865

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.55  E-value=1.2e-14  Score=119.82  Aligned_cols=78  Identities=15%  Similarity=0.395  Sum_probs=63.9

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEe--cCeeEEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA  385 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~--~g~~l~v~  385 (652)
                      ....++|||+|||+++|+++|+++|++||.|++|+|+++    +||||||+|.+.++|.+    +++..+  .|+.|.|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            345679999999999999999999999999999999986    79999999999999983    566655  49999999


Q ss_pred             ecccHHHH
Q 006282          386 VAQRKEER  393 (652)
Q Consensus       386 ~~~~~~~r  393 (652)
                      ++.++..+
T Consensus        80 ~a~~k~~~   87 (89)
T 3d2w_A           80 NAEPKHNK   87 (89)
T ss_dssp             ECC-----
T ss_pred             EcCCCCcC
Confidence            99877543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.55  E-value=3.6e-15  Score=125.15  Aligned_cols=78  Identities=27%  Similarity=0.393  Sum_probs=71.5

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|..+    ..+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            356789999999999999999999999988766    4468899999999999999999999999999999999999997


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        90 ~~   91 (96)
T 1fjc_A           90 EK   91 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.55  E-value=1.9e-15  Score=136.93  Aligned_cols=84  Identities=21%  Similarity=0.239  Sum_probs=73.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEE-----EeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRV-----CRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS  100 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v-----~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~  100 (652)
                      ..++++|||+|||+++|+++|+++|+.||.|.++.+     ++...+++++|||||.|.+.++|.+|++.||+..|.|++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            456799999999999999999999999999876411     222246889999999999999999999999999999999


Q ss_pred             eEeecccCC
Q 006282          101 IRIMYSHRD  109 (652)
Q Consensus       101 i~i~~s~~~  109 (652)
                      |+|.|+...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999998754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.55  E-value=6.4e-15  Score=123.59  Aligned_cols=77  Identities=25%  Similarity=0.398  Sum_probs=70.4

Q ss_pred             ccccceeeecCCCC-CCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~-~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||. .+++++|+++|+.||.|.+|++.       +|||||+|.+.++|.+|+..|||..+.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            34578999999998 99999999999999999999984       67999999999999999999999999999999999


Q ss_pred             cccHH
Q 006282          387 AQRKE  391 (652)
Q Consensus       387 ~~~~~  391 (652)
                      +..+.
T Consensus        80 a~~~~   84 (96)
T 2kvi_A           80 SSSNA   84 (96)
T ss_dssp             EECCC
T ss_pred             cCcCC
Confidence            97653

>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=99.55  E-value=1.4e-14  Score=123.30  Aligned_cols=76  Identities=28%  Similarity=0.527  Sum_probs=70.6

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|.+|+++       +|||||+|.+.++|.+|++.||+..|+|+.|.|.|+.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            346789999999999999999999999999999987       4499999999999999999999999999999999998


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      .+.
T Consensus        82 ~~~   84 (103)
T 2dgu_A           82 PPD   84 (103)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            653

>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=99.54  E-value=8.5e-15  Score=120.78  Aligned_cols=78  Identities=18%  Similarity=0.276  Sum_probs=63.1

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ...+.++|||+|||+++||++|+++|++||+|.+|+|.++     ++|||||+|.+.++|+++.. . ...++|+.|+|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~-~-~~~~~g~~v~v~   79 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG-E-DLIIKGISVHIS   79 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT-C-EEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC-C-CcccCCEEEEEE
Confidence            3456889999999999999999999999999999999874     77999999999999995433 1 334579999999


Q ss_pred             cccCC
Q 006282          105 YSHRD  109 (652)
Q Consensus       105 ~s~~~  109 (652)
                      ++...
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            88754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.54  E-value=3e-14  Score=120.97  Aligned_cols=83  Identities=16%  Similarity=0.260  Sum_probs=73.5

Q ss_pred             cccceeeecCCCC-----CCCHHHHHHHhhhcCCeeEEEEecCC--CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee
Q 006282          309 FQGLNLYIKNLGD-----SIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP  381 (652)
Q Consensus       309 ~~~~~l~V~nlp~-----~~te~~L~~~F~~fG~I~~v~i~~~~--~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~  381 (652)
                      ..+++|+|+|+-.     +-++++|+++|++||.|++|+|+++.  +++++|||||+|.+.++|.+|++.|||+.++|+.
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            3567899999963     23689999999999999999999875  3689999999999999999999999999999999


Q ss_pred             EEEEecccHH
Q 006282          382 LYVAVAQRKE  391 (652)
Q Consensus       382 l~v~~~~~~~  391 (652)
                      |.|.++....
T Consensus        86 i~v~~a~~~~   95 (105)
T 2pe8_A           86 VKACFYNLDK   95 (105)
T ss_dssp             CEEEECCHHH
T ss_pred             EEEEEcCHHH
Confidence            9999998643

>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=99.54  E-value=1.1e-14  Score=132.26  Aligned_cols=77  Identities=19%  Similarity=0.333  Sum_probs=70.7

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC--eeEEEEecc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVAVAQ  388 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g--~~l~v~~~~  388 (652)
                      ...|||+||++.+|+++|+++|++||.|++|+|+.+.   ++|||||+|.+.++|.+|++.|||..|.|  +.|+|.|++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            3569999999999999999999999999999997652   58899999999999999999999999965  999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus       123 ~~  124 (164)
T 1sjr_A          123 LT  124 (164)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=9.7e-15  Score=120.31  Aligned_cols=75  Identities=20%  Similarity=0.341  Sum_probs=69.7

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||.++++++|+++|++| .|.++++.     +++|||||+|.+.++|.+|++.|||..++|+.|.|.|+..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            35789999999999999999999999 99999985     5799999999999999999999999999999999999864


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        78 ~   78 (88)
T 1wg1_A           78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.54  E-value=1e-15  Score=129.78  Aligned_cols=80  Identities=23%  Similarity=0.387  Sum_probs=72.8

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+ +++.+ .+|+++|||||+|.+.++|.+|++ |||..+.|+.|.|.++.
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            5678999999999999999999999999988 55544 468899999999999999999999 99999999999999998


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      .+.
T Consensus        94 ~~~   96 (101)
T 1fj7_A           94 GRD   96 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.3e-14  Score=123.23  Aligned_cols=80  Identities=30%  Similarity=0.436  Sum_probs=72.6

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ....++|||+|||.++++++|+++|+.|+   +|+++.+. +|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            44678999999999999999999999873   67777764 788999999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ++++
T Consensus        89 a~~~   92 (102)
T 2fc8_A           89 AKPK   92 (102)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9865

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=8e-15  Score=125.26  Aligned_cols=80  Identities=21%  Similarity=0.320  Sum_probs=70.3

Q ss_pred             CCCccEEEE--cCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc-----CC
Q 006282           26 QFLTTSLYV--GDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL-----NN   98 (652)
Q Consensus        26 ~~~~~sL~V--~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i-----~G   98 (652)
                      ..++++|||  +||++++||++|+++|++||.|.+|.+..      ++|||||+|.+.++|++|++.||+..|     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345789999  77999999999999999999999998864      258999999999999999999999987     68


Q ss_pred             ceeEeecccCCcc
Q 006282           99 KSIRIMYSHRDPS  111 (652)
Q Consensus        99 ~~i~i~~s~~~~~  111 (652)
                      ++|.|.|+..-+.
T Consensus        96 ~~l~v~~a~~~p~  108 (114)
T 2cq2_A           96 ITLYLNFVEKVQW  108 (114)
T ss_dssp             EECEEEEESCCCC
T ss_pred             cEEEEEecccCcc
Confidence            8999988775543

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=7.5e-15  Score=122.40  Aligned_cols=76  Identities=24%  Similarity=0.361  Sum_probs=68.9

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCC-eeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcC-cEecCeeEEEEe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGT-ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG-KMIVSKPLYVAV  386 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~-I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng-~~~~g~~l~v~~  386 (652)
                      ...++|||+|||.++++++|+++|+.||. |..+.+.      ++|||||+|.+.++|.+|++.||| ..++|+.|.|.|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            35678999999999999999999999999 6666663      488999999999999999999999 999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        80 a~~~   83 (93)
T 2cqh_A           80 SVSK   83 (93)
T ss_dssp             CCCC
T ss_pred             ccCc
Confidence            9865

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=125.31  Aligned_cols=78  Identities=14%  Similarity=0.237  Sum_probs=68.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCC---CCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLST---RRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t---~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ..+++|||+|||+++||++|+++|++||+|. ++++.+..+   ++++|||||+|.+.++|++|++.|+  .++|+.+.+
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            4578999999999999999999999999999 888888887   6999999999999999999999884  367777776


Q ss_pred             eccc
Q 006282          104 MYSH  107 (652)
Q Consensus       104 ~~s~  107 (652)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.54  E-value=2.1e-14  Score=125.58  Aligned_cols=75  Identities=20%  Similarity=0.363  Sum_probs=69.5

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccE-EEEEeCCHHHHHHHHHHhcCcEecC--eeEEEEecc
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS-GFVAFSTPEEASRALAEMNGKMIVS--KPLYVAVAQ  388 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~-afV~F~s~~~A~~A~~~lng~~~~g--~~l~v~~~~  388 (652)
                      ..|||+||++.+|+++|+++|++||.|.+|+++.+    ++|| |||+|.+.++|.+|++.|||..|.|  +.|+|.|++
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak  104 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  104 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecC
Confidence            45889999999999999999999999999998865    3678 9999999999999999999999988  999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus       105 ~~  106 (130)
T 3zzy_A          105 LT  106 (130)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.53  E-value=1.6e-14  Score=118.77  Aligned_cols=73  Identities=22%  Similarity=0.504  Sum_probs=67.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQV----G-------QVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~----G-------~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      ..+.++|||+|||+++|+++|+++|+.|    |       +|.++++.++      +|||||+|.+.++|++|+ .||+.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            4568999999999999999999999999    8       9999998765      589999999999999999 89999


Q ss_pred             ccCCceeEeec
Q 006282           95 PLNNKSIRIMY  105 (652)
Q Consensus        95 ~i~G~~i~i~~  105 (652)
                      .|.|+.|+|.+
T Consensus        76 ~~~g~~l~V~r   86 (87)
T 2hzc_A           76 IFQGQSLKIRR   86 (87)
T ss_dssp             EETTEECEEEC
T ss_pred             EECCeEEEEeC
Confidence            99999999964

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2.3e-14  Score=120.38  Aligned_cols=75  Identities=29%  Similarity=0.469  Sum_probs=69.5

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|+  ++++++|+++|++||.|.+|+|.     +++|||||+|.+.++|.+|+..|||..++|+.|.|.|+.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            45689999996  89999999999999999999984     468999999999999999999999999999999999997


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        86 ~~   87 (97)
T 1x5p_A           86 KQ   87 (97)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=7.7e-14  Score=121.54  Aligned_cols=78  Identities=19%  Similarity=0.273  Sum_probs=68.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccE-EEEEeCCHHHHHHHHhhcCCcccCC--ceeEe
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY-GYVNYANPADAARALDVLNFTPLNN--KSIRI  103 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~-AfV~F~~~e~A~~Al~~ln~~~i~G--~~i~i  103 (652)
                      .....|||+||++.+|+++|+++|++||.|.+|+|...     + |+ |||+|.+.++|.+|++.||+..|.|  +.|+|
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~-Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V   96 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----N-GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI   96 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----S-SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEE
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----C-CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEE
Confidence            33455789999999999999999999999999999652     2 75 9999999999999999999999988  68999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|++...
T Consensus        97 ~~Ak~~~  103 (124)
T 2e5i_A           97 EYARPTR  103 (124)
T ss_dssp             ECCSCSC
T ss_pred             EEecCCc
Confidence            9988653

>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=99.53  E-value=1.4e-14  Score=124.92  Aligned_cols=73  Identities=26%  Similarity=0.560  Sum_probs=69.3

Q ss_pred             ccceeeecCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~-~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.+ +++++|+++|+.||.|.+|++       ++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   98 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            4579999999999 999999999999999999998       47899999999999999999999999999999999987


Q ss_pred             c
Q 006282          389 R  389 (652)
Q Consensus       389 ~  389 (652)
                      .
T Consensus        99 ~   99 (110)
T 1wf1_A           99 E   99 (110)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=4.5e-15  Score=134.44  Aligned_cols=84  Identities=26%  Similarity=0.470  Sum_probs=73.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEE------EEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC------KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP  381 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v------~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~  381 (652)
                      ....++|||+|||.++|+++|+++|+.||.|.++      .+....+|+++|||||+|.+.++|.+|+..|||..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            4467899999999999999999999999999874      1222246889999999999999999999999999999999


Q ss_pred             EEEEecccHH
Q 006282          382 LYVAVAQRKE  391 (652)
Q Consensus       382 l~v~~~~~~~  391 (652)
                      |.|.+++...
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997643

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=3.7e-14  Score=120.44  Aligned_cols=83  Identities=8%  Similarity=0.051  Sum_probs=74.2

Q ss_pred             CCCccEEEEcCCCC-----CCCHHHHHHHHhccCCeEEEEEEeeCCC-CCcccEEEEEeCCHHHHHHHHhhcCCcccCCc
Q 006282           26 QFLTTSLYVGDLDF-----NVTDSQLYDLFSQVGQVLSVRVCRDLST-RRSLGYGYVNYANPADAARALDVLNFTPLNNK   99 (652)
Q Consensus        26 ~~~~~sL~V~nLp~-----~vte~~L~~~Fs~~G~V~~i~v~~d~~t-~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~   99 (652)
                      +.++++|+|+||-.     +-++++|++.|++||+|.+|+|++|..+ ++++|||||+|.+.++|.+|++.||+..|.||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34689999999962     2379999999999999999999999764 68999999999999999999999999999999


Q ss_pred             eeEeecccC
Q 006282          100 SIRIMYSHR  108 (652)
Q Consensus       100 ~i~i~~s~~  108 (652)
                      .|+|.|+..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999998764

>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=99.52  E-value=1.6e-14  Score=125.41  Aligned_cols=75  Identities=24%  Similarity=0.279  Sum_probs=66.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce-----e
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS-----I  101 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~-----i  101 (652)
                      ...++|||+|||+++|+++|+++|+.||+|.+|+|+.|       |||||+|.+.++|++|++.||+..|+|+.     |
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     5


Q ss_pred             EeecccC
Q 006282          102 RIMYSHR  108 (652)
Q Consensus       102 ~i~~s~~  108 (652)
                      +|..+..
T Consensus        87 ~v~~~~~   93 (115)
T 3beg_B           87 RVKVDGP   93 (115)
T ss_dssp             EEEECC-
T ss_pred             EeccCCC
Confidence            5655443

>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=99.52  E-value=1.3e-14  Score=119.64  Aligned_cols=78  Identities=19%  Similarity=0.281  Sum_probs=67.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .++++|||+|||+++||++|+++|+.||+|.+|++.++     ++|||||+|.+.++|++|+..  ...+.|+.|+|.|+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            45799999999999999999999999999999999865     679999999999999876552  35669999999998


Q ss_pred             cCCcc
Q 006282          107 HRDPS  111 (652)
Q Consensus       107 ~~~~~  111 (652)
                      .....
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=4.6e-14  Score=119.07  Aligned_cols=75  Identities=29%  Similarity=0.473  Sum_probs=70.0

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhc--CCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~f--G~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...++|||+|||..+++++|+++|+.|  |.|.+|++.       +|||||+|.+.++|.+|+..|||..|+|+.|.|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   85 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            456789999999999999999999999  999999875       56999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ++++
T Consensus        86 a~~~   89 (99)
T 2cpd_A           86 AKPV   89 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9864

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=3.4e-14  Score=119.14  Aligned_cols=78  Identities=27%  Similarity=0.391  Sum_probs=71.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEE-EecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCK-VMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~-i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+ ++.+..   .|.|||+|.+.++|.+|+..|||..++|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            467899999999999999999999999999995 777642   3449999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        91 ~~   92 (96)
T 2e44_A           91 DE   92 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            76

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.50  E-value=2.7e-14  Score=124.00  Aligned_cols=74  Identities=24%  Similarity=0.333  Sum_probs=66.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee-----EEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP-----LYV  384 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~-----l~v  384 (652)
                      ..++|||+|||+++++++|+++|+.||.|++|+|+.+      |||||+|.+.++|.+|++.|||..|+|+.     |.|
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v   88 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   88 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEe
Confidence            3578999999999999999999999999999999876      79999999999999999999999999988     666


Q ss_pred             Eeccc
Q 006282          385 AVAQR  389 (652)
Q Consensus       385 ~~~~~  389 (652)
                      ..+.+
T Consensus        89 ~~~~~   93 (115)
T 3beg_B           89 KVDGP   93 (115)
T ss_dssp             EECC-
T ss_pred             ccCCC
Confidence            65554

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.50  E-value=5.8e-14  Score=122.31  Aligned_cols=74  Identities=24%  Similarity=0.276  Sum_probs=67.5

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccE-EEEEeCCHHHHHHHHHHhcCcEecC--eeEEEEecc
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS-GFVAFSTPEEASRALAEMNGKMIVS--KPLYVAVAQ  388 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~-afV~F~s~~~A~~A~~~lng~~~~g--~~l~v~~~~  388 (652)
                      ..|||+||++.+++++|+++|++||.|.+|+|+..     .|| |||+|.+.++|.+|++.|||..|.|  +.|.|.+++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            34789999999999999999999999999999763     386 9999999999999999999999987  699999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus       101 ~~  102 (124)
T 2e5i_A          101 PT  102 (124)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=3.7e-14  Score=114.63  Aligned_cols=70  Identities=24%  Similarity=0.397  Sum_probs=63.6

Q ss_pred             ceeeecCCCCCCCHHH----HHHHhhhc-CCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          312 LNLYIKNLGDSIDDEK----LKELFSEF-GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~----L~~~F~~f-G~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      +.|||+|||+.+++++    |+++|++| |.|.+|      +|   |+|||.|.+.++|.+|++.|||..+.||+|+|.+
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            3499999999999987    55899999 599999      22   8999999999999999999999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ++.+
T Consensus        81 A~~~   84 (96)
T 2diu_A           81 TPKN   84 (96)
T ss_dssp             SCCS
T ss_pred             cCCC
Confidence            9865

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.49  E-value=5.8e-14  Score=133.54  Aligned_cols=79  Identities=16%  Similarity=0.312  Sum_probs=73.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      .++|||+|||+++|+++|+++|+.||+|.+|+++++.. ++++|||||+|.+.++|++|++.++ ..|.|++|+|.|...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            58999999999999999999999999999999999864 8999999999999999999999665 589999999998765


Q ss_pred             C
Q 006282          109 D  109 (652)
Q Consensus       109 ~  109 (652)
                      .
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=5.7e-14  Score=117.26  Aligned_cols=75  Identities=20%  Similarity=0.342  Sum_probs=66.6

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .++|||+|||.++++++|+++|+.||.|.+| +....+|+   ||||+|.+.++|.+|+. |||..|+|+.|.|.++..+
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            4689999999999999999999999999998 44333444   99999999999999999 9999999999999977644

>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=99.47  E-value=1.3e-13  Score=113.21  Aligned_cols=70  Identities=21%  Similarity=0.485  Sum_probs=66.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhc----C-------CeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEF----G-------TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~f----G-------~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      ..++|||+|||.++++++|+++|+.|    |       .|.++++..+     +|||||+|.+.++|.+|+ .|||..++
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            45789999999999999999999999    8       9999999865     899999999999999999 99999999


Q ss_pred             CeeEEEE
Q 006282          379 SKPLYVA  385 (652)
Q Consensus       379 g~~l~v~  385 (652)
                      |+.|.|+
T Consensus        79 g~~l~V~   85 (87)
T 2hzc_A           79 GQSLKIR   85 (87)
T ss_dssp             TEECEEE
T ss_pred             CeEEEEe
Confidence            9999987

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=7.7e-14  Score=120.92  Aligned_cols=77  Identities=16%  Similarity=0.238  Sum_probs=67.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-C---CCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-S---GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~---g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ..++|||+|||.++++++|+++|++||.|. ++++.+. +   |+++|||||+|.+.++|.+|++.|+  .++|+.+.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            457899999999999999999999999999 8777765 3   7999999999999999999999985  3788888777


Q ss_pred             eccc
Q 006282          386 VAQR  389 (652)
Q Consensus       386 ~~~~  389 (652)
                      .+..
T Consensus        84 ~~~~   87 (114)
T 2dnl_A           84 SSPT   87 (114)
T ss_dssp             CCSS
T ss_pred             cCCC
Confidence            5543

>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=99.46  E-value=1.3e-13  Score=131.18  Aligned_cols=79  Identities=20%  Similarity=0.278  Sum_probs=73.4

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .++|||+|||.++++++|+++|+.||.|.+|+|.++.+|.++|||||+|.+.++|.+|+..++ ..++|+.|.|.++..-
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHH
Confidence            468999999999999999999999999999999999889999999999999999999998655 5999999999998753

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.45  E-value=1.2e-13  Score=134.16  Aligned_cols=81  Identities=23%  Similarity=0.434  Sum_probs=71.5

Q ss_pred             CCCCccEEEEcCCCCCC---------CHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcc
Q 006282           25 NQFLTTSLYVGDLDFNV---------TDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTP   95 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~v---------te~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~   95 (652)
                      .....++|||+||+.++         +|++|+++|++||+|.+|+|++      ++|||||.|.+.++|+.|++.|++..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            34568999999999998         7999999999999999999985      46899999999999999999999999


Q ss_pred             c------------CCceeEeecccCCcc
Q 006282           96 L------------NNKSIRIMYSHRDPS  111 (652)
Q Consensus        96 i------------~G~~i~i~~s~~~~~  111 (652)
                      |            .|+.|+|.|++.++.
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCC
Confidence            9            899999999998764

>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=99.44  E-value=7.1e-14  Score=115.09  Aligned_cols=75  Identities=17%  Similarity=0.357  Sum_probs=64.6

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.+    ++|||||+|.+.++|.+|+..  ...+.|+.|.|.++.+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCC
Confidence            4578999999999999999999999999999999876    689999999999999764321  2345899999999876


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        78 ~   78 (88)
T 1wf0_A           78 K   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.44  E-value=2.4e-13  Score=115.47  Aligned_cols=83  Identities=16%  Similarity=0.257  Sum_probs=72.1

Q ss_pred             ccceeeecCC--CCCCC--------HHHHHHHhhhcCCeeEEEEecCCC---CCCccEEEEEeCCHHHHHHHHHHhcCcE
Q 006282          310 QGLNLYIKNL--GDSID--------DEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPEEASRALAEMNGKM  376 (652)
Q Consensus       310 ~~~~l~V~nl--p~~~t--------e~~L~~~F~~fG~I~~v~i~~~~~---g~s~g~afV~F~s~~~A~~A~~~lng~~  376 (652)
                      ++++|.|+|+  +.++.        +++|++.|++||.|++|+|+++..   ++++|||||+|.+.++|.+|++.|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4678999998  33443        369999999999999999998864   3689999999999999999999999999


Q ss_pred             ecCeeEEEEecccHHH
Q 006282          377 IVSKPLYVAVAQRKEE  392 (652)
Q Consensus       377 ~~g~~l~v~~~~~~~~  392 (652)
                      ++|+.|.|.++....-
T Consensus        84 f~GR~i~v~~~~~~~f   99 (105)
T 3v4m_A           84 FANRVVVTKYCDPDSY   99 (105)
T ss_dssp             ETTEECEEEEECHHHH
T ss_pred             eCCCEEEEEEeCHHHH
Confidence            9999999999886643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.44  E-value=1.2e-13  Score=134.23  Aligned_cols=79  Identities=22%  Similarity=0.396  Sum_probs=70.4

Q ss_pred             ccceeeecCCCCCC---------CHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEe---
Q 006282          310 QGLNLYIKNLGDSI---------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---  377 (652)
Q Consensus       310 ~~~~l~V~nlp~~~---------te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~---  377 (652)
                      ..++|||+||+..+         ++++|+++|++||.|++|+|+.+     +|||||+|.+.++|.+|++.|+|..|   
T Consensus       133 ~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~~l~~~  207 (240)
T 3u1l_A          133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLLLP  207 (240)
T ss_dssp             CCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCCCCT
T ss_pred             CCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEEecc
Confidence            56789999999998         79999999999999999999864     89999999999999999999999999   


Q ss_pred             ---------cCeeEEEEecccHHHH
Q 006282          378 ---------VSKPLYVAVAQRKEER  393 (652)
Q Consensus       378 ---------~g~~l~v~~~~~~~~r  393 (652)
                               .|+.|.|.||......
T Consensus       208 ~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          208 SDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             TSTTGGGGGGSCCCEEEECC-----
T ss_pred             ccccccccCCCCEEEEEEccCCCCH
Confidence                     8999999999976544

>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=99.42  E-value=8.4e-14  Score=118.14  Aligned_cols=72  Identities=18%  Similarity=0.431  Sum_probs=62.1

Q ss_pred             ecCCCCCCCHHHHHHHh------------hhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEE
Q 006282          316 IKNLGDSIDDEKLKELF------------SEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  383 (652)
Q Consensus       316 V~nlp~~~te~~L~~~F------------~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~  383 (652)
                      +.||+..+++++|+++|            ++||.|++|+|+++..|+++|||||+|.+.++|.+|+..|||+.++|+.|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            34555555665555544            999999999999998899999999999999999999999999999999999


Q ss_pred             EEec
Q 006282          384 VAVA  387 (652)
Q Consensus       384 v~~~  387 (652)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.41  E-value=1.1e-12  Score=113.23  Aligned_cols=86  Identities=13%  Similarity=0.131  Sum_probs=72.8

Q ss_pred             CCCCCCccEEEEcCCCCCCC-----------HHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc
Q 006282           23 SGNQFLTTSLYVGDLDFNVT-----------DSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL   91 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vt-----------e~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l   91 (652)
                      ...+.++++|+|+||-...+           +++|+++|++||+|.+|.| .|+   .++|||||+|.+.++|++|++.|
T Consensus         9 ~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~l   84 (112)
T 2dit_A            9 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTL   84 (112)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHc
Confidence            34566799999999944332           6899999999999999966 543   37899999999999999999999


Q ss_pred             CCcccCCceeEeecccCCccc
Q 006282           92 NFTPLNNKSIRIMYSHRDPSI  112 (652)
Q Consensus        92 n~~~i~G~~i~i~~s~~~~~~  112 (652)
                      |+..|.|++|+|.|+......
T Consensus        85 ng~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           85 DGRWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             TTCEETTEECEEEECCSCCCS
T ss_pred             CCCEECCcEEEEEEeCCCCCc
Confidence            999999999999998765443

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.40  E-value=4.1e-13  Score=116.28  Aligned_cols=82  Identities=17%  Similarity=0.331  Sum_probs=71.7

Q ss_pred             ccceeeecCCC--CCC---CHHHHHHHhhhcCCeeEEEEecCC-----CCCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          310 QGLNLYIKNLG--DSI---DDEKLKELFSEFGTITSCKVMRDP-----SGISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       310 ~~~~l~V~nlp--~~~---te~~L~~~F~~fG~I~~v~i~~~~-----~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      ++++|+|+|+-  .++   .+++|++.|++||.|++|+|+++.     +++++||+||+|.+.++|.+|++.|||+.++|
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            57789999983  233   258999999999999999999874     35678999999999999999999999999999


Q ss_pred             eeEEEEecccHH
Q 006282          380 KPLYVAVAQRKE  391 (652)
Q Consensus       380 ~~l~v~~~~~~~  391 (652)
                      +.|.|.++....
T Consensus        99 R~i~v~~~~~~~  110 (118)
T 3ue2_A           99 RKVVAEVYDQER  110 (118)
T ss_dssp             EECEEEEECHHH
T ss_pred             cEEEEEEcChHh
Confidence            999999987643

>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=99.38  E-value=7.6e-13  Score=114.56  Aligned_cols=81  Identities=10%  Similarity=0.166  Sum_probs=72.0

Q ss_pred             CccEEEEcCCC--CCC---CHHHHHHHHhccCCeEEEEEEeeCC----CCCcccEEEEEeCCHHHHHHHHhhcCCcccCC
Q 006282           28 LTTSLYVGDLD--FNV---TDSQLYDLFSQVGQVLSVRVCRDLS----TRRSLGYGYVNYANPADAARALDVLNFTPLNN   98 (652)
Q Consensus        28 ~~~sL~V~nLp--~~v---te~~L~~~Fs~~G~V~~i~v~~d~~----t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G   98 (652)
                      ++++|+|+|+-  .++   -+++|++.|++||+|.+|+|+++..    +++++|++||+|.+.++|.+|++.||+..|.|
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            58899999993  223   3789999999999999999999975    46788999999999999999999999999999


Q ss_pred             ceeEeecccC
Q 006282           99 KSIRIMYSHR  108 (652)
Q Consensus        99 ~~i~i~~s~~  108 (652)
                      |.|+|.+...
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998653

>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=99.37  E-value=7e-13  Score=112.61  Aligned_cols=82  Identities=18%  Similarity=0.214  Sum_probs=72.6

Q ss_pred             CCccEEEEcCC--CCCCC--------HHHHHHHHhccCCeEEEEEEeeCCC--CCcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           27 FLTTSLYVGDL--DFNVT--------DSQLYDLFSQVGQVLSVRVCRDLST--RRSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        27 ~~~~sL~V~nL--p~~vt--------e~~L~~~Fs~~G~V~~i~v~~d~~t--~~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      .+++.|.|.|+  +.++.        +++|++.|++||+|.+|+|+++..+  ++++|+|||+|.+.++|.+|++.||+.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            36899999999  44443        3689999999999999999999765  468999999999999999999999999


Q ss_pred             ccCCceeEeecccC
Q 006282           95 PLNNKSIRIMYSHR  108 (652)
Q Consensus        95 ~i~G~~i~i~~s~~  108 (652)
                      .|.||.|+|.+...
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999998654

>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=99.37  E-value=1.4e-12  Score=112.58  Aligned_cols=80  Identities=24%  Similarity=0.323  Sum_probs=68.9

Q ss_pred             ccccceeeecCCCCCCC-----------HHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcE
Q 006282          308 KFQGLNLYIKNLGDSID-----------DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKM  376 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~t-----------e~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~  376 (652)
                      ...+++|+|+||-...+           +++|+++|++||.|.+|.| .+.  .++|||||+|.+.++|.+|+..|||..
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            34577899999954332           5899999999999999966 443  379999999999999999999999999


Q ss_pred             ecCeeEEEEecccH
Q 006282          377 IVSKPLYVAVAQRK  390 (652)
Q Consensus       377 ~~g~~l~v~~~~~~  390 (652)
                      ++|+.|.|.++..+
T Consensus        89 ~~gr~l~v~~a~~~  102 (112)
T 2dit_A           89 FGGRQITAQAWDGT  102 (112)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCcEEEEEEeCCC
Confidence            99999999998764

>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=99.36  E-value=2e-13  Score=115.81  Aligned_cols=72  Identities=26%  Similarity=0.409  Sum_probs=64.1

Q ss_pred             EcCCCCCCCHHHHHHHH------------hccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           34 VGDLDFNVTDSQLYDLF------------SQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        34 V~nLp~~vte~~L~~~F------------s~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      +.+|++.+++++|+++|            ++||+|.+|+|+++.. ++++|||||.|.+.++|.+|++.||+..|.||.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56677777888777666            9999999999999865 7899999999999999999999999999999999


Q ss_pred             Eeecc
Q 006282          102 RIMYS  106 (652)
Q Consensus       102 ~i~~s  106 (652)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99886

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=1e-11  Score=103.93  Aligned_cols=76  Identities=20%  Similarity=0.232  Sum_probs=65.9

Q ss_pred             ccEEEEcCCC-------CCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           29 TTSLYVGDLD-------FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        29 ~~sL~V~nLp-------~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ..+|.|.-..       .++||++|+++|++||.|.+|+|+     ++++|||||+|.+.++|++|++.++  .+.|++|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            6688887765       458999999999999999999998     3678999999999999999999754  4689999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+...+.
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999887654

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.27  E-value=2e-11  Score=104.82  Aligned_cols=81  Identities=14%  Similarity=0.173  Sum_probs=68.7

Q ss_pred             ccceeeecCCCCCC----------CHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          310 QGLNLYIKNLGDSI----------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       310 ~~~~l~V~nlp~~~----------te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      ++++|.++|+=..-          -+++|++.|++||.|++|+|.++.   ++||+||+|.+.++|.+|++.|||+.++|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            46678888883221          135899999999999999998763   58999999999999999999999999999


Q ss_pred             eeEEEEecccHHHH
Q 006282          380 KPLYVAVAQRKEER  393 (652)
Q Consensus       380 ~~l~v~~~~~~~~r  393 (652)
                      +.|.|.++....-.
T Consensus        83 R~i~v~~~~~~~y~   96 (114)
T 3s6e_A           83 KMITAAYVPLPTYH   96 (114)
T ss_dssp             EECEEEEECHHHHH
T ss_pred             EEEEEEEEcHHHHH
Confidence            99999999866443

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=1.4e-11  Score=103.03  Aligned_cols=64  Identities=20%  Similarity=0.367  Sum_probs=57.5

Q ss_pred             CCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          321 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       321 ~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ..+++++|+++|++||.|.+|+|+    ++++|||||+|.+.++|.+|++.+++  +.|++|.|.|++.+
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~   90 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQ   90 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCC
Confidence            568999999999999999999998    36899999999999999999998555  67999999998754

>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=99.22  E-value=1.6e-11  Score=125.75  Aligned_cols=77  Identities=25%  Similarity=0.489  Sum_probs=67.2

Q ss_pred             ccccceeeecC--CCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec---Ce--
Q 006282          308 KFQGLNLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---SK--  380 (652)
Q Consensus       308 ~~~~~~l~V~n--lp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~---g~--  380 (652)
                      ..++.+|||+|  |+..+|+++|+++|++||+|++|++..     +||||||+|.+.++|.+|++.|||+.+.   |+  
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            44677999999  578999999999999999999987754     4899999999999999999999999883   34  


Q ss_pred             eEEEEeccc
Q 006282          381 PLYVAVAQR  389 (652)
Q Consensus       381 ~l~v~~~~~  389 (652)
                      .|+|.++..
T Consensus        90 ~ly~~~~~~   98 (345)
T 3tht_A           90 TLYLNFVEK   98 (345)
T ss_dssp             ECEEEECSS
T ss_pred             EEEEEEeec
Confidence            788988853

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.19  E-value=3.7e-11  Score=103.12  Aligned_cols=80  Identities=18%  Similarity=0.195  Sum_probs=68.2

Q ss_pred             CCCCccEEEEcCCC--CCC--------CHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           25 NQFLTTSLYVGDLD--FNV--------TDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        25 ~~~~~~sL~V~nLp--~~v--------te~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      ++.++++|.|.|+=  .+.        -+++|++.|++||.|.+|.|+++.    ++|+|||.|.+.++|.+|++.||+.
T Consensus         3 ~p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~   78 (114)
T 3s6e_A            3 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGR   78 (114)
T ss_dssp             CCCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCC
Confidence            45578899999993  221        145789999999999999997763    5799999999999999999999999


Q ss_pred             ccCCceeEeecccC
Q 006282           95 PLNNKSIRIMYSHR  108 (652)
Q Consensus        95 ~i~G~~i~i~~s~~  108 (652)
                      .|.||.|+|.|+..
T Consensus        79 ~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           79 WFAGKMITAAYVPL   92 (114)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EECCEEEEEEEEcH
Confidence            99999999998753

>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=99.16  E-value=3.2e-11  Score=123.49  Aligned_cols=76  Identities=21%  Similarity=0.325  Sum_probs=64.5

Q ss_pred             CCCCccEEEEcC--CCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC---Cc
Q 006282           25 NQFLTTSLYVGD--LDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN---NK   99 (652)
Q Consensus        25 ~~~~~~sL~V~n--Lp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~---G~   99 (652)
                      ...++.+|||+|  |+.++||++|+++|++||.|.+|++.+      ++|||||+|.+.+||++|++.||+..+.   |+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            456789999999  578999999999999999999987743      4589999999999999999999998773   44


Q ss_pred             --eeEeecc
Q 006282          100 --SIRIMYS  106 (652)
Q Consensus       100 --~i~i~~s  106 (652)
                        ++.+.+.
T Consensus        88 ~~~ly~~~~   96 (345)
T 3tht_A           88 KITLYLNFV   96 (345)
T ss_dssp             EEECEEEEC
T ss_pred             ceEEEEEEe
Confidence              4555554

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.01  E-value=9e-10  Score=94.48  Aligned_cols=84  Identities=23%  Similarity=0.260  Sum_probs=73.9

Q ss_pred             ccccccceeeecCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCC-HHHHHHHHHHhc--CcEecCee
Q 006282          306 VDKFQGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFST-PEEASRALAEMN--GKMIVSKP  381 (652)
Q Consensus       306 ~~~~~~~~l~V~nlp~~-~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s-~~~A~~A~~~ln--g~~~~g~~  381 (652)
                      ..-..++.|||+||+++ +++++|+++|+.||.|..|.+..+..     .|||.|.+ .++|..|+..+|  +..|.|..
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            34557899999999999 99999999999999999999998743     69999999 899999999995  77889999


Q ss_pred             EEEEecccHHHHH
Q 006282          382 LYVAVAQRKEERR  394 (652)
Q Consensus       382 l~v~~~~~~~~r~  394 (652)
                      +.+.+..-.+++.
T Consensus        88 ~~~evL~GeeE~~  100 (121)
T 1owx_A           88 VTWEVLEGEVEKE  100 (121)
T ss_dssp             EEEEECCHHHHHH
T ss_pred             EEEEECCCHHHHH
Confidence            9999887666554

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.00  E-value=8.3e-10  Score=88.45  Aligned_cols=73  Identities=21%  Similarity=0.388  Sum_probs=62.6

Q ss_pred             cccceeeecCCC----CCCCH----HHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCe
Q 006282          309 FQGLNLYIKNLG----DSIDD----EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK  380 (652)
Q Consensus       309 ~~~~~l~V~nlp----~~~te----~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~  380 (652)
                      ++..+|+|.-.+    .++-+    .+|.+.|+.||+|..++++.|       .+||+|.+.++|.+|++ |||..++||
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHh-cCCeEeCCe
Confidence            445577777665    34444    689999999999999999987       39999999999999998 999999999


Q ss_pred             eEEEEeccc
Q 006282          381 PLYVAVAQR  389 (652)
Q Consensus       381 ~l~v~~~~~  389 (652)
                      .|+|+++.+
T Consensus        77 ~LkV~lkt~   85 (91)
T 2dnr_A           77 TITIALKSP   85 (91)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999999875

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.93  E-value=2.8e-09  Score=85.39  Aligned_cols=75  Identities=24%  Similarity=0.302  Sum_probs=63.9

Q ss_pred             CCCccEEEEcCCCC----CCCH----HHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           26 QFLTTSLYVGDLDF----NVTD----SQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        26 ~~~~~sL~V~nLp~----~vte----~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      .++..+|+|.-++.    ++-.    .+|.+.|++||.|.++|+..|.        +||+|.+.++|.+|++ ||+..+.
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            34577899988772    3433    6689999999999999999873        8999999999999999 9999999


Q ss_pred             CceeEeecccCC
Q 006282           98 NKSIRIMYSHRD  109 (652)
Q Consensus        98 G~~i~i~~s~~~  109 (652)
                      ||.|+|.+...+
T Consensus        75 Gr~LkV~lkt~d   86 (91)
T 2dnr_A           75 NRTITIALKSPS   86 (91)
T ss_dssp             TEEEEEEECCCS
T ss_pred             CeEEEEEeCCCC
Confidence            999999877654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.93  E-value=2e-09  Score=92.35  Aligned_cols=75  Identities=17%  Similarity=0.116  Sum_probs=66.2

Q ss_pred             CCCccEEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCC-HHHHHHHHhhcC--CcccCCcee
Q 006282           26 QFLTTSLYVGDLDFN-VTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN-PADAARALDVLN--FTPLNNKSI  101 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~-vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~-~e~A~~Al~~ln--~~~i~G~~i  101 (652)
                      =..++.|||+||+++ +++++|+++|+.||+|..|.+.+|..      .|||.|.+ .++|..|+..+|  +..|+|..+
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            346899999999999 99999999999999999999998865      49999999 899999999995  677889888


Q ss_pred             Eeecc
Q 006282          102 RIMYS  106 (652)
Q Consensus       102 ~i~~s  106 (652)
                      ++...
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            77543

>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=98.81  E-value=6.3e-09  Score=83.71  Aligned_cols=74  Identities=12%  Similarity=0.194  Sum_probs=63.5

Q ss_pred             ccccceeeecCCCC-----CCCH----HHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          308 KFQGLNLYIKNLGD-----SIDD----EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       308 ~~~~~~l~V~nlp~-----~~te----~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      .++..+|+|.-++.     ++-+    .+|.+.|+.||+|..+++..|       -+||+|.+.++|.+|++ |||..++
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-------~~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-------cEEEEEcChHHHHHHHh-cCCeeeC
Confidence            45667888888763     2333    579999999999999999998       39999999999999998 9999999


Q ss_pred             CeeEEEEeccc
Q 006282          379 SKPLYVAVAQR  389 (652)
Q Consensus       379 g~~l~v~~~~~  389 (652)
                      ||.|+|++..+
T Consensus        84 Gr~L~V~~k~~   94 (95)
T 1ufw_A           84 GRAVKISGPSS   94 (95)
T ss_dssp             TEEEEEECCCC
T ss_pred             CeEEEEeccCC
Confidence            99999998653

>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=98.80  E-value=1.3e-08  Score=98.99  Aligned_cols=71  Identities=17%  Similarity=0.282  Sum_probs=63.2

Q ss_pred             CCCHHHHHHHhhhcCCeeEEEEecCC-----CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHHH
Q 006282          322 SIDDEKLKELFSEFGTITSCKVMRDP-----SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEE  392 (652)
Q Consensus       322 ~~te~~L~~~F~~fG~I~~v~i~~~~-----~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~~  392 (652)
                      +-.+++|++.|++||.|.+++|.++.     +++++|++||+|.+.++|.+|+..|||+.++||.|.+.+....+-
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~f  215 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERF  215 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHHH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHHHh
Confidence            34568999999999999999998653     458999999999999999999999999999999999999886543

>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=98.74  E-value=1.3e-08  Score=81.80  Aligned_cols=74  Identities=16%  Similarity=0.201  Sum_probs=63.3

Q ss_pred             CCCCCccEEEEcCCCCC-----CCH----HHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           24 GNQFLTTSLYVGDLDFN-----VTD----SQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~-----vte----~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      ...++..+|+|.-++++     +-.    .+|.+.|++||.|..+|+..|.        +||+|.+.++|.+|++ ||+.
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~   80 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGM   80 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGS
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCe
Confidence            34556889999998754     322    4588999999999999999884        9999999999999999 9999


Q ss_pred             ccCCceeEeecc
Q 006282           95 PLNNKSIRIMYS  106 (652)
Q Consensus        95 ~i~G~~i~i~~s  106 (652)
                      .+.||.|+|.+-
T Consensus        81 ~v~Gr~L~V~~k   92 (95)
T 1ufw_A           81 KVKGRAVKISGP   92 (95)
T ss_dssp             EETTEEEEEECC
T ss_pred             eeCCeEEEEecc
Confidence            999999999763

>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=98.69  E-value=2.9e-08  Score=96.47  Aligned_cols=80  Identities=10%  Similarity=0.149  Sum_probs=67.6

Q ss_pred             ccEEEEcCCC-----CCCCHHHHHHHHhccCCeEEEEEEeeCCCC----CcccEEEEEeCCHHHHHHHHhhcCCcccCCc
Q 006282           29 TTSLYVGDLD-----FNVTDSQLYDLFSQVGQVLSVRVCRDLSTR----RSLGYGYVNYANPADAARALDVLNFTPLNNK   99 (652)
Q Consensus        29 ~~sL~V~nLp-----~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~----~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~   99 (652)
                      +..+.+.++-     .+-.+++|++.|++||.|.+++|+++..++    +++|++||+|.+.++|.+|++.||+..|.||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            4455555552     223578899999999999999999776554    8999999999999999999999999999999


Q ss_pred             eeEeecccC
Q 006282          100 SIRIMYSHR  108 (652)
Q Consensus       100 ~i~i~~s~~  108 (652)
                      .|++.+...
T Consensus       204 ~i~~~~~~~  212 (222)
T 3dxb_A          204 KVVAEVYDQ  212 (222)
T ss_dssp             BCEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999998764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.49  E-value=8.3e-07  Score=72.64  Aligned_cols=73  Identities=15%  Similarity=0.197  Sum_probs=67.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhc-----CCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEF-----GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~f-----G~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ..++|-+-||||.+++..|+.+.++|     |.|+.+.+..|..     -|+|+|.+...|.+|.-.|+|..|.|+.|++
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~-----GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN-----GAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT-----EEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC-----ceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            35689999999999999999999999     9999999999954     4999999999999999999999999999998


Q ss_pred             Eec
Q 006282          385 AVA  387 (652)
Q Consensus       385 ~~~  387 (652)
                      .-.
T Consensus        95 gTv   97 (117)
T 2l9w_A           95 GTI   97 (117)
T ss_dssp             ECH
T ss_pred             cCH
Confidence            743

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.99  E-value=8.9e-05  Score=60.34  Aligned_cols=88  Identities=22%  Similarity=0.232  Sum_probs=71.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhc-----cCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQ-----VGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~-----~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ...+|.|.|||++++++.|.-+|+.     =|+|.+++...        +-|+|.|.+.+.|++.|+. ....|+|.+|.
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            4689999999999999999999976     25999987754        3699999999999999994 35678899999


Q ss_pred             eecccCCcccccCCCcceeecCCCcccc
Q 006282          103 IMYSHRDPSIRKSGTGNIFIKNLDKSID  130 (652)
Q Consensus       103 i~~s~~~~~~~~~~~~~lfV~nLp~~~t  130 (652)
                      |.....      ....++++.+|++.++
T Consensus        78 V~P~~~------~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           78 LRPAPP------RAPARLLLQGLPPGTS   99 (104)
T ss_dssp             EEECCC------CCCCCCCCCSCCCCCC
T ss_pred             EEcCCC------CCcceEeeecCCCCCC
Confidence            974322      1245799999998765

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.78  E-value=9.8e-05  Score=60.51  Aligned_cols=72  Identities=19%  Similarity=0.204  Sum_probs=65.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhcc-----CCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQV-----GQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~-----G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ...++|-+-+||..++.+.|+.+.+.+     |.+..|.+..|-      +-|+|+|.+..+|-+|.-.|++..|.|+.|
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            346899999999999999999999999     999999887763      469999999999999998899999999999


Q ss_pred             Eee
Q 006282          102 RIM  104 (652)
Q Consensus       102 ~i~  104 (652)
                      +|.
T Consensus        93 r~g   95 (117)
T 2l9w_A           93 RSG   95 (117)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            984

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.69  E-value=5.6e-05  Score=61.90  Aligned_cols=75  Identities=17%  Similarity=0.252  Sum_probs=63.2

Q ss_pred             ccEEEEcCCCCCC-CH----HHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           29 TTSLYVGDLDFNV-TD----SQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        29 ~~sL~V~nLp~~v-te----~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      -++|+|.||+.+| +.    +.++++|..|+++.+....+.      ..=.-|+|.++++|.+|...|++..|.|+.++|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3589999999876 32    467899999999988777653      223689999999999999999999999999999


Q ss_pred             ecccCC
Q 006282          104 MYSHRD  109 (652)
Q Consensus       104 ~~s~~~  109 (652)
                      .+.+..
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998843

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.59  E-value=0.00012  Score=59.88  Aligned_cols=73  Identities=19%  Similarity=0.255  Sum_probs=63.3

Q ss_pred             cceeeecCCCCCC-CH----HHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          311 GLNLYIKNLGDSI-DD----EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       311 ~~~l~V~nlp~~~-te----~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      .++|+|.||+.++ ..    +.++++|..|+.+.+...++.     =.-..|.|.+.++|.+|...||+..++|+.++|-
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            4579999998766 32    577999999999998887764     2358999999999999999999999999999999


Q ss_pred             ecc
Q 006282          386 VAQ  388 (652)
Q Consensus       386 ~~~  388 (652)
                      +++
T Consensus        80 Fgq   82 (104)
T 1wey_A           80 FAQ   82 (104)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            998

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.45  E-value=0.00037  Score=56.12  Aligned_cols=68  Identities=13%  Similarity=0.108  Sum_probs=57.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCC--cccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR--SLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~--s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      +.|.||+||+.+||+++.+.++.+..+....-+..+.+.+  ...-|||+|.+.+++....+.+++..|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            5799999999999999999999998888777777665433  3357999999999999999999877663

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.14  E-value=0.0019  Score=51.89  Aligned_cols=61  Identities=23%  Similarity=0.318  Sum_probs=47.7

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN   92 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln   92 (652)
                      ...+.-.-.++| ++|.++...||.++|+.||-| .|+=+.|  |     -|||.|.+++.|..|+..++
T Consensus        10 d~~p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD--T-----sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           10 DLQPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC--C-----eEEEEecCHHHHHHHHHhcc
Confidence            333444567777 999999999999999999854 3444444  3     69999999999999999764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.07  E-value=0.0021  Score=52.33  Aligned_cols=69  Identities=23%  Similarity=0.372  Sum_probs=57.3

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhh-----cCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSE-----FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~-----fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      .+++|.|.|||..++++.|.-+|+.     -|.|.+++...       +-|+|+|.+.+.|++.++ -....+.+.+|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLA-QADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhc-CCcceecCeEEEE
Confidence            4678999999999999999999986     36899998765       369999999999999886 3355777788888


Q ss_pred             Ee
Q 006282          385 AV  386 (652)
Q Consensus       385 ~~  386 (652)
                      .-
T Consensus        79 ~P   80 (104)
T 2dhx_A           79 RP   80 (104)
T ss_dssp             EE
T ss_pred             Ec
Confidence            73

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.85  E-value=0.003  Score=53.19  Aligned_cols=74  Identities=16%  Similarity=0.138  Sum_probs=58.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC-ceeEe
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN-KSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G-~~i~i  103 (652)
                      .....+.|.|-+.|++ .-..|.+.|++||.|.+....      ....+.+|.|.+..+|++||. .|+..|.| -.|-|
T Consensus        20 ~~~~~~wVtVFGFp~~-~~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV   91 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQA-SASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGV   91 (119)
T ss_dssp             -CGGGGEEEEECCCGG-GHHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEE
T ss_pred             CCCCCCEEEEECCCHH-HHHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEE
Confidence            3455789999999988 477788899999999988762      123599999999999999999 69988875 44555


Q ss_pred             ecc
Q 006282          104 MYS  106 (652)
Q Consensus       104 ~~s  106 (652)
                      .+.
T Consensus        92 ~p~   94 (119)
T 1wwh_A           92 KPC   94 (119)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            554

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.70  E-value=0.005  Score=51.87  Aligned_cols=75  Identities=12%  Similarity=0.165  Sum_probs=60.1

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC-eeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS-KPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g-~~l~v~~~  387 (652)
                      ...+.|.|-+.+.+. ...|..+|+.||+|.+.....     ...+-.|.|.+..+|.+|+. .||..++| -.|-|..-
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            345689999999884 677889999999999988621     25699999999999999999 79999985 56666654


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus        95 ~d~   97 (119)
T 1wwh_A           95 IDK   97 (119)
T ss_dssp             CCH
T ss_pred             CCH
Confidence            433

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.56  E-value=0.003  Score=50.93  Aligned_cols=53  Identities=26%  Similarity=0.422  Sum_probs=43.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN   92 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln   92 (652)
                      .++| ++|.++...||.++|+.||-| .|+=+-|  |     -|||.|.+++.|..|+..++
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidD--T-----sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD--T-----SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEET--T-----EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcC--C-----eEEEEecCHHHHHHHHHhcc
Confidence            4566 999999999999999999933 3444444  3     69999999999999999775

>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=96.51  E-value=0.0048  Score=49.55  Aligned_cols=54  Identities=30%  Similarity=0.450  Sum_probs=45.4

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhc
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN  373 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~ln  373 (652)
                      ..++| ++|.++.-.||.++|+.||.| .|+.+.|.      .|||.|.+++.|..|+..++
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            34666 999999999999999999844 46666663      69999999999999999764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.38  E-value=0.0024  Score=51.65  Aligned_cols=70  Identities=14%  Similarity=0.068  Sum_probs=51.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCC--cccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR--SLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~--s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      .+-.|.||.||+.+||+++.+.++.+=.+....-+..+.+.+  ...-|||+|.+.+|.....+..++..|.
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            466899999999999999988887764443333333332221  2256999999999999999999887663

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.33  E-value=0.015  Score=46.79  Aligned_cols=68  Identities=12%  Similarity=0.214  Sum_probs=56.2

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC---CCCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---SGISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~---~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      ++|.|++||..+|++++.+.++....+.....+...   .-..-.-|+|.|.+.+++....+.++|..|.+
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            479999999999999999999999887766665443   12234569999999999999999999998853

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.18  E-value=0.0052  Score=49.52  Aligned_cols=53  Identities=28%  Similarity=0.420  Sum_probs=45.4

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhc
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN  373 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~ln  373 (652)
                      .++| ++|.++.-.||.++|+.|| =..|+.+.|.      .|||.|.+++.|..|+..++
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            4667 9999999999999999998 4456666664      69999999999999999764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.88  E-value=0.0035  Score=66.28  Aligned_cols=57  Identities=9%  Similarity=0.186  Sum_probs=44.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhh
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV   90 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~   90 (652)
                      ..+||+|. .|..+++++|.++|++||+|.++....++.     -||.|+|.+.+++..+++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHhc
Confidence            36899998 799999999999999999999987776543     5999999999999988774

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.27  E-value=0.027  Score=48.04  Aligned_cols=77  Identities=23%  Similarity=0.323  Sum_probs=57.3

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEE-EecCC-------------CC-CCccEEEEEeCCHHHHHHHHHHhcCcE
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCK-VMRDP-------------SG-ISKGSGFVAFSTPEEASRALAEMNGKM  376 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~-i~~~~-------------~g-~s~g~afV~F~s~~~A~~A~~~lng~~  376 (652)
                      +.|.|-+.|.+. ...+-+.|++||.|.+.. +.++.             -+ ...++.-|+|++..+|.+|+. .||..
T Consensus         8 ~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            357788886654 456778999999997732 21100             00 135688999999999999998 99999


Q ss_pred             ecCeeEEEEecccH
Q 006282          377 IVSKPLYVAVAQRK  390 (652)
Q Consensus       377 ~~g~~l~v~~~~~~  390 (652)
                      |+|..|-|....+.
T Consensus        86 i~G~mIGV~Py~~~   99 (132)
T 3p3d_A           86 FNGVLLGVIPYTKD   99 (132)
T ss_dssp             ETTEECEEEECCHH
T ss_pred             eCcEEEEEEECCHH
Confidence            99998888877543

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.81  E-value=0.026  Score=48.12  Aligned_cols=76  Identities=21%  Similarity=0.234  Sum_probs=54.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEeeC------------CCC-CcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLS-VRVCRDL------------STR-RSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~-i~v~~d~------------~t~-~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      .+.|.|-+.|++ ....+.+.|++||.|.+ +.+.++.            ... ...++..|.|.+..+|.+||. .|+.
T Consensus         7 e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            567888899776 56677789999999866 2111100            000 124688999999999999999 6999


Q ss_pred             ccCCceeEeecc
Q 006282           95 PLNNKSIRIMYS  106 (652)
Q Consensus        95 ~i~G~~i~i~~s  106 (652)
                      .|.|.-|-|.+.
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999987766654

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.53  E-value=0.067  Score=56.49  Aligned_cols=54  Identities=20%  Similarity=0.286  Sum_probs=40.9

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA  370 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~  370 (652)
                      ++|+|. .+..+++.+|.++|+.||.|.++....+ .|   -|+.|+|.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~-~g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES-FG---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS-SS---EEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc-CC---eEEEEEeCCHHHHHHHHh
Confidence            479997 7999999999999999999999977654 23   599999999999987765

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.45  E-value=0.16  Score=41.03  Aligned_cols=69  Identities=12%  Similarity=0.213  Sum_probs=50.8

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC--C-CCCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--S-GISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~--~-g~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      +-+|.|++||+.+|++++.+.++..=++.....+...  . ...-..|+|.|.+.++.....+.++|..|.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            3469999999999999999998876554322222111  1 1123458999999999999999999998853

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=85.64  E-value=1.9  Score=46.39  Aligned_cols=56  Identities=23%  Similarity=0.401  Sum_probs=45.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF   93 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~   93 (652)
                      ...++|+ +|..+...+|.++|+.||.| +|+-+-|       ..|||.|.+.++|..++++++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            4577787 99999999999999999954 4443332       2699999999999999998863

>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*

Probab=80.32  E-value=0.34  Score=51.22  Aligned_cols=6  Identities=67%  Similarity=1.054  Sum_probs=2.4

Q ss_pred             ceeecC
Q 006282          119 NIFIKN  124 (652)
Q Consensus       119 ~lfV~n  124 (652)
                      ++++-+
T Consensus        70 ~~ll~~   75 (448)
T 2z73_A           70 NMFIIN   75 (448)
T ss_dssp             HHHHHH
T ss_pred             chHHHH
Confidence            344433

---

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	652
d1nmra_	85	a.144.1.1 (A:) poly(A) binding protein {Protozoan	3e-32
d1g9la_	144	a.144.1.1 (A:) poly(A) binding protein {Human (Hom	1e-30
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-28
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-27
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-27
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-09
d1ifwa_	92	a.144.1.1 (A:) poly(A) binding protein {Baker's ye	6e-28
d1i2ta_	61	a.144.1.1 (A:) hyperplastic discs protein {Human (	1e-26
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-22
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-19
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-19
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-15
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-22
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-21
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-18
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-20
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-17
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	9e-19
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	9e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-18
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-17
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-18
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-18
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-18
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-18
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-18
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	7e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-18
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-17
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-17
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-17
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-14
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-17
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-17
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-16
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-17
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-16
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-17
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-16
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-16
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	9e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-16
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-14
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-14
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-16
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-16
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-16
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-16
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	9e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-16
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-15
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-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:) 6e-16
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-14
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:) 1e-12
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:) 1e-11
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	8e-16
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	5e-10
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-15
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-15
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-15
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-12
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-14
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	7e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-13
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-11
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-14
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-13
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-14
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-14
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-14
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-14
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-13
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-13
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	9e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-11
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-13
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-13
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-13
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-11
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-13
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-13
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-13
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-12
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	9e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	7e-13
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	7e-13
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-11
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-12
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	9e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-12
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-11
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-12
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	7e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	9e-12
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-11
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-11
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-07
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	6e-11
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	3e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-09
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	5e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-09
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	9e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	8e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-08
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	7e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	9e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.002
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	6e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	6e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-06

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]} Length = 85

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

 Score =  117 bits (295), Expect = 3e-32
 Identities = 42/72 (58%), Positives = 52/72 (72%)

Query: 557 ALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALK 616
            LST LAN +PEQQ+ +LGE LY  +  +   AAAKVTGMLLEMD  E+L+LL++P  L 
Sbjct: 10  NLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLD 69

Query: 617 AKVAEAMEVLRS 628
           AKV EA+EVL  
Sbjct: 70  AKVQEALEVLNR 81

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 144

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  115 bits (288), Expect = 1e-30
 Identities = 50/156 (32%), Positives = 81/156 (51%), Gaps = 17/156 (10%)

Query: 488 GPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDA 547
           GP+       P +   +P     Y+Y  G        +      +  P            
Sbjct: 1   GPLGSAAAATPAVR-TVPQ----YKYAAGVRNPQQHLNAQPQVTMQQPA----------V 45

Query: 548 SVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLH 607
            V    P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH
Sbjct: 46  HVQGQEPLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 103

Query: 608 LLESPEALKAKVAEAMEVLRSVAQQQANNPADQLAS 643
           +LESPE+L++KV EA+ VL++   ++A   A   A+
Sbjct: 104 MLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSAT 139

>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 =  110 bits (274), Expect = 2e-28
 Identities = 48/187 (25%), Positives = 76/187 (40%), Gaps = 10/187 (5%)

Query: 108 RDPS-IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQF 165
           ++P  +RK     +FI  L      ++L   F  +G +  C +  D  + +S+GFGFV +
Sbjct: 1   KEPEQLRK-----LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 55

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDL 225
              E    A++     +            R+  +   A  T    +FV  + E T +  L
Sbjct: 56  ATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLT-VKKIFVGGIKEDTEEHHL 114

Query: 226 KKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
           +  F +YG I    +M D G GK + F FV F++ D   K V        +     V KA
Sbjct: 115 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA 173

Query: 285 QKKSERE 291
             K E  
Sbjct: 174 LSKQEMA 180

>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 =  107 bits (266), Expect = 2e-27
 Identities = 39/187 (20%), Positives = 75/187 (40%), Gaps = 16/187 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L   TTDE L+  F ++GT+T  VVMRD +  +S+ FGFV +   ++   A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
             K                      +    +  +          +++  + +  ++  L+
Sbjct: 69  PHKVDGRVVEPK-------------RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 115

Query: 330 ELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
           + F ++G I   ++M D   G  +G  FV F   +   + +       +      V  A 
Sbjct: 116 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKAL 174

Query: 389 RKEERRA 395
            K+E  +
Sbjct: 175 SKQEMAS 181

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  106 bits (264), Expect = 5e-27
 Identities = 50/174 (28%), Positives = 75/174 (43%), Gaps = 5/174 (2%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A++  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 92  NFTPLNNKSIRIMYSHRDPSIRKSGT---GNIFIKNLDKSIDHKALHDTFSSFGNILSCK 148
                           R+ S R         IF+  + +  +   L D F  +G I   +
Sbjct: 69  PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 128

Query: 149 IATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
           I TD GSG+ +GF FV F++ +S    +       +N     V   L KQE  +
Sbjct: 129 IMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMAS 181

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (133), Expect = 1e-09
 Identities = 29/114 (25%), Positives = 46/114 (40%), Gaps = 1/114 (0%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+I  L     DE L+  F ++GT+T C VMRDP +  S+G GFV ++T EE   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSG 426
             K+            R++ +R        ++    +                G
Sbjct: 69  PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 122

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  105 bits (263), Expect = 6e-28
 Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 2/87 (2%)

Query: 552 PMPITALSTALANASPEQQRTLLGESLYPLVEQL--ERDAAAKVTGMLLEMDQTEVLHLL 609
           P+     +        ++QR  LGE LY  V       +AA K+TGM+L++   EV  LL
Sbjct: 2   PLGSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLL 61

Query: 610 ESPEALKAKVAEAMEVLRSVAQQQANN 636
           ES E  +    EA     S  ++Q   
Sbjct: 62  ESDELFEQHYKEASAAYESFKKEQEQQ 88

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  100 bits (251), Expect = 1e-26
 Identities = 27/59 (45%), Positives = 42/59 (71%)

Query: 570 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRS 628
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++ +
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIA 59

>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 = 90.0 bits (223), Expect = 1e-22
 Identities = 48/79 (60%), Positives = 60/79 (75%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           SLYVGDL  +VT++ LY+ FS  G +LS+RVCRD+ TRRSLGY YVN+  PADA RALD 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 91  LNFTPLNNKSIRIMYSHRD 109
           +NF  +  K +RIM+S RD
Sbjct: 62  MNFDVIKGKPVRIMWSQRD 80

>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 = 81.5 bits (201), Expect = 1e-19
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 269 LNGKKFDDREWYVGKAQK 286
           +N      +   +  +Q+
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 29/78 (37%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           +LY+ +L   + +  L E FS  G I S +V RD  +  S G  +V F  P +A RAL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 372 MNGKMIVSKPLYVAVAQR 389
           MN  +I  KP+ +  +QR
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 69.9 bits (171), Expect = 1e-15
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           ++++ +L   +    L++ FS  G ILS ++  D  + +S G+ +V F+    A+ A+D 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 178 LNGMLINDKQVFV 190
           +N  +I  K V +
Sbjct: 62  MNFDVIKGKPVRI 74

>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 = 88.6 bits (219), Expect = 4e-22
 Identities = 62/90 (68%), Positives = 79/90 (87%), Gaps = 1/90 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
           PS+RKSG GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+  D +G SKG+GFV FE +E
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQE 59

Query: 170 SAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           +A+ AI+K+NGML+ND++VFVG F  ++ER
Sbjct: 60  AAERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 85.5 bits (211), Expect = 5e-21
 Identities = 34/86 (39%), Positives = 55/86 (63%), Gaps = 1/86 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           K+   N+F+KNLD+S  ++ L   F  +G I S  V+ D +G SK +GFV+FE  + A +
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAER 63

Query: 265 AVEALNGKKFDDREWYVGKAQKKSER 290
           A+E +NG   +DR+ +VG+ + + ER
Sbjct: 64  AIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 78.2 bits (192), Expect = 2e-18
 Identities = 38/81 (46%), Positives = 55/81 (67%), Gaps = 1/81 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 68

Query: 373 NGKMIVSKPLYVAVAQRKEER 393
           NG ++  + ++V   + ++ER
Sbjct: 69  NGMLLNDRKVFVGRFKSRKER 89

>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 = 63.1 bits (153), Expect = 4e-13
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 2/78 (2%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             ++++ +LD ++ +  LYD FS  G +LS +V  D     S GYG+V++     A RA+
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAI 65

Query: 89  DVLNFTPLNNKSIRIMYS 106
           + +N   LN++ + +   
Sbjct: 66  EKMNGMLLNDRKVFVGRF 83

>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 = 86.9 bits (215), Expect = 2e-21
 Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 3/93 (3%)

Query: 202 VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD--GKSKCFGFVNFENA 259
           V  K   + + V+N+       +++++F  +G + +  + +     G  + FGFV+F   
Sbjct: 2   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

Query: 260 DDAAKAVEAL-NGKKFDDREWYVGKAQKKSERE 291
            DA KA  AL +      R   +  A  +   +
Sbjct: 62  QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 77.7 bits (191), Expect = 3e-18
 Identities = 18/85 (21%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALA 370
            + ++N+    +  +++ELFS FG + + ++ +    +G  +G GFV F T ++A +A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 371 EM-NGKMIVSKPLYVAVAQRKEERR 394
            + +   +  + L +  A  +   +
Sbjct: 70  ALCHSTHLYGRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 77.3 bits (190), Expect = 6e-18
 Identities = 19/87 (21%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS-TRRSLGYGYVNYANPADAARA 87
           T+ + V ++ F     ++ +LFS  G++ +VR+ + ++ T    G+G+V++    DA +A
Sbjct: 8   TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

Query: 88  LDVL-NFTPLNNKSIRIMYSHRDPSIR 113
            + L + T L  + + + ++  + +++
Sbjct: 68  FNALCHSTHLYGRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.9 bits (176), Expect = 3e-16
 Identities = 20/91 (21%), Positives = 46/91 (50%), Gaps = 3/91 (3%)

Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD--GSGQSKGFGFVQFENKES 170
           +K  T  I ++N+    + + + + FS+FG + + ++     G+G  +GFGFV F  K+ 
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 171 AQNAIDKL-NGMLINDKQVFVGHFLRKQERE 200
           A+ A + L +   +  +++ +     +   +
Sbjct: 64  AKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 83.1 bits (205), Expect = 8e-20
 Identities = 23/105 (21%), Positives = 48/105 (45%), Gaps = 3/105 (2%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             ++++NL    T E++  IFG+YG I    +      +++   +V +E+  DA  A + 
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN 313
           L+G    +R   V         ++    + E+ +K  + +  G+N
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKL-LKEKYGIN 109

>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 = 75.4 bits (185), Expect = 4e-17
 Identities = 18/93 (19%), Positives = 44/93 (47%), Gaps = 3/93 (3%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LYI+NL   I  E++ ++F ++G I         +  ++G+ +V +    +A  A   ++
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQI--RVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 374 GKMIVSKPLYVAVAQ-RKEERRARLQAQFSQMR 405
           G  + ++ L V      +  ++   + +  Q++
Sbjct: 68  GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLK 100

>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 = 73.5 bits (180), Expect = 2e-16
 Identities = 24/114 (21%), Positives = 54/114 (47%), Gaps = 16/114 (14%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++I+NL   I  + ++D F  +G I   ++    + +++G  +V +E+   A+NA D L+
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG 233
           G  + ++ + V ++   +                + +D    +E LK +  +YG
Sbjct: 68  GFNVCNRYLVVLYYNANRAF--------------QKMDTKKKEEQLKLLKEKYG 107

>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 = 71.2 bits (174), Expect = 1e-15
 Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 3/87 (3%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              LY+ +L + +T  ++YD+F + G +  +RV     TR   G  YV Y +  DA  A 
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAC 63

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKS 115
           D L+   + N+ + ++Y + + + +K 
Sbjct: 64  DHLSGFNVCNRYLVVLYYNANRAFQKM 90

>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 = 79.3 bits (195), Expect = 9e-19
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 4/81 (4%)

Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD----GDGKSKCFGFVNFENADDAAKAVE 267
           F+KNL+ STT+E LK +F + G I S  + +     G   S  FGFV ++  + A KA++
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 268 ALNGKKFDDREWYVGKAQKKS 288
            L G   D  +  V  +++ +
Sbjct: 62  QLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 75.1 bits (184), Expect = 2e-17
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 4/82 (4%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTPEEASRAL 369
           L+IKNL  S  +E LK +FS+ G I SC + +        +S G GFV +  PE+A +AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 370 AEMNGKMIVSKPLYVAVAQRKE 391
            ++ G  +    L V +++R  
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.1 bits (166), Expect = 6e-15
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLS---VRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           L++ +L+F+ T+  L  +FS+VG + S    +         S+G+G+V Y  P  A +AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 89  DVLNFTPLNNKSIRIMYSHRDP 110
             L    ++   + +  S R  
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.7 bits (157), Expect = 9e-14
 Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD----GSGQSKGFGFVQFENKESAQNAI 175
           +FIKNL+ S   + L   FS  G I SC I+      G   S GFGFV+++  E AQ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 176 DKLNGMLINDKQVFV 190
            +L G  ++  ++ V
Sbjct: 61  KQLQGHTVDGHKLEV 75

>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 = 78.8 bits (194), Expect = 2e-18
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           ++V NL   TT+E + ++F + G I   ++  D     +  F FV + +  DA  A+  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
           NG + DDR           E  Q
Sbjct: 70  NGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 75.4 bits (185), Expect = 2e-17
 Identities = 27/86 (31%), Positives = 49/86 (56%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           + +LYVG+L F  T+ Q+Y+LFS+ G +  + +  D   + + G+ +V Y + ADA  A+
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRK 114
             +N T L+++ IR  +       R+
Sbjct: 67  RYINGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 71.5 bits (175), Expect = 5e-16
 Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 7/97 (7%)

Query: 299 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS-GFV 357
           E+ +K++        LY+ NL     +E++ ELFS+ G I    +  D    +     FV
Sbjct: 1   EKLLKKSC------TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 54

Query: 358 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 394
            + +  +A  A+  +NG  +  + +        +E R
Sbjct: 55  EYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR 91

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.0 bits (158), Expect = 1e-13
 Identities = 20/80 (25%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 112 IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKES 170
           ++KS T  +++ NL      + +++ FS  G+I    +  D     + GF FV++ ++  
Sbjct: 4   LKKSCT--LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 61

Query: 171 AQNAIDKLNGMLINDKQVFV 190
           A+NA+  +NG  ++D+ +  
Sbjct: 62  AENAMRYINGTRLDDRIIRT 81

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.1 bits (192), Expect = 2e-18
 Identities = 26/71 (36%), Positives = 39/71 (54%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++  N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 271 GKKFDDREWYV 281
           G   D R   +
Sbjct: 63  GVPLDGRPMNI 73

>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 = 76.9 bits (189), Expect = 4e-18
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ + N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 374 GKMIVSKPLYVAVAQ 388
           G  +  +P+ + +  
Sbjct: 63  GVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.5 bits (175), Expect = 3e-16
 Identities = 20/73 (27%), Positives = 37/73 (50%)

Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
           G + + NLD  +    + + F+ FG +    +  D SG+S G   V FE K  A  A+ +
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 178 LNGMLINDKQVFV 190
            NG+ ++ + + +
Sbjct: 61  YNGVPLDGRPMNI 73

>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 = 67.3 bits (164), Expect = 9e-15
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L V +LDF V+D+ + +LF++ G +    V  D  + RSLG   V++   ADA +A+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 61

Query: 92  NFTPLNNKSIRIMYS 106
           N  PL+ + + I   
Sbjct: 62  NGVPLDGRPMNIQLV 76

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.4 bits (190), Expect = 3e-18
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 269
           ++V  L E   D+ L   F  +G IT   +  D + +  + F FV FE A+DAA A++ +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 270 NGKKFDDREWYVGKAQKKSERE 291
           N  +   R   V  A+    +E
Sbjct: 68  NESELFGRTIRVNLAKPMRIKE 89

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.3 bits (169), Expect = 3e-15
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           LY+  L + +DD+ L   F  FG IT  ++  D  +   +G  FV F   E+A+ A+  M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 373 NGKMIVSKPLYVAVAQRKEER 393
           N   +  + + V +A+    +
Sbjct: 68  NESELFGRTIRVNLAKPMRIK 88

>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 = 67.4 bits (164), Expect = 1e-14
 Identities = 23/76 (30%), Positives = 39/76 (51%)

Query: 31  SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
            LYVG L   V D  L+  F   G +  +++  D  T +  G+ +V +    DAA A+D 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 91  LNFTPLNNKSIRIMYS 106
           +N + L  ++IR+  +
Sbjct: 67  MNESELFGRTIRVNLA 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 2e-13
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           +++  L + +D K LH  F  FG+I   +I  D  + + +GF FV+FE  E A  AID +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 179 NGMLINDKQVFVGHFLRKQERE 200
           N   +  + + V      + +E
Sbjct: 68  NESELFGRTIRVNLAKPMRIKE 89

>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 = 77.3 bits (190), Expect = 4e-18
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 269 LNGKKFDDREWYVGKAQ 285
           LNG    ++   V  A+
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 72.3 bits (177), Expect = 2e-16
 Identities = 28/77 (36%), Positives = 47/77 (61%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  ++TD +LY LF  +G + + R+ RD  T  S GY +V++ +  D+ RA+ 
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 90  VLNFTPLNNKSIRIMYS 106
           VLN   + NK +++ Y+
Sbjct: 63  VLNGITVRNKRLKVSYA 79

>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 = 72.0 bits (176), Expect = 3e-16
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 371
           NL +  L   + D +L  LF   G I +C++MRD   G S G  FV F++  ++ RA+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K L V+ A+
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 65.0 bits (158), Expect = 7e-14
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCK-IATDGSGQSKGFGFVQFENKESAQN 173
           S T N+ +  L + +  + L+  F + G I +C+ +    +G S G+ FV F ++  +Q 
Sbjct: 1   SNT-NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 59

Query: 174 AIDKLNGMLINDKQVFV 190
           AI  LNG+ + +K++ V
Sbjct: 60  AIKVLNGITVRNKRLKV 76

>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 = 77.4 bits (190), Expect = 4e-18
 Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           K+    + V N+     D DL+++FG++G I    ++ + +  SK FGFV FEN+ DA +
Sbjct: 8   KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSADADR 66

Query: 265 AVEALNGKKFDDREWYVGKAQKK 287
           A E L+G   + R+  V  A  +
Sbjct: 67  AREKLHGTVVEGRKIEVNNATAR 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.8 bits (165), Expect = 1e-14
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++ N+     D  L+++F +FG I   +++ +    SKG GFV F    +A RA  ++
Sbjct: 13  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKL 71

Query: 373 NGKMIVSKPLYVAVAQRK 390
           +G ++  + + V  A  +
Sbjct: 72  HGTVVEGRKIEVNNATAR 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 7e-13
 Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 2/88 (2%)

Query: 19  AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
           ++G S ++     L+V ++ F   D  L  +F Q G++L V +  +   R S G+G+V +
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTF 58

Query: 79  ANPADAARALDVLNFTPLNNKSIRIMYS 106
            N ADA RA + L+ T +  + I +  +
Sbjct: 59  ENSADADRAREKLHGTVVEGRKIEVNNA 86

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 114 KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQN 173
           KS    + + N+        L   F  FG IL  +I  +    SKGFGFV FEN   A  
Sbjct: 8   KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSADADR 66

Query: 174 AIDKLNGMLINDKQVFVGH 192
           A +KL+G ++  +++ V +
Sbjct: 67  AREKLHGTVVEGRKIEVNN 85

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.1 bits (189), Expect = 5e-18
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSA--VVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           +F+ NLD    ++ L   F  +G I     ++     G SK + F+NF + D +  A+EA
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
           +NG+   +R   V  A KK  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.6 bits (180), Expect = 7e-17
 Identities = 25/82 (30%), Positives = 47/82 (57%), Gaps = 2/82 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR--DPSGISKGSGFVAFSTPEEASRALAE 371
           ++I NL   ID++ L + FS FG I     +     +G SKG  F+ F++ + +  A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
           MNG+ + ++P+ V+ A +K+ +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.6 bits (167), Expect = 4e-15
 Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSV-RVCRDLSTRRSLGYGYVNYANPADAARALDV 90
           +++G+LD  + +  LYD FS  G +L   ++ RD  T  S GY ++N+A+   +  A++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 91  LNFTPLNNKSIRIMYSHRDPS 111
           +N   L N+ I + Y+ +  S
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.9 bits (160), Expect = 4e-14
 Identities = 30/82 (36%), Positives = 48/82 (58%), Gaps = 2/82 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIAT--DGSGQSKGFGFVQFENKESAQNAIDK 177
           IFI NLD  ID K L+DTFS+FG IL          +G SKG+ F+ F + +++  AI+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 178 LNGMLINDKQVFVGHFLRKQER 199
           +NG  + ++ + V +  +K  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 75.4 bits (185), Expect = 2e-17
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 3/83 (3%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAA 263
             K  N++V NL  + TD+ L  IFG+YG+I    ++RD   G+ +   FV +   ++A 
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 264 KAVEALNGKKFD--DREWYVGKA 284
           +A+ ALN    +   +   V  A
Sbjct: 63  EAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 73.8 bits (181), Expect = 6e-17
 Identities = 27/84 (32%), Positives = 49/84 (58%), Gaps = 3/84 (3%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
           +  +  NLY+ NL  +I D++L  +F ++G+I    ++RD  +G  +G  FV ++  EEA
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 366 SRALAEMNGKMI--VSKPLYVAVA 387
             A++ +N  +    S+PL V +A
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 70.8 bits (173), Expect = 8e-16
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 24  GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPAD 83
           G     T+LYV +L   +TD QL  +F + G ++   + RD  T R  G  +V Y    +
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 84  AARALDVLNFTPLN--NKSIRIMY 105
           A  A+  LN       ++ + +  
Sbjct: 61  AQEAISALNNVIPEGGSQPLSVRL 84

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 65.7 bits (160), Expect = 4e-14
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+++ NL ++I    L   F  +G+I+   I  D  +G+ +G  FV++  +E AQ AI  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 178 LNGMLIN 184
           LN ++  
Sbjct: 68  LNNVIPE 74

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.3 bits (185), Expect = 2e-17
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 209 NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           + VF+ NL+       D++ IF +YG I    V +        F FV + N  +A  AV 
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG-------FAFVQYVNERNARAAVA 68

Query: 268 ALNGKKFDDREWYVGKAQKKSERE 291
             +G+    +   +  A +     
Sbjct: 69  GEDGRMIAGQVLDINLAAEPKVNR 92

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.8 bits (181), Expect = 9e-17
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 313 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
            ++I NL    +    ++ +FS++G I  C V +       G  FV +     A  A+A 
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARAAVAG 69

Query: 372 MNGKMIVSKPLYVAVAQRKEERR 394
            +G+MI  + L + +A   +  R
Sbjct: 70  EDGRMIAGQVLDINLAAEPKVNR 92

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.4 bits (175), Expect = 6e-16
 Identities = 21/105 (20%), Positives = 52/105 (49%), Gaps = 13/105 (12%)

Query: 19  AAGASGN---QFLTTSLYVGDLD-FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYG 74
           ++G+SG    + + + +++G+L+   V  S +  +FS+ G+++   V +        G+ 
Sbjct: 2   SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFA 53

Query: 75  YVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGN 119
           +V Y N  +A  A+   +   +  + + I  +  +P + +SG  +
Sbjct: 54  FVQYVNERNARAAVAGEDGRMIAGQVLDINLA-AEPKVNRSGPSS 97

>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 = 64.5 bits (157), Expect = 2e-13
 Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 114 KSGTGNIFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
           +S    +FI NL+   +    +   FS +G I+ C +        KGF FVQ+ N+ +A+
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNAR 64

Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQERET 201
            A+   +G +I  + + +      +   +
Sbjct: 65  AAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>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 = 75.1 bits (184), Expect = 3e-17
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             ++V NL    T+  + ++F + G   S  ++ +    +  + FV F    DAA A+ A
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALAA 67

Query: 269 LNGKKFDDREWYVGKAQKKSERE 291
           +NG+K   +E  V  A   S ++
Sbjct: 68  MNGRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 1e-14
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 1/81 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY+ NL   + +  + +LFS+ G   SCK++ +    +    FV F    +A+ ALA MN
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-TSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 374 GKMIVSKPLYVAVAQRKEERR 394
           G+ I+ K + V  A     ++
Sbjct: 70  GRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 9e-14
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 3/85 (3%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            +LYVG+L  +VT+  +  LFSQ+G   S ++  +     +  Y +V +    DAA AL 
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAALA 66

Query: 90  VLNFTPLNNKSIRIMYSHRDPSIRK 114
            +N   +  K +++ ++   PS +K
Sbjct: 67  AMNGRKILGKEVKVNWA-TTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +++ NL + +    +   FS  G   SCK+ T+    +  + FV+F     A  A+  +N
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 180 GMLINDKQVFVGHFLRKQERE 200
           G  I  K+V V        ++
Sbjct: 70  GRKILGKEVKVNWATTPSSQK 90

>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 = 75.1 bits (184), Expect = 4e-17
 Identities = 26/83 (31%), Positives = 47/83 (56%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
            N+F+ +L +   D+DL ++F  +G + SA V  D     SKCFGFV+++N   A  A++
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
           ++NG +   +   V   + K++ 
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKNDS 101

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.3 bits (174), Expect = 9e-16
 Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRA 368
           +G NL+I +L     D+ L ++F  FG + S KV  D    +SK  GFV++  P  A  A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERR 394
           +  MNG  I  K L V + + K + +
Sbjct: 77  IQSMNGFQIGMKRLKVQLKRSKNDSK 102

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (148), Expect = 2e-12
 Identities = 24/97 (24%), Positives = 43/97 (44%)

Query: 12  MSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSL 71
           ++  +  AAG+        +L++  L     D  L  +F   G V+S +V  D  T  S 
Sbjct: 1   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR 108
            +G+V+Y NP  A  A+  +N   +  K +++     
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 97

>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 = 58.2 bits (140), Expect = 3e-11
 Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQNAIDK 177
           N+FI +L +    + L   F  FGN++S K+  D     SK FGFV ++N  SAQ AI  
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 178 LNGMLINDKQVFVGHFLRKQER 199
           +NG  I  K++ V     K + 
Sbjct: 80  MNGFQIGMKRLKVQLKRSKNDS 101

>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 = 74.3 bits (182), Expect = 4e-17
 Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 6/90 (6%)

Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           + +++ NL+E    ++LKK    IF  +G I   +V R      +   FV F+    A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATN 61

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQEL 294
           A+ ++ G  F D+   +  A+  S+   ++
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 70.8 bits (173), Expect = 8e-16
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 314 LYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +YI NL + I  ++LK     +FS FG I    V R      +G  FV F     A+ AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63

Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARL 397
             M G     KP+ +  A+   +  A++
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 59.3 bits (143), Expect = 8e-12
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 7/85 (8%)

Query: 29  TTSLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
             ++Y+ +L+  +   +L    + +FS+ GQ+L + V R L  R   G  +V +   + A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSA 59

Query: 85  ARALDVLNFTPLNNKSIRIMYSHRD 109
             AL  +   P  +K +RI Y+  D
Sbjct: 60  TNALRSMQGFPFYDKPMRIQYAKTD 84

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 120 IFIKNLDKSIDHKAL----HDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
           I+I NL++ I    L    H  FS FG IL   ++     + +G  FV F+   SA NA+
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63

Query: 176 DKLNGMLINDKQVFVGHFLRKQER 199
             + G    DK + + +     + 
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDI 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 = 74.3 bits (182), Expect = 5e-17
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             V+V  LDE  ++  L ++F + G + +  + +D   G+ + +GFV F + +DA  A++
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 268 ALNGKKFDDREWYVGKAQKKSE 289
            ++  K   +   V KA   ++
Sbjct: 70  IMDMIKLYGKPIRVNKASAHNK 91

>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 = 69.7 bits (170), Expect = 2e-15
 Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
           ++ Q   +Y+  L + + +  L ELF + G + +  + +D  +G  +G GFV F + E+A
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEE 392
             A+  M+   +  KP+ V  A    +
Sbjct: 65  DYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 68.1 bits (166), Expect = 7e-15
 Identities = 25/78 (32%), Positives = 45/78 (57%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             ++YVG LD  V++  L++LF Q G V++  + +D  T +  GYG+V + +  DA  A+
Sbjct: 9   DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 89  DVLNFTPLNNKSIRIMYS 106
            +++   L  K IR+  +
Sbjct: 69  KIMDMIKLYGKPIRVNKA 86

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 20/90 (22%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
           P   ++    +++  LD+ +    L + F   G +++  +  D  +GQ +G+GFV+F ++
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 169 ESAQNAIDKLNGMLINDKQVFVGHFLRKQE 198
           E A  AI  ++ + +  K + V       +
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 73.6 bits (180), Expect = 1e-16
 Identities = 14/92 (15%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM---RDGDGKSKCFGFVNFENADDAAKAVE 267
           +F+  + +    E++ +   +       V++        K++ F FV +E+   AA A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 268 ALNGKKF--DDREWYVGKAQKKSEREQELKGQ 297
            L   +      +  V  A+ + + ++++   
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 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 = 64.7 bits (157), Expect = 1e-13
 Identities = 11/92 (11%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM---RDPSGISKGSGFVAFSTPEEASRALA 370
           L+I  +      E++ E  ++        ++         ++G  FV + +   A+ A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 371 EMNGK--MIVSKPLYVAVAQRKEERRARLQAQ 400
           ++      +    + V  A+ + +    +   
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 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 = 57.8 bits (139), Expect = 3e-11
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIA---TDGSGQSKGFGFVQFENKESAQNAID 176
           +FI  + K    + + +  +     +   I         +++GF FV++E+  +A  A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 177 KLNG--MLINDKQVFVGHFLRKQERE 200
           KL    + +   Q+ V     + + +
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVD 89

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 5e-11
 Identities = 12/85 (14%), Positives = 32/85 (37%), Gaps = 4/85 (4%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLS--VRVCRDLSTRRSLGYGYVNYANPADAARA 87
             L++G +       ++ +  ++V + +   +         ++ G+ +V Y +   AA A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 88  LDVLNFTP--LNNKSIRIMYSHRDP 110
              L      L    I + ++  + 
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEI 86

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.5 bits (180), Expect = 1e-16
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             ++Y G +   +TD  +   FS  GQ++ +RV  +        Y +V ++    AA A+
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAI 71

Query: 89  DVLNFTPLNNKSIRIMYSHRDPS 111
             +N T +    ++  +    P 
Sbjct: 72  VSVNGTTIEGHVVKCYWGKESPD 94

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.8 bits (173), Expect = 1e-15
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            V+   +    TD+ +++ F  +G I    V  +     K + FV F   + AA A+ ++
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 74

Query: 270 NGKKFDDREWYVGKAQKK 287
           NG   +         ++ 
Sbjct: 75  NGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.1 bits (166), Expect = 9e-15
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 7/93 (7%)

Query: 298 FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFV 357
           FE  + ++  K     +Y   +   + D+ +++ FS FG I   +V  +         FV
Sbjct: 7   FEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFV 59

Query: 358 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 390
            FST E A+ A+  +NG  I    +     +  
Sbjct: 60  RFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.1 bits (148), Expect = 3e-12
 Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 12/97 (12%)

Query: 97  NNKSIRI--MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS 154
           N K +R   + +   P         ++   +   +  + +  TFS FG I+  ++  +  
Sbjct: 1   NTKQLRFEDVVNQSSPKNCT-----VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-- 53

Query: 155 GQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVG 191
              KG+ FV+F   ESA +AI  +NG  I    V   
Sbjct: 54  ---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 87

>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 = 72.8 bits (178), Expect = 2e-16
 Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVE 267
             +FV+NL  ++++EDL+K+F  YG ++      D   K  K F FV F   + A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 268 ALNGKKFDDREWYVGKAQKKSEREQ 292
            ++G+ F  R  +V  +  K E  Q
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 67.4 bits (164), Expect = 2e-14
 Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 1/96 (1%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG+   +  L+V +L +  ++  L  LFS  G +  +    D  T++  G+ +V +  
Sbjct: 1   GSSGSS-GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF 59

Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
           P  A +A   ++      + + ++ S       +SG
Sbjct: 60  PEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.4 bits (164), Expect = 2e-14
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE 371
            L+++NL  +  +E L++LFS +G ++      D      KG  FV F  PE A +A AE
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 372 MNGKMIVSKPLYVAVAQRKEERRAR 396
           ++G++   + L+V  +  K+E    
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQS 94

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.4 bits (151), Expect = 1e-12
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQFENKESAQN 173
           SG+G +F++NL  +   + L   FS++G +       D   +  KGF FV F   E A  
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQERE 200
           A  +++G +   + + V     K+E  
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.9 bits (176), Expect = 3e-16
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
           T+ + +FV NL    T+E+++K+F +YG      + +D     K FGF+  E    A  A
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 60

Query: 266 VEALNGKKFDDREWYVGKAQKKS 288
              L+      ++  V  A   +
Sbjct: 61  KVELDNMPLRGKQLRVRFACHSA 83

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 308 KFQGLN-LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
            F   + L++ NL   I +E++++LF ++G      + +D        GF+   T   A 
Sbjct: 4   TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAE 58

Query: 367 RALAEMNGKMIVSKPLYVAVAQRK 390
            A  E++   +  K L V  A   
Sbjct: 59  IAKVELDNMPLRGKQLRVRFACHS 82

>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 = 60.8 bits (147), Expect = 3e-12
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           + L+VG+L  ++T+ ++  LF + G+   V + +D        +G++       A  A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

Query: 90  VLNFTPLNNKSIRIMYSHRDPSI 112
            L+  PL  K +R+ ++    S+
Sbjct: 63  ELDNMPLRGKQLRVRFACHSASL 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           +    +F+ NL   I  + +   F  +G      I      + KGFGF++ E +  A+ A
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-----HKDKGFGFIRLETRTLAEIA 60

Query: 175 IDKLNGMLINDKQVFV 190
             +L+ M +  KQ+ V
Sbjct: 61  KVELDNMPLRGKQLRV 76

>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 = 71.7 bits (175), Expect = 3e-16
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 267
             + V  L   TT+ DL+++F +YG I    ++ D    +S+ F FV FEN DDA +A E
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 268 ALNGKKFDDREWYV 281
             NG + D R   V
Sbjct: 70  RANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.0 bits (168), Expect = 3e-15
 Identities = 25/83 (30%), Positives = 39/83 (46%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G   N      L V  L    T+  L ++FS+ G +  V +  D  +RRS G+ +V + N
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 81  PADAARALDVLNFTPLNNKSIRI 103
             DA  A +  N   L+ + IR+
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (152), Expect = 5e-13
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L +  L     +  L+E+FS++G I    ++ D  S  S+G  FV F   ++A  A   
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 372 MNGKMIVSKPLYV 384
            NG  +  + + V
Sbjct: 71  ANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 4e-12
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
            + +  L      + L + FS +G I    I  D  S +S+GF FV FEN + A+ A ++
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 178 LNGMLINDKQVFV 190
            NGM ++ +++ V
Sbjct: 71  ANGMELDGRRIRV 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 = 71.6 bits (175), Expect = 3e-16
 Identities = 17/80 (21%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L     D+ +K++   +G + +  +++D   G SK + F  + + +   +A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 270 NGKKFDDREWYVGKAQKKSE 289
           NG +  D++  V +A   ++
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 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 = 65.8 bits (160), Expect = 5e-14
 Identities = 18/75 (24%), Positives = 37/75 (49%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L   + D Q+ +L +  G + +  + +D +T  S GY +  Y +     +A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 92  NFTPLNNKSIRIMYS 106
           N   L +K + +  +
Sbjct: 64  NGMQLGDKKLLVQRA 78

>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 = 65.0 bits (158), Expect = 7e-14
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+I  L + ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 373 NGKMIVSKPLYVAVAQRKEE 392
           NG  +  K L V  A    +
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 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 = 60.8 bits (147), Expect = 3e-12
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI  L   ++   + +  +SFG + +  +  D  +G SKG+ F ++ +      AI  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 179 NGMLINDKQVFVGH 192
           NGM + DK++ V  
Sbjct: 64  NGMQLGDKKLLVQR 77

>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 = 72.0 bits (176), Expect = 4e-16
 Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
             + V NL E T + DL+++F  +G+I+   + +D   G+SK F F++F   +DAA+A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 268 ALNGKKFDDREWYVGKAQKKS 288
            ++G  +D     V  A+  +
Sbjct: 69  GVSGFGYDHLILNVEWAKPST 89

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (160), Expect = 5e-14
 Identities = 15/78 (19%), Positives = 42/78 (53%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             ++ V +L  +  ++ L +LF   G +  + + +D +T +S G+ ++++    DAARA+
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 89  DVLNFTPLNNKSIRIMYS 106
             ++    ++  + + ++
Sbjct: 68  AGVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 2e-13
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            + + NL +   +  L+ELF  FG+I+   + +D  +G SKG  F++F   E+A+RA+A 
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 372 MNGKMIVSKPLYVAVAQRKE 391
           ++G       L V  A+   
Sbjct: 70  VSGFGYDHLILNVEWAKPST 89

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 4e-12
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
           P+ R      I + NL +      L + F  FG+I    +A D  +GQSKGF F+ F  +
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 169 ESAQNAIDKLNGMLINDKQVFV 190
           E A  AI  ++G   +   + V
Sbjct: 61  EDAARAIAGVSGFGYDHLILNV 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.3 bits (174), Expect = 4e-16
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
           N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 269 LNGKKFDDREWYVGKAQ 285
           LNG +   +   V  A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (159), Expect = 4e-14
 Identities = 33/82 (40%), Positives = 51/82 (62%), Gaps = 2/82 (2%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+L V  L  N+T  +   LF  +G++ S ++ RD  T +SLGYG+VNY +P DA +A++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 90  VLNFTPLNNKSIRIMYSHRDPS 111
            LN   L  K+I++ Y+   PS
Sbjct: 63  TLNGLRLQTKTIKVSYA--RPS 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.4 bits (156), Expect = 1e-13
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 372 MNGKMIVSKPLYVAVAQ 388
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.0 bits (142), Expect = 9e-12
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
           N+ +  L +++  +     F S G I SCK+  D  +GQS G+GFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 178 LNGMLINDKQVFVGH 192
           LNG+ +  K + V +
Sbjct: 64  LNGLRLQTKTIKVSY 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 = 72.0 bits (176), Expect = 5e-16
 Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 267
             VF   L       DL+  F   G +    ++ D +  +SK   +V F        A+ 
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 78

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
            L G++       V  +Q +  R
Sbjct: 79  -LTGQRLLGVPIIVQASQAEKNR 100

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 2e-14
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            ++   L   I    L++ FS  G +   +++ D  S  SKG  +V F   +    A+  
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G 78

Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
           + G+ ++  P+ V  +Q ++ R
Sbjct: 79  LTGQRLLGVPIIVQASQAEKNR 100

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.0 bits (163), Expect = 3e-14
 Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +++   L   +    L D FS VG+V  VR+  D ++RRS G  YV +        A+
Sbjct: 18  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 77

Query: 89  DVLNFTPLNNKSIRIMYS 106
             L    L    I +  S
Sbjct: 78  G-LTGQRLLGVPIIVQAS 94

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 1e-11
 Identities = 27/100 (27%), Positives = 44/100 (44%), Gaps = 4/100 (4%)

Query: 101 IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKG 159
           +R    +  P  R + T  +F   L   I  + L D FS+ G +   +I +D  S +SKG
Sbjct: 4   VREPVDNLSPEERDART--VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 61

Query: 160 FGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
             +V+F   +S   AI  L G  +    + V     ++ R
Sbjct: 62  IAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR 100

>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 = 71.2 bits (174), Expect = 5e-16
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 265
           K +++ V  L   TT++DLK+ F  +G +    V +D   G SK FGFV F   +   K 
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 266 VEALNGKKFDDREWYVGKAQKKSERE 291
           +   +    D R         K  ++
Sbjct: 67  MSQRH--MIDGRWCDCKLPNSKQSQD 90

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.8 bits (168), Expect = 4e-15
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 5/93 (5%)

Query: 302 MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFS 360
           +K  V K    +L +  L     ++ LKE FS FG +   +V +D  +G SKG GFV F+
Sbjct: 1   VKRAVQK--TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 58

Query: 361 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 393
             E   + +++ +  MI  +     +   K+ +
Sbjct: 59  EYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.4 bits (159), Expect = 6e-14
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           T+ L V  L +  T+  L + FS  G+VL V+V +DL T  S G+G+V +       + +
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 89  DVLNFTPLNNKSIRIMYS 106
              +   ++ +       
Sbjct: 68  SQRHM--IDGRWCDCKLP 83

>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 = 63.8 bits (155), Expect = 2e-13
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 3/85 (3%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
           T ++ +  L      + L + FS+FG +L  ++  D  +G SKGFGFV+F   E+    +
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 176 DKLNGMLINDKQVFVGHFLRKQERE 200
            + +   I+ +         KQ ++
Sbjct: 68  SQRHM--IDGRWCDCKLPNSKQSQD 90

>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 = 71.6 bits (175), Expect = 6e-16
 Identities = 15/77 (19%), Positives = 34/77 (44%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
           ++  ++V ++   +   +E   ++  +YG +    V  +         +V F   +DA K
Sbjct: 24  RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEK 83

Query: 265 AVEALNGKKFDDREWYV 281
           AV  LN + F+ +  + 
Sbjct: 84  AVIDLNNRWFNGQPIHA 100

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 2e-14
 Identities = 13/72 (18%), Positives = 34/72 (47%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           ++ ++   D   +E   E+  ++G +    V  +      G+ +V F   E+A +A+ ++
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 373 NGKMIVSKPLYV 384
           N +    +P++ 
Sbjct: 89  NNRWFNGQPIHA 100

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 1e-12
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 1/95 (1%)

Query: 12  MSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSL 71
              P   +  A G +   + + + +      +    ++  + G+V  + VC +      +
Sbjct: 10  YRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLV 68

Query: 72  GYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS 106
           G  YV +    DA +A+  LN    N + I    S
Sbjct: 69  GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>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 = 59.7 bits (144), Expect = 1e-11
 Identities = 12/92 (13%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 104 MYSH-----RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSK 158
           +Y +     +     +S   ++ ++        +   +    +G +    +  +      
Sbjct: 9   IYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLV 68

Query: 159 GFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           G  +V+F  +E A+ A+  LN    N + +  
Sbjct: 69  GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

>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 = 71.8 bits (175), Expect = 8e-16
 Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN-ADDAAKAVEA 268
             F  +LD+ T  EDL  +F  +G I     +R         G + F+  A +A    + 
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKD 67

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQG 311
            N      R   V     + E E+E   +  +  +E+++K++ 
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKS 110

>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 = 55.2 bits (132), Expect = 5e-10
 Identities = 18/95 (18%), Positives = 30/95 (31%), Gaps = 6/95 (6%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP-EEASRALA 370
           L  +  +L D    E L  LFS  G I     +R         G + F    +EA     
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAK 66

Query: 371 EMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMR 405
           + N   +  +   V     + E       +  + +
Sbjct: 67  DANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQ 101

>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 = 49.8 bits (118), Expect = 4e-08
 Identities = 20/95 (21%), Positives = 31/95 (32%), Gaps = 6/95 (6%)

Query: 107 HRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFE 166
           H      K G    F  +LD     + LH  FS+ G I           +    G + F+
Sbjct: 1   HHGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-----RGAKEGIILFK 55

Query: 167 NK-ESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
            K + A       N   +  +   V   + + E E
Sbjct: 56  EKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVE 90

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (99), Expect = 1e-05
 Identities = 18/108 (16%), Positives = 32/108 (29%), Gaps = 18/108 (16%)

Query: 8   HQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLST 67
           H   +    G               + GDLD       L+ LFS  G++  +   R    
Sbjct: 1   HHGSLEEKIGC-----------LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG--- 46

Query: 68  RRSLGYGYVNYANPADAA-RALDVLNFTPLNNKSIRIMYSHRDPSIRK 114
                 G + +   A  A       N   L  ++  + +   +  + K
Sbjct: 47  ---AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEK 91

>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 = 70.1 bits (171), Expect = 1e-15
 Identities = 20/73 (27%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKA 265
           +  N++V  L ++ T ++L+++F +YG I ++ ++ D     S+  GF+ F+   +A +A
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 266 VEALNGKKFDDRE 278
           ++ LNG+K     
Sbjct: 65  IKGLNGQKPSGAT 77

>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 = 68.9 bits (168), Expect = 3e-15
 Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG-ISKGSGFVAFSTPEEASRALAE 371
           NLY+  L  ++  ++L++LFS++G I + +++ D    +S+G GF+ F    EA  A+  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 372 MNGKMI--VSKPLYVAVA 387
           +NG+     ++P+ V  A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 1e-13
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +LYV  L   +T  +L  LFSQ G++++ R+  D  T  S G G++ +    +A  A+
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 89  DVLNFTPLNNKSIRI 103
             LN    +  +  I
Sbjct: 66  KGLNGQKPSGATEPI 80

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 111 SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQFENKE 169
           SIR +   N+++  L K++  K L   FS +G I++ +I  D     S+G GF++F+ + 
Sbjct: 3   SIRDA---NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 59

Query: 170 SAQNAIDKLNGMLINDK 186
            A+ AI  LNG   +  
Sbjct: 60  EAEEAIKGLNGQKPSGA 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 = 70.9 bits (173), Expect = 1e-15
 Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 6/98 (6%)

Query: 194 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFG 252
           L +++RE    K +F  +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FG
Sbjct: 10  LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 65

Query: 253 FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSER 290
           FV F +  +   A+        D R     +A  + E 
Sbjct: 66  FVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES 102

>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 = 68.6 bits (167), Expect = 8e-15
 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS+  E   A+  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
                I  + +    A  +EE 
Sbjct: 81  ARPHSIDGRVVEPKRAVAREES 102

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 3/102 (2%)

Query: 99  KSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQS 157
           K++  +   R    ++     +FI  L      ++L + +  +G +  C +  D  S +S
Sbjct: 3   KTLETVPLERKKREKEQFR-KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 61

Query: 158 KGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           +GFGFV F +      A+       I+ + V     + ++E 
Sbjct: 62  RGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAREES 102

>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 = 57.4 bits (138), Expect = 6e-11
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             L++G L F  T+  L + + Q G++    V RD +++RS G+G+V +++ A+   A+ 
Sbjct: 21  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 80

Query: 90  VLNFTPLNNKSIRI 103
                 ++ + +  
Sbjct: 81  -ARPHSIDGRVVEP 93

>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 = 70.1 bits (171), Expect = 1e-15
 Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 204 IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 263
             +    ++V+NL  ST++E ++K F          V      K + + FV+F N +DA 
Sbjct: 4   TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAV 58

Query: 264 KAVEALNGKKFDDREWYVGKAQKKSER 290
           +A++ALNGK  D     V  A+   + 
Sbjct: 59  EAMKALNGKVLDGSPIEVTLAKPVDKD 85

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 3e-12
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LY++NL  S  +E +++ F+        +V        +   FV FS  E+A  A+  +N
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALN 65

Query: 374 GKMIVSKPLYVAVAQRKEER 393
           GK++   P+ V +A+  ++ 
Sbjct: 66  GKVLDGSPIEVTLAKPVDKD 85

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 16/87 (18%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           S    ++++NL  S   + +   F++       ++      + + + FV F N+E A  A
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEA 60

Query: 175 IDKLNGMLINDKQVFVGHFLRKQERET 201
           +  LNG +++   + V    +  ++++
Sbjct: 61  MKALNGKVLDGSPIEV-TLAKPVDKDS 86

>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 = 57.0 bits (137), Expect = 6e-11
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LYV +L  + ++  +   F+ +      RV      ++   Y +V+++N  DA  A+  L
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKAL 64

Query: 92  NFTPLNNKSIRIMYS 106
           N   L+   I +  +
Sbjct: 65  NGKVLDGSPIEVTLA 79

>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 = 70.2 bits (171), Expect = 2e-15
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 9/91 (9%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---------GDGKSKCFGFVNFENA 259
           + ++V+ L++S T +DL   F + G +                   GK K    V++E+ 
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 260 DDAAKAVEALNGKKFDDREWYVGKAQKKSER 290
             A  AVE  +GK F   +  V  A+KK   
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 62.9 bits (152), Expect = 8e-13
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 9/96 (9%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFV 357
           +      +Y++ L DS+  + L + F + G +   K    P         +G  KG   V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 358 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 393
           ++  P  A  A+   +GK      L V++A++K   
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 20/90 (22%), Positives = 38/90 (42%), Gaps = 8/90 (8%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQV--------LSVRVCRDLSTRRSLGYGYVNYAN 80
            +++YV  L+ +VT   L D F Q G V          + +  D  T +  G   V+Y +
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDP 110
           P  A  A++  +        +++  + + P
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>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 = 56.7 bits (136), Expect = 1e-10
 Identities = 20/100 (20%), Positives = 39/100 (39%), Gaps = 10/100 (10%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD---------GSGQSKG 159
           DP      +  I+++ L+ S+    L D F   G +   K              +G+ KG
Sbjct: 1   DPDEDSDNS-AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 59

Query: 160 FGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
              V +E+  +A+ A++  +G      ++ V    +K   
Sbjct: 60  DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 68.9 bits (168), Expect = 3e-15
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 373 NGKMIVSKPLYVAVA 387
           +   + SK +   VA
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.3 bits (164), Expect = 1e-14
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L   TT E L++ FG++G +   +VMRD    +S+ FGFV F +     K +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 270 NGKKFDDREWYVGKA 284
           +  + D +      A
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.8 bits (160), Expect = 3e-14
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++G L +  T   L + F Q G+V    V RD  T+RS G+G+V + + A   + L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 92  NFTPLNNKSIRI 103
           +   L++K+I  
Sbjct: 62  SRHELDSKTIDP 73

>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 = 63.1 bits (153), Expect = 3e-13
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI  L      + L + F  FG +  C +  D  + +S+GFGFV F ++      +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 179 NGMLINDKQVFV 190
           +   ++ K +  
Sbjct: 62  SRHELDSKTIDP 73

>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 = 68.1 bits (166), Expect = 4e-15
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 269
           +F+  L   TT +DLK  F ++G +    +  D     S+ FGFV F+ ++   K ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 270 NGKKFDDREWYVGKA 284
              K + +     +A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.8 bits (155), Expect = 1e-13
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           +++G L ++ T   L D FS+ G+V+   +  D  T RS G+G+V +       + +D  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 92  NFTPLNNKSIRI 103
               LN K I  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 60.0 bits (145), Expect = 4e-12
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           ++I  L      + LK+ FS+FG +  C +  DP +G S+G GFV F   E   + + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 373 NGKMIVSKPLYVAVA 387
               +  K +    A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI  L      K L D FS FG ++ C +  D  +G+S+GFGFV F+  ES    +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 179 NGMLINDKQVFV 190
               +N K +  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 67.4 bits (164), Expect = 1e-14
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N +++ NL  + T +DL+++FG+     +  V+         + FV++ + + A +A+E 
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIET 56

Query: 269 LNGK-KFDDREWYVGKAQKKSER 290
           L+GK +   +   V  +  K  R
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLR 79

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 7e-13
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           LYI NL  ++  + L++LF +     + +V+        G  FV +     A RA+  ++
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLS 58

Query: 374 GKMIV-SKPLYVAVAQRKEER 393
           GK+ +  K + V  +  K+ R
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 79

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 2e-11
 Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           ++I NL  ++    L   F      L+ ++         G+ FV + ++  A  AI+ L+
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLS 58

Query: 180 GML-INDKQVFVGHFLRKQER 199
           G + ++ K + V + + K+ R
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 79

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 3e-09
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LY+G+L   VT   L  LF      L+ +V          GY +V+Y +   A RA++ L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETL 57

Query: 92  N-FTPLNNKSIRIMYS 106
           +    L+ K + + YS
Sbjct: 58  SGKVELHGKIMEVDYS 73

>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 = 67.5 bits (164), Expect = 1e-14
 Identities = 34/81 (41%), Positives = 52/81 (64%), Gaps = 1/81 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 269
           +FV  L   T ++ L+++F +YG I+  VV++D + + S+ FGFV FEN DDA  A+ A+
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 270 NGKKFDDREWYVGKAQKKSER 290
           NGK  D R+  V +A K S+ 
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDN 88

>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 = 65.2 bits (158), Expect = 1e-13
 Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCK-VMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L++  L    +++ L+++FS++G I+    V    +  S+G GFV F   ++A  A+  M
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
           NGK +  + + V  A +  + R+
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDNRS 90

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 4e-11
 Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 1/86 (1%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQN 173
           S  G +F+  L    + ++L   FS +G I    +  D  + +S+GFGFV FEN + A++
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQER 199
           A+  +NG  ++ +Q+ V    +  + 
Sbjct: 63  AMMAMNGKSVDGRQIRVDQAGKSSDN 88

>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 = 57.4 bits (138), Expect = 5e-11
 Identities = 27/82 (32%), Positives = 46/82 (56%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L+VG L F+  +  L  +FS+ GQ+  V V +D  T+RS G+G+V + N  DA  A+  +
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 92  NFTPLNNKSIRIMYSHRDPSIR 113
           N   ++ + IR+  + +    R
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDNR 89

>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 = 67.4 bits (164), Expect = 2e-14
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             +  KNL  + T+++LK++F +   I          G      ++ F++  DA K +E 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG----IAYIEFKSEADAEKNLEE 72

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
             G + D R   +    +K   
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGT 94

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 63.5 bits (154), Expect = 3e-13
 Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +L   +L FN+T+ +L ++F    ++            +S G  Y+ + + ADA + L
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNL 70

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIR 113
           +      ++ +S+ + Y+      R
Sbjct: 71  EEKQGAEIDGRSVSLYYTGEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 63.5 bits (154), Expect = 3e-13
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L  KNL  +I +++LKE+F +   I          G SKG  ++ F +  +A + L E 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 373 NGKMIVSKPLYVAVAQRKEERR 394
            G  I  + + +     K   R
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 8/89 (8%)

Query: 106 SH--RDPSIRK--SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFG 161
           SH   DP   K       +  KNL  +I    L + F     I          G+SKG  
Sbjct: 1   SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIA 56

Query: 162 FVQFENKESAQNAIDKLNGMLINDKQVFV 190
           +++F+++  A+  +++  G  I+ + V +
Sbjct: 57  YIEFKSEADAEKNLEEKQGAEIDGRSVSL 85

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +F+  L   TTDE L+  F ++GT+T  VVMRD +  +S+ FGFV +   ++   A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 67

Query: 270 NGKKFDDREWYVGKA 284
              K D R     +A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 3e-12
 Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           L+I  L     DE L+  F ++GT+T C VMRDP +  S+G GFV ++T EE   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67

Query: 373 NGKMIVSKPLYVAVA 387
               +  + +    A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           L++G L F  TD  L   F Q G +    V RD +T+RS G+G+V YA   +   A++  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-A 67

Query: 92  NFTPLNNKSIRI 103
               ++ + +  
Sbjct: 68  RPHKVDGRVVEP 79

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-11
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           +FI  L      ++L   F  +G +  C +  D  + +S+GFGFV +   E    A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67

Query: 179 NGMLINDKQVFV 190
               ++ + V  
Sbjct: 68  RPHKVDGRVVEP 79

>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 = 65.5 bits (159), Expect = 4e-14
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           +FV  L  +TT ED+K  F ++G +  A++M D    + + FGFV FE+ D   K  E +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 270 NGKKFDDREWYVGKA 284
           +  + +++     KA
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.7 bits (144), Expect = 4e-12
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG L  N T   +   F Q G+V    +  D +T R  G+G+V + +     +  + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 92  NFTPLNNKSIRI 103
           +F  +NNK +  
Sbjct: 61  HFHEINNKMVEC 72

>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 = 57.8 bits (139), Expect = 2e-11
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +++  L  +   E +K  F +FG +    +M D  +   +G GFV F + +   +   E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 373 NGKMIVSKPLYVAVA 387
           +   I +K +    A
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIAT-DGSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  L  +   + +   F  FG +    +     + + +GFGFV FE+++  +    ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 179 NGMLINDKQVFV 190
           +   IN+K V  
Sbjct: 61  HFHEINNKMVEC 72

>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 = 66.2 bits (161), Expect = 4e-14
 Identities = 22/104 (21%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 13  SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
           SG  GV  G +GN      +YVG+L  ++    + D+F + G +  + +           
Sbjct: 1   SG-GGVIRGPAGNN--DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP---P 54

Query: 73  YGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
           + +V + +P DA  A+   +    +   +R+ +       R +G
Sbjct: 55  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG---RGTG 95

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 1e-13
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           ++V NL      +D++ +F +YG I    +          F FV FE+  DA  AV   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAVYGRD 74

Query: 271 GKKFDDREWYVGKAQKKSER 290
           G  +D     V     +S R
Sbjct: 75  GYDYDGYRLRVEFP--RSGR 92

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           +Y+ NL   I  + ++++F ++G I    +            FV F  P +A  A+   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAEDAVYGRD 74

Query: 374 GKMIVSKPLYVAVAQRK 390
           G       L V   +  
Sbjct: 75  GYDYDGYRLRVEFPRSG 91

>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 = 55.8 bits (134), Expect = 2e-10
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFEN 167
           R P+        I++ NL   I  K + D F  +G I    +          F FV+FE+
Sbjct: 7   RGPAGNNDCR--IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFED 62

Query: 168 KESAQNAIDKLNGMLINDKQVFV 190
              A++A+   +G   +  ++ V
Sbjct: 63  PRDAEDAVYGRDGYDYDGYRLRV 85

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 65.9 bits (160), Expect = 4e-14
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
             +FV ++ E   ++++++ F +YG I +  +  D   G SK +  V +E    A  A E
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 268 ALNGKKFDDREWYVGKAQKK 287
           ALNG +   +   V     K
Sbjct: 68  ALNGAEIMGQTIQVDWCFVK 87

>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 = 60.9 bits (147), Expect = 2e-12
 Identities = 16/78 (20%), Positives = 34/78 (43%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
             L+V  +     + ++ + F   G++ ++ +  D  T  S GY  V Y     A  A +
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 90  VLNFTPLNNKSIRIMYSH 107
            LN   +  ++I++ +  
Sbjct: 68  ALNGAEIMGQTIQVDWCF 85

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 60.9 bits (147), Expect = 3e-12
 Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRA 368
           +G  L++ ++ +   +++++E F ++G I +  +  D     SKG   V + T ++A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 369 LAEMNGKMIVSKPLYVAVAQRK 390
              +NG  I+ + + V     K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>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 = 52.4 bits (125), Expect = 3e-09
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
            +F+ ++ +      + + F  +G I +  +  D  +G SKG+  V++E  + A  A + 
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 178 LNGMLINDKQVFV 190
           LNG  I  + + V
Sbjct: 69  LNGAEIMGQTIQV 81

>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 = 65.0 bits (158), Expect = 6e-14
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
           +FV  L   T +E +++ FG +G + S  +  D    K + F F+ F+  +   K +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 270 NGKKFDDREWYVGKA 284
                   +  +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (157), Expect = 8e-14
 Identities = 11/72 (15%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG L  +  + ++ + F   G+V S+ +  D  T +  G+ ++ +       + ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 92  NFTPLNNKSIRI 103
            +  +      I
Sbjct: 61  KYHNVGLSKCEI 72

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 3e-12
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           +++  L     +EK++E F  FG + S ++  D  +   +G  F+ F   E   + + E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 373 NGKMIVSKPLYVAVA 387
               +      + VA
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (144), Expect = 5e-12
 Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
           IF+  L      + + + F  FG + S ++  D  + + +GF F+ F+ +E  +  ++K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 179 NGMLINDKQVFV 190
               +   +  +
Sbjct: 61  KYHNVGLSKCEI 72

>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 = 65.4 bits (159), Expect = 7e-14
 Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 6/84 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + VFV       T+++L++ F +YG +    + +        F FV F +   A      
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA----FAFVTFADDQIAQSLCG- 60

Query: 269 LNGKKFDDREWYVGKAQKKSEREQ 292
                      ++  A+ K     
Sbjct: 61  -EDLIIKGISVHISNAEPKHNSNS 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 1e-11
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG+  +F+      +    L + FS +G+++   I        + F FV F + + AQ+ 
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSL 58

Query: 175 IDKLNGMLINDKQVFVGHFLRKQERET 201
                 ++I    V + +   K    +
Sbjct: 59  CG--EDLIIKGISVHISNAEPKHNSNS 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 12/82 (14%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            +++      + +++L+E FS++G +    + +     +    FV F+  + A       
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFA----FVTFADDQIAQSLC--G 60

Query: 373 NGKMIVSKPLYVAVAQRKEERR 394
              +I    ++++ A+ K    
Sbjct: 61  EDLIIKGISVHISNAEPKHNSN 82

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 8e-09
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 11/86 (12%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG    ++ ++VG    ++T+ +L + FSQ G V+ V +      +    + +V +A+
Sbjct: 1   GSSG----SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFAD 51

Query: 81  PADAARALDVLNFTPLNNKSIRIMYS 106
              A           +   S+ I  +
Sbjct: 52  DQIAQSLCG--EDLIIKGISVHISNA 75

>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 = 65.1 bits (158), Expect = 1e-13
 Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 10/99 (10%)

Query: 193 FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG 252
            LR +  ETV+  T+   V    L    +   L  +  + G + + ++  +     K + 
Sbjct: 5   LLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYS 59

Query: 253 FVNFENADDAAKAVEALNGKKFDDRE-----WYVGKAQK 286
           F  +   +++ +A   LNGK+  D        Y+   +K
Sbjct: 60  FARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 98

>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 = 52.8 bits (126), Expect = 3e-09
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 10/84 (11%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           Q L +    LG+ +   +L  +  + G + +  +  +         F  + T EE+ RA 
Sbjct: 19  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-----YSFARYRTTEESKRAY 73

Query: 370 AEMNGKMIV-----SKPLYVAVAQ 388
             +NGK +V        LY+   +
Sbjct: 74  VTLNGKEVVDDLGQKITLYLNFVE 97

>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 = 49.3 bits (117), Expect = 4e-08
 Identities = 13/88 (14%), Positives = 28/88 (31%), Gaps = 7/88 (7%)

Query: 102 RIMYSHRDPSIRKSGTGNIFIK--NLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKG 159
             +  H         T ++ +    L   +    L       G + +  +       +K 
Sbjct: 3   HTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-----PPNKP 57

Query: 160 FGFVQFENKESAQNAIDKLNGMLINDKQ 187
           + F ++   E ++ A   LNG  + D  
Sbjct: 58  YSFARYRTTEESKRAYVTLNGKEVVDDL 85

>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 = 45.1 bits (106), Expect = 1e-06
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 29 TTSLYV--GDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
          T SL V  G L   V+ +QL  +  + G V ++ +  +        Y +  Y    ++ R
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKR 71

Query: 87 ALDVLN 92
          A   LN
Sbjct: 72 AYVTLN 77

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.2 bits (158), Expect = 1e-13
 Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 1/91 (1%)

Query: 203 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC-FGFVNFENADD 261
           A+     +VFV N+    T+E LK IF E G + S  ++ D +      +GF  +++ + 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 262 AAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
           A  A+  LNG++F  R   V  A  +  +E+
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>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 = 58.6 bits (141), Expect = 3e-11
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 3/96 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE 371
           ++++ N+     +E+LK++FSE G + S +++ D      KG GF  +   E A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPV 407
           +NG+    + L V  A  ++ +            PV
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEEL--KSLGTGAPV 103

>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 = 4e-11
 Identities = 24/93 (25%), Positives = 52/93 (55%), Gaps = 2/93 (2%)

Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQFEN 167
           DP++ +S   ++F+ N+      + L D FS  G ++S ++  D      KG+GF ++++
Sbjct: 1   DPAVDRS-LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERE 200
           +E+A +A+  LNG   + + + V +   ++ +E
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 2e-10
 Identities = 28/93 (30%), Positives = 52/93 (55%), Gaps = 3/93 (3%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             S++VG++ +  T+ QL D+FS+VG V+S R+  D  T +  GYG+  Y +   A  A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 89  DVLNFTPLNNKSIRIMYSHRDPS---IRKSGTG 118
             LN    + +++R+  +  + +   ++  GTG
Sbjct: 68  RNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             + V+N+  + + +++   F  Y  I  +V ++  + G       V FE+ D+A  AV 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 268 ALNGKKFDDREWYV 281
            LN +    R+  +
Sbjct: 70  DLNDRPIGSRKVKL 83

>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 = 60.8 bits (147), Expect = 3e-12
 Identities = 14/76 (18%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
            + ++N+  ++  +++ + F  +  I     ++    G+  G   VAF + +EA+ A+ +
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 372 MNGKMIVSKPLYVAVA 387
           +N + I S+ + + + 
Sbjct: 71  LNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.3 bits (143), Expect = 9e-12
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENK 168
            S  K G   I ++N+  ++    + D F  +  I     +  +  G   G   V FE++
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 169 ESAQNAIDKLNGMLINDKQVFV 190
           + A  A+  LN   I  ++V +
Sbjct: 62  DEATAAVIDLNDRPIGSRKVKL 83

>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 = 58.1 bits (140), Expect = 2e-11
 Identities = 16/83 (19%), Positives = 35/83 (42%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           GAS  +   T + V ++ F V+  ++ D F     +      +        G   V + +
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 81  PADAARALDVLNFTPLNNKSIRI 103
             +A  A+  LN  P+ ++ +++
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKL 83

>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 = 64.4 bits (156), Expect = 2e-13
 Identities = 17/77 (22%), Positives = 34/77 (44%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
            N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF   E+ +     +  
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 269 LNGKKFDDREWYVGKAQ 285
            NGK            +
Sbjct: 79  FNGKFIKTPPGVSAPTE 95

>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 = 63.7 bits (154), Expect = 4e-13
 Identities = 31/95 (32%), Positives = 48/95 (50%)

Query: 294 LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKG 353
           LK    QA      +    NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G
Sbjct: 1   LKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 60

Query: 354 SGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
            GF    + E+    +   NGK I + P   A  +
Sbjct: 61  VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>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 = 50.9 bits (121), Expect = 1e-08
 Identities = 24/73 (32%), Positives = 36/73 (49%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           N++I NL  S+D + L +    FG ++S +I  D SG S+G GF + E+ E  +  I   
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 179 NGMLINDKQVFVG 191
           NG  I        
Sbjct: 80  NGKFIKTPPGVSA 92

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 4e-07
 Identities = 10/77 (12%), Positives = 26/77 (33%), Gaps = 1/77 (1%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T+LY+ +L  ++ + +L ++       +        S+  S G G+    +       + 
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPF-GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 90  VLNFTPLNNKSIRIMYS 106
             N   +         +
Sbjct: 78  HFNGKFIKTPPGVSAPT 94

>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 = 63.3 bits (153), Expect = 3e-13
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTIT-SAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
           +++ N   S T  +++ +  +   +  S  +       S+ F +++  + +DA   VE L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 270 NGKKFDDREWYVGKAQ 285
           NG K +        + 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 59.4 bits (143), Expect = 6e-12
 Identities = 13/77 (16%), Positives = 29/77 (37%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            +L++ +   + T   + DL   +  V        L    S  + Y++  +  DA   ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 90  VLNFTPLNNKSIRIMYS 106
            LN   +   ++    S
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.5 bits (138), Expect = 3e-11
 Identities = 12/76 (15%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAEM 372
           L++ N   S     +++L  +   +     +       S+   ++  ++ E+A   + ++
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 373 NGKMIVSKPLYVAVAQ 388
           NG  I    L   V+ 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.6 bits (120), Expect = 1e-08
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNIL-SCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +++ N   S   + + D       +  S ++ +     S+ F ++   +KE A+  ++KL
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 179 NGMLINDKQVFV 190
           NG+ I    +  
Sbjct: 64  NGLKIEGYTLVT 75

>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 = 63.9 bits (155), Expect = 3e-13
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
           L + ++NL   +  + L ++FS+FGT+         +   +    + ++ P  A  A   
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN---QFQALLQYADPVSAQHAKLS 64

Query: 372 MNGKMIV--SKPLYVAVAQRKEERRAR 396
           ++G+ I      L +  ++        
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNVKY 91

>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 = 63.5 bits (154), Expect = 5e-13
 Identities = 14/87 (16%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
           +    + V+NL    T + L +IF ++GT+   +        ++    + + +   A  A
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHA 61

Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQ 292
             +L+G+   +    +     K     
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKLTSLN 88

>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 = 59.3 bits (143), Expect = 2e-11
 Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 7/96 (7%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           S    I ++NL   +    LH  FS FG +L     T     ++    +Q+ +  SAQ+A
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHA 61

Query: 175 IDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
              L+G  I +        LR    +  ++  K+NN
Sbjct: 62  KLSLDGQNIYNA----CCTLRIDFSKLTSLNVKYNN 93

>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 = 57.7 bits (139), Expect = 6e-11
 Identities = 22/106 (20%), Positives = 43/106 (40%), Gaps = 18/106 (16%)

Query: 12  MSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSL 71
           M+G + V             + V +L + VT   L+ +FS+ G VL +        + + 
Sbjct: 1   MAGQSPV-----------LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQ 45

Query: 72  GYGYVNYANPADAARALDVLNFTPL--NNKSIRIMYS-HRDPSIRK 114
               + YA+P  A  A   L+   +     ++RI +S     +++ 
Sbjct: 46  FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY 91

>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 = 63.7 bits (154), Expect = 4e-13
 Identities = 16/103 (15%), Positives = 31/103 (30%), Gaps = 10/103 (9%)

Query: 313 NLYIKNLGDSIDDEK-----LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASR 367
            L      D +  E       + LF  +   T+ +  +           + FS P  A+ 
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAAD 61

Query: 368 ALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMG 410
           A   ++    + K + +  AQ      + L          + G
Sbjct: 62  ARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSSG 104

>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 = 56.7 bits (136), Expect = 1e-10
 Identities = 16/96 (16%), Positives = 35/96 (36%), Gaps = 15/96 (15%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDS-----QLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           G+SG+    + L     + +V        +   LF    +  + +  +            
Sbjct: 1   GSSGS----SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVR 50

Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPS 111
           +N++NP  AA A   L+ T    K +++ ++     
Sbjct: 51  INFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI 86

>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 = 56.0 bits (134), Expect = 2e-10
 Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 10/92 (10%)

Query: 209 NNVFVKNLDES-----TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 263
           + +     ++       T    + +F  Y   T+    +           +NF N   AA
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAA 60

Query: 264 KAVEALNGKKFDDREWYVGKAQKKSEREQELK 295
            A   L+  +F  +E  +  AQ        L 
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>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 = 52.5 bits (125), Expect = 3e-09
 Identities = 11/92 (11%), Positives = 28/92 (30%), Gaps = 10/92 (10%)

Query: 115 SGTGNIFIKNLDKSIDH-----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
           SG+  +     +  +             F ++    + +       +S     + F N  
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPL 57

Query: 170 SAQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
           SA +A  +L+      K++ +          +
Sbjct: 58  SAADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>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 = 62.8 bits (152), Expect = 5e-13
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 209 NNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMR--DGDGKSKCFGFVNFENADDAAKA 265
             + ++NL     DE+ L++ F  +G+I    +         + C  F+ FEN D A +A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 266 VEALNGKKFDDREWYVGKAQKK 287
           ++ +N     +RE  V  A KK
Sbjct: 65  LQ-MNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 310 QGLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA--FSTPEEAS 366
           +G  + I+NL  + +D+  L+E F  FG+I    +       S  +      F   + A 
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 367 RALAEMNGKMIVSKPLYVAVAQRK 390
           RAL +MN  ++ ++ + V++A +K
Sbjct: 63  RAL-QMNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.1 bits (124), Expect = 3e-09
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 3/83 (3%)

Query: 30  TSLYVGDLDFNVTDSQ-LYDLFSQVGQVLSVRVCRDL-STRRSLGYGYVNYANPADAARA 87
             + + +L   + D   L + F   G +  + +         +    ++ + N   A RA
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 88  LDVLNFTPLNNKSIRIMYSHRDP 110
           L  +N + L N+ I +  + + P
Sbjct: 65  LQ-MNRSLLGNREISVSLADKKP 86

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.9 bits (108), Expect = 4e-07
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 119 NIFIKNLDKS-IDHKALHDTFSSFGNILSCKIAT--DGSGQSKGFGFVQFENKESAQNAI 175
            I I+NL    +D   L ++F  FG+I    I         +    F+ FENK+SA+ A+
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 176 DKLNGMLINDKQVFV 190
            ++N  L+ ++++ V
Sbjct: 66  -QMNRSLLGNREISV 79

>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 = 63.3 bits (153), Expect = 5e-13
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             +++KNL    T+ DL  +F  +       +      G+ +   F+ F N + A +A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
            +NG K   +   +   + K +R
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQR 101

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.2 bits (145), Expect = 6e-12
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
            LY+KNL   + +  L  LF+ F       +     +G  +G  F+ F   E A +AL  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
           +NG  +  K L +   + K++R
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQR 101

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 9e-10
 Identities = 19/80 (23%), Positives = 35/80 (43%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
              LY+ +L   VT+  L  LF++  +     +   + T R  G  ++ + N   A +AL
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 89  DVLNFTPLNNKSIRIMYSHR 108
            ++N   L  K + I +   
Sbjct: 78  HLVNGYKLYGKILVIEFGKN 97

>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 = 49.8 bits (118), Expect = 3e-08
 Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 4/97 (4%)

Query: 104 MYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGF 162
           M+S  +P         +++KNL   +  + L   F+ F       I     +G+ +G  F
Sbjct: 8   MFSSYNPG---EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF 64

Query: 163 VQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQER 199
           + F NKE A  A+  +NG  +  K + +     K++R
Sbjct: 65  ITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR 101

>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 = 62.7 bits (151), Expect = 7e-13
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
            T   N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  K
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 265 AVEALNGKKFDDREWYVGKAQKK 287
           A+E L G K    E  + K + +
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGR 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 50.3 bits (119), Expect = 1e-08
 Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
           SH       +   N+FI NL+ +     L    S         +    +G ++ FG+V F
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 166 ENKESAQNAIDKLNGMLINDKQVFVGHFLRK 196
           E+ E  + A++ L G+ +   ++ +     +
Sbjct: 62  ESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.6 bits (152), Expect = 7e-13
 Identities = 17/96 (17%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 195 RKQERETVAIKTKFNNVFVKNLDESTTD--EDLKKIFGEYGTITSAVVMRDGDGKSKCFG 252
           R +    V IK  F+ +  ++      +  EDL+    ++G I   ++            
Sbjct: 4   RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVA 60

Query: 253 FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS 288
            V+F + ++A   ++ L+G+ F  R+         +
Sbjct: 61  SVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT 96

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.8 bits (142), Expect = 2e-11
 Identities = 19/111 (17%), Positives = 36/111 (32%), Gaps = 16/111 (14%)

Query: 282 GKAQKKSEREQELKGQFEQA-MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 340
           G ++ + ER   +K  F     ++       +             E L+   S+FG I  
Sbjct: 1   GPSRMRHERVVIIKNMFHPMDFEDDPLVLNEI------------REDLRVECSKFGQIRK 48

Query: 341 CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE 391
             +         G   V+F  PEEA   +  ++G+    + +         
Sbjct: 49  LLLFDRHP---DGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT 96

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 2e-08
 Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 3/57 (5%)

Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           L    S FG I    +         G   V F + E A   I  L+G     +Q+  
Sbjct: 36  LRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

>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 = 45.3 bits (107), Expect = 1e-06
 Identities = 14/83 (16%), Positives = 25/83 (30%), Gaps = 4/83 (4%)

Query: 25  NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
           N F         L  N     L    S+ GQ+  + +          G   V++ +P +A
Sbjct: 15  NMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEA 70

Query: 85  ARALDVLNFTPLNNKSIRIMYSH 107
              +  L+      + I      
Sbjct: 71  DYCIQTLDGRWFGGRQITAQAWD 93

>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 = 62.1 bits (150), Expect = 1e-12
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 7/89 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
             VF++NL   + +E L ++  ++G +    V+       SK   F  F   + A K + 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 268 ALN------GKKFDDREWYVGKAQKKSER 290
           A +      G K D R+  V  A  + E 
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.3 bits (140), Expect = 3e-11
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 7/94 (7%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEA 365
           D  +G  ++I+NL    ++E L E+  +FG +   +V+  P    SKG  F  F T E A
Sbjct: 4   DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 63

Query: 366 SRALAEMN------GKMIVSKPLYVAVAQRKEER 393
            + LA  +      G  +  + L V +A  ++E 
Sbjct: 64  QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.0 bits (129), Expect = 9e-10
 Identities = 14/83 (16%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
            ++++ +L F+  +  L ++  Q G +  VRV     T  S G  +  +     A + L 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 90  VLNF------TPLNNKSIRIMYS 106
             +         L+ + +++  +
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLA 91

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (117), Expect = 3e-08
 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
           PS    G   +FI+NL    + +AL +    FG++   ++     +  SKG  F QF  +
Sbjct: 2   PSDVTEGK-TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 169 ESAQNAIDKLNGMLINDKQVFVGHFLR 195
           E+AQ  +   +           G  L+
Sbjct: 61  EAAQKCLAAASLEAEGGGLKLDGRQLK 87

>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 = 62.4 bits (151), Expect = 1e-12
 Identities = 31/94 (32%), Positives = 45/94 (47%), Gaps = 3/94 (3%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAK 264
           T F  +FV  L   TTD  L+K F  +G I  AVV+ D    KS+ +GFV   +   A +
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 67

Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 298
           A +  N    D R+  V  A   + + + L+  F
Sbjct: 68  ACKDPNP-IIDGRKANVNLAYLGA-KPRSLQTGF 99

>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 = 58.6 bits (141), Expect = 3e-11
 Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
            T ++VG L ++ TD+ L   F   G +    V  D  T +S GYG+V  A+ A A RA 
Sbjct: 10  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 89  DVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
              N   ++ +   +  ++     R   TG
Sbjct: 70  KDPNPI-IDGRKANVNLAYLGAKPRSLQTG 98

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 4e-10
 Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE 371
            +++  L     D  L++ F  FG I    V+ D     S+G GFV  +    A RA  +
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 372 MNGKMIVSKPLYVAVAQRKEERRARLQAQFS 402
            N  +I  +   V +A    + R+ LQ  F+
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRS-LQTGFA 100

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 4e-09
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 106 SHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQ 164
           S +D +  K     IF+  L       +L   F  FG+I    + TD  +G+S+G+GFV 
Sbjct: 4   SQKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 58

Query: 165 FENKESAQNAIDKLNGMLINDKQVFV 190
             ++ +A+ A    N + I+ ++  V
Sbjct: 59  MADRAAAERACKDPNPI-IDGRKANV 83

>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 = 61.7 bits (149), Expect = 1e-12
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
            K  +V++K      T +D+K+   + G + +  + R      K   FV F++ + A K 
Sbjct: 4   VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 63

Query: 266 VEALNGKKFDDREWYV 281
           VE   G+K+ + +  +
Sbjct: 64  VE-TPGQKYKETDLLI 78

>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 = 53.2 bits (127), Expect = 1e-09
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 4/80 (5%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           ++YIK        + +KE   + G + + ++ R      KGS FV F + E A + + E 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 66

Query: 373 NGKMIVSKPLYVAVAQRKEE 392
            G+      L +     K++
Sbjct: 67  PGQKYKETDLLI---LFKDD 83

>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 = 4e-09
 Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
           +++IK          + +     G +L+ ++        KG  FV F++ ESA+  + + 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 66

Query: 179 NGMLINDKQVFV 190
            G    +  + +
Sbjct: 67  PGQKYKETDLLI 78

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 13/82 (15%), Positives = 32/82 (39%), Gaps = 2/82 (2%)

Query: 25  NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
           N     S+Y+     + T   + +     GQVL++++ R    +   G  +V + +   A
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESA 60

Query: 85  ARALDVLNFTPLNNKSIRIMYS 106
            + ++           + I++ 
Sbjct: 61  KKFVE-TPGQKYKETDLLILFK 81

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 266
           K N ++V   D   T   L+  F  +G I    +        +   FV +E  + A +AV
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAV 56

Query: 267 EALNGKKFDDREWYVGKAQKK 287
             LNG + +  +  V  A+K+
Sbjct: 57  AELNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
           +G  LY+      +    L+  FS FG I    +            FV +   E A +A+
Sbjct: 4   KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR-----NCAFVTYEKMESADQAV 56

Query: 370 AEMNGKMIVSKPLYVAVAQRK 390
           AE+NG  + S  L V +A+++
Sbjct: 57  AELNGTQVESVQLKVNIARKQ 77

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
             +LYV   D  +T + L   FS  G ++ + +             +V Y     A +A+
Sbjct: 5   GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAV 56

Query: 89  DVLNFTPLNNKSIRIMYSHRDP 110
             LN T + +  +++  + + P
Sbjct: 57  AELNGTQVESVQLKVNIARKQP 78

>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 = 47.3 bits (112), Expect = 1e-07
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            +++   D  +    L   FS FGNI+   +        +   FV +E  ESA  A+ +L
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAEL 59

Query: 179 NGMLINDKQVFV 190
           NG  +   Q+ V
Sbjct: 60  NGTQVESVQLKV 71

>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 = 60.5 bits (146), Expect = 3e-12
 Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 269
           +FV  + E T +  L+  F +YG I    +M D      + F FV F++ D   K V   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-Q 63

Query: 270 NGKKFDDREWYVGKA 284
                +     V KA
Sbjct: 64  KYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 305 TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE 363
           TV K     +++  + +  ++  L++ F ++G I   ++M D  SG  +G  FV F   +
Sbjct: 1   TVKK-----IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 55

Query: 364 EASRALAEMNGKMIVSKPLYVAVA 387
              + +       +      V  A
Sbjct: 56  SVDKIV-IQKYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 11/72 (15%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           ++VG +  +  +  L D F Q G++  + +  D  + +  G+ +V + +     + +   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-Q 63

Query: 92  NFTPLNNKSIRI 103
            +  +N  +  +
Sbjct: 64  KYHTVNGHNCEV 75

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 7/81 (8%)

Query: 111 SIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKE 169
           +++K     IF+  + +  +   L D F  +G I   +I TD GSG+ +GF FV F++ +
Sbjct: 1   TVKK-----IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 55

Query: 170 SAQNAIDKLNGMLINDKQVFV 190
           S    +       +N     V
Sbjct: 56  SVDKIV-IQKYHTVNGHNCEV 75

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 4e-12
 Identities = 12/81 (14%), Positives = 29/81 (35%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
            F+ NL    T+E +K+ F         +     + +             D+  +  +LN
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLN 77

Query: 271 GKKFDDREWYVGKAQKKSERE 291
            +   ++   V  A +  +++
Sbjct: 78  EESLGNKRIRVDVADQAQDKD 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 3e-10
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKV-MRDPSGISKGSGFVAFSTPEEASRALAEM 372
            ++ NL   + +E +KE F                    KG G+  F   +    AL  +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SL 76

Query: 373 NGKMIVSKPLYVAVAQRKEERR 394
           N + + +K + V VA + +++ 
Sbjct: 77  NEESLGNKRIRVDVADQAQDKD 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 8e-10
 Identities = 21/103 (20%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 19  AAGASGNQFLT---TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           ++G+SG++       + ++G+L ++VT+  + + F  +            +  R  G+GY
Sbjct: 2   SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
             + +      AL  LN   L NK IR+  + +        + 
Sbjct: 62  AEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 46.6 bits (110), Expect = 3e-07
 Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKI-ATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            F+ NL   +  +++ + F                  + KGFG+ +FE+ +S  +A+  L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SL 76

Query: 179 NGMLINDKQVFVGHFLRKQERET 201
           N   + +K++ V    + Q++++
Sbjct: 77  NEESLGNKRIRVDVADQAQDKDS 99

>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 = 60.6 bits (146), Expect = 4e-12
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
              + N+  S T  D+ +         +AV +   + G+      V F+N DDA K+   
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER- 68

Query: 269 LNGKKFDDREWYVGKAQKKSEREQE 293
           L+ KK + RE +V     +  RE E
Sbjct: 69  LHRKKLNGREAFVHVVTLEDMREIE 93

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (127), Expect = 2e-09
 Identities = 13/86 (15%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
           +  +I N+  SI    + +         +   +    +G   G   V F   ++A ++  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 67

Query: 371 EMNGKMIVSKPLYVAVAQRKEERRAR 396
            ++ K +  +  +V V   ++ R   
Sbjct: 68  RLHRKKLNGREAFVHVVTLEDMREIE 93

>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 = 49.8 bits (118), Expect = 3e-08
 Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 2/88 (2%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQN 173
           S      I N+  SI    +           +        +GQ  G   VQF+N++ A+ 
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 174 AIDKLNGMLINDKQVFVGHFLRKQERET 201
           +  +L+   +N ++ FV     +  RE 
Sbjct: 66  SE-RLHRKKLNGREAFVHVVTLEDMREI 92

>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 = 48.7 bits (115), Expect = 7e-08
 Identities = 11/80 (13%), Positives = 29/80 (36%), Gaps = 1/80 (1%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
              ++ ++ F++T   +      +    +       +  + LG   V + N  DA ++  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 90  VLNFTPLNNKSIRIMYSHRD 109
            L+   LN +   +     +
Sbjct: 69  -LHRKKLNGREAFVHVVTLE 87

>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 = 59.8 bits (144), Expect = 6e-12
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 7/80 (8%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG------DGKSKCFGFVNFENADDAAK 264
           ++V N+    T+E +   F     +                 + K F F+ F + D+  +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 265 AVEALNGKKFDDREWYVGKA 284
           A+   +G  F  +   + + 
Sbjct: 64  AMA-FDGIIFQGQSLKIRRP 82

>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 = 58.2 bits (140), Expect = 3e-11
 Identities = 11/77 (14%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRV-----CRDLSTRRSLGYGYVNYANPADAAR 86
           LYVG++ F +T+  + D F+   ++  +          +   +   + ++ + +  +  +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 87  ALDVLNFTPLNNKSIRI 103
           A+   +      +S++I
Sbjct: 64  AMA-FDGIIFQGQSLKI 79

>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 = 56.7 bits (136), Expect = 9e-11
 Identities = 13/79 (16%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG------SGQSKGFGFVQFENKESAQN 173
           +++ N+   I  +A+ D F++   +     A           Q K F F++F + +    
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 174 AIDKLNGMLINDKQVFVGH 192
           A+   +G++   + + +  
Sbjct: 64  AMA-FDGIIFQGQSLKIRR 81

>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 = 55.5 bits (133), Expect = 2e-10
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP------SGISKGSGFVAFSTPEEASR 367
           LY+ N+   I +E + + F+    +                   K   F+ F + +E ++
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 368 ALAEMNGKMIVSKPLYV 384
           A+   +G +   + L +
Sbjct: 64  AM-AFDGIIFQGQSLKI 79

>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 = 60.7 bits (146), Expect = 9e-12
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF-GFVNFENADDAAKAVE 267
            N+ V  +  +  +  L+++F  YG I S  ++ D + +     GFV F++   A +A+ 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
            LNG    ++   V  A    +R
Sbjct: 103 GLNGFNILNKRLKVALAASGHQR 125

>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 = 56.8 bits (136), Expect = 2e-10
 Identities = 26/111 (23%), Positives = 52/111 (46%), Gaps = 1/111 (0%)

Query: 287 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD 346
           + ++ Q+ + Q     +   +     NL +  +  ++D+ +L++LF  +G I S K++ D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 347 PSGISKGSGFVA-FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 396
                        F +   A +A+A +NG  I++K L VA+A    +R   
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGI 128

>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 = 56.1 bits (134), Expect = 5e-10
 Identities = 31/122 (25%), Positives = 56/122 (45%), Gaps = 4/122 (3%)

Query: 5   QVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD 64
           Q+Q   Q    +      +    +  +L V  +   V + QL  LF + G + SV++  D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 65  LSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH----RDPSIRKSGTGNI 120
             TR+S GYG+V + + + A +A+  LN   + NK +++  +     R       G GN 
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137

Query: 121 FI 122
           ++
Sbjct: 138 YL 139

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 53.4 bits (127), Expect = 4e-09
 Identities = 28/96 (29%), Positives = 45/96 (46%), Gaps = 1/96 (1%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGF-GFVQFENKESAQNAIDK 177
           N+ +  +  ++D   L   F  +G I S KI  D   +     GFV+F++  SAQ AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFV 213
           LNG  I +K++ V       +R  +A      N ++
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>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 = 59.0 bits (142), Expect = 1e-11
 Identities = 20/82 (24%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             V V  L  S + +DLK    E G       +   D +    G V +   +D   A+  
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMREAGD------VCYADVQKDGMGMVEYLRKEDMEYALRK 69

Query: 269 LNGKKFDDREWYVGKAQKKSER 290
           L+  KF   E      +   ER
Sbjct: 70  LDDTKFRSHEGETSYIRVYPER 91

>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 = 52.5 bits (125), Expect = 3e-09
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +  L  S   + LK+   E G +    V +D  G       V +   E+   AL +++
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMG------MVEYLRKEDMEYALRKLD 71

Query: 374 GKMIVSKPLYVAVAQRKEERRA 395
                S     +  +   ER +
Sbjct: 72  DTKFRSHEGETSYIRVYPERSS 93

>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 = 45.2 bits (106), Expect = 1e-06
 Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 7/92 (7%)

Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
           P  R+S    + +  L  S   + L D     G++    +      Q  G G V++  KE
Sbjct: 9   PPTRRSDF-RVLVSGLPPSGSWQDLKDHMREAGDVCYADV------QKDGMGMVEYLRKE 61

Query: 170 SAQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
             + A+ KL+       +    +     ER +
Sbjct: 62  DMEYALRKLDDTKFRSHEGETSYIRVYPERSS 93

>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 = 58.2 bits (140), Expect = 1e-11
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
           ++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 270 NGKKFDDR 277
                  +
Sbjct: 61  KASGVQAQ 68

>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 = 54.8 bits (131), Expect = 2e-10
 Identities = 19/71 (26%), Positives = 37/71 (52%)

Query: 32  LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
           LY+  L    TD  L  L    G+++S +   D +T +  GYG+V++ +P+ A +A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 92  NFTPLNNKSIR 102
             + +  +  +
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.2 bits (119), Expect = 1e-08
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
           LYI+ L     D+ L +L   +G I S K + D  +   KG GFV F +P  A +A+  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 373 NGKMIVSKPL 382
               + ++  
Sbjct: 61  KASGVQAQMA 70

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 8e-08
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
           ++I+ L      + L      +G I+S K   D  + + KG+GFV F++  +AQ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 179 NGMLINDKQV 188
               +  +  
Sbjct: 61  KASGVQAQMA 70

>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 = 58.7 bits (141), Expect = 1e-11
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 209 NNVFVKNLDESTTDEDLKKIF---GEYGTITSAVVMRD----GDGKSKCFGFVNFENADD 261
           N VFV  L +   D ++ K     G++G I   V+       G        +V +  ++D
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 262 AAKAVEALNGKKFDDR 277
           A +A++ +N    D R
Sbjct: 69  ALRAIQCVNNVVVDGR 84

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.1 bits (124), Expect = 3e-09
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 310 QGLNLYIKNLGDSIDDE---KLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTP 362
           Q   +++  L   + D    K  E F +FG I    +        S     S +V +   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 363 EEASRALAEMNGKMIVSKPLYVA 385
           E+A RA+  +N  ++  + L  +
Sbjct: 67  EDALRAIQCVNNVVVDGRTLKAS 89

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (117), Expect = 3e-08
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 32  LYVGDLDFNVTDSQLYDLF---SQVGQVLSVRVCRDLSTRRS---LGYGYVNYANPADAA 85
           ++V  L   + D ++        + G++  V +    S   S       YV Y    DA 
Sbjct: 11  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 70

Query: 86  RALDVLNFTPLNNKSIRI 103
           RA+  +N   ++ ++++ 
Sbjct: 71  RAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.7 bits (115), Expect = 5e-08
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 7/85 (8%)

Query: 111 SIRKSGTGNIFIKNLDKSI---DHKALHDTFSSFGNILSCKIATD----GSGQSKGFGFV 163
           S+R      +F+  L + +   +     + F  FG I    I       GS       +V
Sbjct: 2   SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYV 61

Query: 164 QFENKESAQNAIDKLNGMLINDKQV 188
            +   E A  AI  +N ++++ + +
Sbjct: 62  TYIRSEDALRAIQCVNNVVVDGRTL 86

>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 = 58.1 bits (140), Expect = 4e-11
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 215 NLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS---KCFGFVNFENADDAAKAVEALNG 271
           + +     ED++    +YG + S  + R  DG         FV F +  D  KA++ L G
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 272 KKFDDRE 278
           +KF +R 
Sbjct: 81  RKFANRV 87

>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 = 50.8 bits (121), Expect = 2e-08
 Identities = 16/94 (17%), Positives = 38/94 (40%), Gaps = 13/94 (13%)

Query: 314 LYIKNL---GDSIDD-------EKLKELFSEFGTITSCKVMRDP---SGISKGSGFVAFS 360
           L + N+    + +DD       E +++  S++G + S ++ R          G  FV F+
Sbjct: 7   LCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFT 66

Query: 361 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 394
           +  +  +A+  + G+   ++ +           R
Sbjct: 67  SVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHR 100

>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 = 46.1 bits (109), Expect = 5e-07
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 3/60 (5%)

Query: 134 LHDTFSSFGNILSCKIATD---GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
           + D  S +G + S +I            G  FV+F +    Q A+  L G    ++ V  
Sbjct: 31  VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90

>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 = 56.8 bits (136), Expect = 6e-11
 Identities = 22/84 (26%), Positives = 30/84 (35%), Gaps = 6/84 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           N V V  L  S + +DLK    E G       +   D      G V F   +D   AV  
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMREAGD------VCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 269 LNGKKFDDREWYVGKAQKKSEREQ 292
           L+  KF   E      + K +  +
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPR 78

>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 = 43.7 bits (102), Expect = 3e-06
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + +  L  S   + LK+   E G +    V RD       +G V F   E+ + A+ +++
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVEFVRKEDMTYAVRKLD 56

Query: 374 GKMIVSKPLYVAVAQRKEERR 394
                S     A  + K +  
Sbjct: 57  NTKFRSHEGETAYIRVKVDGP 77

>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 = 39.9 bits (92), Expect = 5e-05
 Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 6/80 (7%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + +  L  S   + L D     G++    +         G G V+F  KE    A+ KL+
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKLD 56

Query: 180 GMLINDKQVFVGHFLRKQER 199
                  +    +   K + 
Sbjct: 57  NTKFRSHEGETAYIRVKVDG 76

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
           + + VKNL + +  +++  +  +Y      V             FV   N + A  A++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKR------TAFVTLLNGEQAQNAIQM 59

Query: 269 LNGKKFDDREWYVGKAQKKS 288
            +   F  ++  V      +
Sbjct: 60  FHQYSFRGKDLIVQLQPTDA 79

>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 = 54.7 bits (131), Expect = 4e-10
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           SG+  I +KNL +  + + +HD    +              ++K   FV   N E AQNA
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD------RNKRTAFVTLLNGEQAQNA 56

Query: 175 IDKLNGMLINDKQVFV 190
           I   +      K + V
Sbjct: 57  IQMFHQYSFRGKDLIV 72

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            + +KNL    + +++ +L  ++               +K + FV     E+A  A+   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR------NKRTAFVTLLNGEQAQNAIQMF 60

Query: 373 NGKMIVSKPLYVAVAQRK 390
           +      K L V +    
Sbjct: 61  HQYSFRGKDLIVQLQPTD 78

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 3e-09
 Identities = 14/94 (14%), Positives = 32/94 (34%), Gaps = 11/94 (11%)

Query: 21  GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
           G+SG    ++ + V +L  +    +++DL             +     R+    +V   N
Sbjct: 1   GSSG----SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLN 49

Query: 81  PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRK 114
              A  A+ + +      K + +     D  +  
Sbjct: 50  GEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCS 83

>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 = 55.8 bits (134), Expect = 2e-10
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           TT L+VG L  N + + L   F + G + ++   +  S      + Y+ Y +   A  A 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAAC 70

Query: 89  DVLNFTPLN--NKSIRIMYSHRDPS 111
             +   PL   ++ +R+ ++   PS
Sbjct: 71  AKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 5e-10
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             ++V  L  +T+   L + F  +G+I +   ++        F ++ +E+ D A  A   
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAK 72

Query: 269 LNGKKFD--DREWYVGKAQKK 287
           + G      DR   V  A+  
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSG 93

>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 = 48.5 bits (115), Expect = 6e-08
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++  LG +     L   F  FG+I +   ++  S       ++ + + + A  A A+M
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-----FAYIQYESLDAAQAACAKM 73

Query: 373 NGKMI--VSKPLYVAVAQRK 390
            G  +    + L V  A+  
Sbjct: 74  RGFPLGGPDRRLRVDFAKSG 93

>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 = 43.9 bits (103), Expect = 3e-06
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 11/88 (12%)

Query: 97  NNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ 156
           +  S +I Y   +P+ R      +++  L  +    AL   F  FG+I +         +
Sbjct: 3   SGSSGKIGYGKANPTTR------LWVGGLGPNTSLAALAREFDRFGSIRTIDH-----VK 51

Query: 157 SKGFGFVQFENKESAQNAIDKLNGMLIN 184
              F ++Q+E+ ++AQ A  K+ G  + 
Sbjct: 52  GDSFAYIQYESLDAAQAACAKMRGFPLG 79

>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 = 54.0 bits (129), Expect = 1e-09
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           ++++ L +S+ +  L E   +FGTI    +M            V F   + A   +    
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFENIDSAKECVTFAA 72

Query: 374 GK--MIVSKPLYVAVAQRKEERR 394
                I  +  +   +  K   R
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITR 95

>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 = 54.0 bits (129), Expect = 1e-09
 Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             V V+ L ES  + DL +   ++GTI   ++M       K    V FEN D A + V  
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTF 70

Query: 269 LNGKKF--DDREWYVGKAQKKSER 290
                     ++ +   +  K   
Sbjct: 71  AADVPVYIAGQQAFFNYSTSKRIT 94

>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 = 53.3 bits (127), Expect = 2e-09
 Identities = 17/106 (16%), Positives = 35/106 (33%), Gaps = 11/106 (10%)

Query: 19  AAGASGNQFLT---TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           ++G+SG+         ++V  L  +V ++ L +   + G +  V +              
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QAL 55

Query: 76  VNYANPADAARALDVLNFTP--LNNKSIRIMYSHRDPSIRKSGTGN 119
           V + N   A   +      P  +  +     YS      R   +G 
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>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 = 42.9 bits (100), Expect = 7e-06
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL- 178
           + ++ L +S+    L +    FG I    +        K    V+FEN +SA+  +    
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMM-----MPFKRQALVEFENIDSAKECVTFAA 72

Query: 179 -NGMLINDKQVFVGHFLRKQER 199
              + I  +Q F  +   K+  
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRIT 94

>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 = 52.5 bits (125), Expect = 1e-09
 Identities = 20/75 (26%), Positives = 25/75 (33%), Gaps = 2/75 (2%)

Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
            V VKNL +S     + K F   G I    V      K+  F  + F   D A  A+   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITK- 59

Query: 270 NGKKFDDREWYVGKA 284
             K     E  V   
Sbjct: 60  THKVVGQNEIIVSHL 74

>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 = 44.5 bits (104), Expect = 1e-06
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T++ V +L  +   +++Y  F   G ++ V V   L       +  + +A    A  A+ 
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR--FARIEFARYDGALAAIT 58

Query: 90  VLNFTPLNNKSIRI 103
             +   +    I +
Sbjct: 59  KTHKV-VGQNEIIV 71

>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 = 42.5 bits (99), Expect = 5e-06
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 2/72 (2%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            + +KNL  S +  K+ + F   G I    V        +    + F+  + A  A+   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAI-TK 59

Query: 373 NGKMIVSKPLYV 384
             K++    + V
Sbjct: 60  THKVVGQNEIIV 71

>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 = 41.0 bits (95), Expect = 2e-05
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            + +KNL KS +   ++  F   G I+   +A       + F  ++F   + A  AI   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAI-TK 59

Query: 179 NGMLINDKQVFVGH 192
              ++   ++ V H
Sbjct: 60  THKVVGQNEIIVSH 73

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.0 bits (126), Expect = 3e-09
 Identities = 17/96 (17%), Positives = 30/96 (31%), Gaps = 5/96 (5%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             +  KNL   T   ++++ F  +G++   ++             V F    +A KA   
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRH 65

Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 304
           L   KF     Y+  A          K   +     
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPA 101

>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 = 45.7 bits (107), Expect = 1e-06
 Identities = 22/103 (21%), Positives = 34/103 (33%), Gaps = 8/103 (7%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            +  KNL       +++E FS FG++    +          +  V F  P EA +A   +
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-----ITAIVEFLEPLEARKAFRHL 66

Query: 373 NGKMIVSKPLYVAVAQRKEERRA---RLQAQFSQMRPVAMGPS 412
                   PLY+  A       A   +             GPS
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPS 109

>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 = 38.8 bits (89), Expect = 2e-04
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 5/72 (6%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
            I  KNL        + +TFS FG++    +      +      V+F     A+ A   L
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRHL 66

Query: 179 NGMLINDKQVFV 190
                +   +++
Sbjct: 67  AYSKFHHVPLYL 78

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.3 bits (120), Expect = 9e-09
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V V    +++    L + F +YG I   V+          +  + +++   A KA+   +
Sbjct: 7   VTVFGFPQASASYILLQ-FAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KD 59

Query: 271 GKKFDDRE-WYVGKAQKKSERE 291
           G+ F +     V     K+  E
Sbjct: 60  GRIFGESIMIGVKPCIDKNVME 81

>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 = 39.9 bits (93), Expect = 4e-05
 Identities = 10/78 (12%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 374
            +     +     L + F+++G I    +             + + +  +A +AL   +G
Sbjct: 8   TVFGFPQASASYILLQ-FAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKAL-SKDG 60

Query: 375 KMIVSKP-LYVAVAQRKE 391
           ++      + V     K 
Sbjct: 61  RIFGESIMIGVKPCIDKN 78

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (87), Expect = 4e-04
 Identities = 10/67 (14%), Positives = 29/67 (43%), Gaps = 7/67 (10%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           + +    ++     L   F+ +GNIL   ++         +  +++++K  A+ A+   +
Sbjct: 7   VTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKAL-SKD 59

Query: 180 GMLINDK 186
           G +  + 
Sbjct: 60  GRIFGES 66

>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 = 36.5 bits (84), Expect = 8e-04
 Identities = 10/72 (13%), Positives = 22/72 (30%), Gaps = 8/72 (11%)

Query: 30  TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
           T + V           +   F+Q G +L   +           + ++ Y +   A +AL 
Sbjct: 5   TWVTVFGFPQASAS-YILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKALS 57

Query: 90  VLNFTPLNNKSI 101
             +        +
Sbjct: 58  -KDGRIFGESIM 68

>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 = 51.3 bits (122), Expect = 1e-08
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 209 NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
           + + V NL+ E  T + L  +FG YG +    ++ +     K    V   + + A  A+ 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMS 58

Query: 268 ALNGKKFDDREWYVGKAQKKS 288
            LNG K   +   +  ++ ++
Sbjct: 59  HLNGHKLHGKPIRITLSKHQN 79

>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 = 3e-08
 Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 314 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
           L + NL  + +  + L  LF  +G +   K++ +          V  +   +A  A++ +
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMSHL 60

Query: 373 NGKMIVSKPLYVAVAQRKEERRAR 396
           NG  +  KP+ + +++ +  +  R
Sbjct: 61  NGHKLHGKPIRITLSKHQNVQLPR 84

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 116 GTGNIFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
           G   + + NL+ + +  ++L   F  +G++   KI        K    VQ  +   AQ A
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQLA 56

Query: 175 IDKLNGMLINDKQVFV 190
           +  LNG  ++ K + +
Sbjct: 57  MSHLNGHKLHGKPIRI 72

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (118), Expect = 4e-08
 Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 3/99 (3%)

Query: 195 RKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGF 253
           +K+ R     +  F  V++K L     ++ +   F +   +  ++ +  G  GK+   GF
Sbjct: 6   QKRSRSRSPHEAGFC-VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF 64

Query: 254 VNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 292
           V F N  D   A+   + +   +R   V    KK   E+
Sbjct: 65  VEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEK 102

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (100), Expect = 1e-05
 Identities = 16/87 (18%), Positives = 36/87 (41%), Gaps = 2/87 (2%)

Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRA 368
            G  +Y+K L    +++ + + F +   +     +   P+G + G GFV F    +   A
Sbjct: 17  AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 76

Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRA 395
           L   + + + ++ + V    +K     
Sbjct: 77  L-CRHKQYMGNRFIQVHPITKKGMLEK 102

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (86), Expect = 7e-04
 Identities = 21/105 (20%), Positives = 47/105 (44%), Gaps = 4/105 (3%)

Query: 108 RDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 166
           R  S  ++G   +++K L    ++K + D F     +        G +G++ G GFV+F 
Sbjct: 10  RSRSPHEAGF-CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 68

Query: 167 NKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETV-AIKTKFNN 210
           N+   + A+   +   + ++ + V    +K   E +  I+ +  +
Sbjct: 69  NEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQS 112

>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 = 49.4 bits (117), Expect = 4e-08
 Identities = 13/80 (16%), Positives = 24/80 (30%), Gaps = 2/80 (2%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           V ++ L    T+ D+   F     +    +    DG+      V F   +DA  A+   +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRV-HIEIGPDGRVTGEADVEFATHEDAVAAMA-KD 75

Query: 271 GKKFDDREWYVGKAQKKSER 290
                 R   +         
Sbjct: 76  KANMQHRYVELFLNSTAGTS 95

>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 = 2e-07
 Identities = 15/102 (14%), Positives = 42/102 (41%), Gaps = 6/102 (5%)

Query: 19  AAGASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
           ++G+SG+ F +T+   +++  L +  T++ +Y+ FS +  +                   
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG--EAD 59

Query: 76  VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGT 117
           V +A   DA  A+   +   + ++ + +  +    +     +
Sbjct: 60  VEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGSGPS 100

>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 = 47.0 bits (111), Expect = 3e-07
 Identities = 13/91 (14%), Positives = 31/91 (34%), Gaps = 2/91 (2%)

Query: 304 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 363
            +     G  ++++ L     +  +   FS    +    +   P G   G   V F+T E
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHE 66

Query: 364 EASRALAEMNGKMIVSKPLYVAVAQRKEERR 394
           +A  A+   +   +  + + + +        
Sbjct: 67  DAVAAM-AKDKANMQHRYVELFLNSTAGTSG 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 = 42.0 bits (98), Expect = 1e-05
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 3/78 (3%)

Query: 114 KSGTGN-IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
           +S TG+ + ++ L        +++ FS    +          G+  G   V+F   E A 
Sbjct: 11  QSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE-IGPDGRVTGEADVEFATHEDAV 69

Query: 173 NAIDKLNGMLINDKQVFV 190
            A+   +   +  + V +
Sbjct: 70  AAM-AKDKANMQHRYVEL 86

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (116), Expect = 5e-08
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
             V ++ L    + E++ + F     + + + +     G+S    FV F + + A KA++
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75

Query: 268 ALNGKKFDDREWYVGKAQKKSER 290
             + ++   R   + K+ +   R
Sbjct: 76  -KHKERIGHRYIEIFKSSRAEVR 97

>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 = 45.2 bits (106), Expect = 1e-06
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEA 365
           D      + ++ L      E++ + FS    + +   +     G S G  FV F++ E A
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEERRA 395
            +AL + + + I  + + +  + R E R +
Sbjct: 71  EKAL-KKHKERIGHRYIEIFKSSRAEVRTS 99

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L++ N+  S+ +E LK LFS  G +                  +   + EEA +AL ++
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA---LIQMGSVEEAVQALIDL 68

Query: 373 NGKMIV-SKPLYVAVAQ 388
           +   +  +  L V+ ++
Sbjct: 69  HNHDLGENHHLRVSFSK 85

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + + N+  S ++EDLK +F   G +   V       K +    +   + ++A +A+  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGV---VKGFKFFQKDRKMALIQMGSVEEAVQALID 67

Query: 269 LNGKKFDD 276
           L+     +
Sbjct: 68  LHNHDLGE 75

>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 = 46.3 bits (109), Expect = 3e-07
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           + +L++ ++  +V++  L  LFS  G V    V      ++      +   +  +A +AL
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQAL 65

Query: 89  DVLNFTPL-NNKSIRIMYS 106
             L+   L  N  +R+ +S
Sbjct: 66  IDLHNHDLGENHHLRVSFS 84

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 9e-05
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
           +  + + N+  S+  + L   FSS G ++          + +    +Q  + E A  A+ 
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALI 66

Query: 177 KLNGMLINDKQVFVGHFLR 195
            L+   + +      H LR
Sbjct: 67  DLHNHDLGE-----NHHLR 80

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (108), Expect = 3e-07
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 6/78 (7%)

Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
           + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 271 GKKFDDREWYVGKAQKKS 288
             +  +RE  V      +
Sbjct: 55  QSRLRERELSVQLQPTDA 72

>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 = 42.6 bits (99), Expect = 5e-06
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           + I+ L   + ++++ +L S+       ++        KG+ FV     E+A  A+   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD------YELKYCFVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 374 GKMIVSKPLYVAVAQRK 390
              +  + L V +    
Sbjct: 55  QSRLRERELSVQLQPTD 71

>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 = 35.7 bits (81), Expect = 0.002
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           I I+ L   + ++ +HD  S +              + KG  FV   N E A+ AI+  +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCF------VDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 180 GMLINDKQVFV 190
              + ++++ V
Sbjct: 55  QSRLRERELSV 65

>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 = 45.6 bits (107), Expect = 5e-07
 Identities = 18/79 (22%), Positives = 27/79 (34%), Gaps = 5/79 (6%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             +F+ NL E T +  L  +F ++                    FV F     +  A EA
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGF----KEVRLVPNRHDIAFVEFTTELQSNAAKEA 64

Query: 269 LNGKKFDD-REWYVGKAQK 286
           L G K        +  A+K
Sbjct: 65  LQGFKITPTHAMKITFAKK 83

>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 = 42.1 bits (98), Expect = 8e-06
 Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
           L++ NL +  ++  L  LF++F      +++ +   I+    FV F+T  +++ A   + 
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIA----FVEFTTELQSNAAKEALQ 66

Query: 374 GKMIV-SKPLYVAVAQR 389
           G  I  +  + +  A++
Sbjct: 67  GFKITPTHAMKITFAKK 83

>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 = 39.8 bits (92), Expect = 6e-05
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 4/77 (5%)

Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
           +F+ NL +  +   L   F+ F      ++            FV+F  +  +  A + L 
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP----NRHDIAFVEFTTELQSNAAKEALQ 66

Query: 180 GMLINDKQVFVGHFLRK 196
           G  I         F +K
Sbjct: 67  GFKITPTHAMKITFAKK 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 = 45.6 bits (107), Expect = 6e-07
 Identities = 15/83 (18%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
            L+I+ L   + + ++  L   FG +T+  +++  +       F+  +T E A   +   
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN-----QAFLELATEEAAITMVNYY 64

Query: 373 NGK--MIVSKPLYVAVAQRKEER 393
           +     + ++P+Y+  +  KE +
Sbjct: 65  SAVTPHLRNQPIYIQYSNHKELK 87

>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 = 43.7 bits (102), Expect = 3e-06
 Identities = 10/81 (12%), Positives = 26/81 (32%), Gaps = 7/81 (8%)

Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
             + ++ L    T+ ++  +   +G +           K K   F+     + A   V  
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKV-----TNILMLKGKNQAFLELATEEAAITMVNY 63

Query: 269 LNGKK--FDDREWYVGKAQKK 287
            +       ++  Y+  +  K
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHK 84

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 29  TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
           +  L++  L   VT++++  L    G+        ++   +     ++  A    A   +
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGK------VTNILMLKGKNQAFLELATEEAAITMV 61

Query: 89  DV--LNFTPLNNKSIRIMYSHR 108
           +        L N+ I I YS+ 
Sbjct: 62  NYYSAVTPHLRNQPIYIQYSNH 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 = 38.3 bits (88), Expect = 2e-04
 Identities = 9/83 (10%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK- 177
            + I+ L   +    +      FG + +  +      + K   F++   +E+A   ++  
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYY 64

Query: 178 -LNGMLINDKQVFVGHFLRKQER 199
                 + ++ +++ +   K+ +
Sbjct: 65  SAVTPHLRNQPIYIQYSNHKELK 87

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.5 bits (107), Expect = 7e-07
 Identities = 15/84 (17%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 314 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA-- 370
           ++I +         +L +L   FG I++  ++   +       F+  +T E+A  A+   
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN-----EAFIEMATTEDAQAAVDYY 65

Query: 371 EMNGKMIVSKPLYVAVAQRKEERR 394
                ++  KP+ V ++Q+ +  +
Sbjct: 66  TTTPALVFGKPVRVHLSQKYKRIK 89

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.5 bits (107), Expect = 8e-07
 Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 8/83 (9%)

Query: 211 VFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA- 268
           V + +          L ++   +G I++ +++           F+     +DA  AV+  
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYY 65

Query: 269 -LNGKKFDDREWYVGKAQKKSER 290
                    +   V  +QK    
Sbjct: 66  TTTPALVFGKPVRVHLSQKYKRI 88

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 13/92 (14%), Positives = 28/92 (30%), Gaps = 5/92 (5%)

Query: 23  SGNQFLTTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP 81
            G       +++ D         QL  L    G + +  +   ++      +  +     
Sbjct: 2   KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINE----AFIEMATTED 57

Query: 82  ADAARALDVLNFTPLNNKSIRIMYSHRDPSIR 113
           A AA          +  K +R+  S +   I+
Sbjct: 58  AQAAVDYYTTTPALVFGKPVRVHLSQKYKRIK 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	652
d1g9la_	144	poly(A) binding protein {Human (Homo sapiens) [Tax	99.97
d1nmra_	85	poly(A) binding protein {Protozoan (Trypanosoma cr	99.96
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1ifwa_	92	poly(A) binding protein {Baker's yeast (Saccharomy	99.95
d1i2ta_	61	hyperplastic discs protein {Human (Homo sapiens) [	99.95
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.95
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.8
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.8
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.8
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.8
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.79
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.78
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.78
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.76
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.76
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.75
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.75
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.75
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.75
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.74
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.74
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.73
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.73
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.73
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.73
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.73
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.72
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.72
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.72
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.72
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.71
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.7
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.7
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.7
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.7
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.7
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.7
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.69
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.69
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.69
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.69
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.67
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.67
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.66
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.66
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.66
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.66
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.66
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.66
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.65
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.65
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.65
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.65
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.65
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.64
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.64
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.63
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.63
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.63
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.63
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.63
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.63
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.62
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.62
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.62
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.62
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.62
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.61
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.6
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.6
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.6
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.6
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.6
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.59
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.58
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.57
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.57
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.57
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	99.55
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.55
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.53
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.53
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.52
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	99.47
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.44
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.4
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.39
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.33
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.33
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.3
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.28
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.25
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.24
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.22
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.2
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.85
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.58
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.53
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.31
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.73
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.23
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.5
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.87

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=7e-33  Score=237.46  Aligned_cols=90  Identities=41%  Similarity=0.677  Sum_probs=83.3

Q ss_pred             CCCCCCccccchhhhhcCChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHH
Q 006282          548 SVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLR  627 (652)
Q Consensus       548 ~~~~~~~~~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~  627 (652)
                      +.+.+.+.++++++|+++++++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||+
T Consensus        44 ~~~~~~q~pltas~la~a~p~eQkq~LGE~Lyp~I~~~~p~~A~KITGMLLEmd~~ell~lL~~~~~L~~kV~EA~~vL~  123 (144)
T d1g9la_          44 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQ  123 (144)
T ss_dssp             SCCCCSCCCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTTTSSSHHHHHHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcccHHHHhhCCHHHHHHHHHHHHHHHHHHhChhhccchhhhhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHH
Confidence            33455677899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcCCc
Q 006282          628 SVAQQQANNP  637 (652)
Q Consensus       628 ~~~~~~~~~~  637 (652)
                      +|+.+++.+.
T Consensus       124 ~~~~~~~~~~  133 (144)
T d1g9la_         124 AHQAKEAAQK  133 (144)
T ss_dssp             TTSSSTTCCC
T ss_pred             HHhccHHHHH
Confidence            9998875543

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

Probab=99.96  E-value=2.1e-31  Score=206.38  Aligned_cols=75  Identities=56%  Similarity=0.776  Sum_probs=72.6

Q ss_pred             ccchhhhhcCChHHHHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 006282          556 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVA  630 (652)
Q Consensus       556 ~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~~  630 (652)
                      ..++++|++++|++||++|||+|||+|++++|++||||||||||||++||++||+|++.|++||+||++||++|+
T Consensus         9 ~~~a~~la~~~p~eqK~~LGE~Lyp~V~~~~p~~AgKITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~h~   83 (85)
T d1nmra_           9 QNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRHM   83 (85)
T ss_dssp             CTTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTTCCC
T ss_pred             hHHHHHHhhCCHHHHHHHHHHHHHHHHHHHCcccccchhHHhhCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHhc
Confidence            459999999999999999999999999999999999999999999999999999999999999999999999875

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.6e-28  Score=231.35  Aligned_cols=172  Identities=27%  Similarity=0.450  Sum_probs=152.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++||++|+++|++||.|.+++++++..+++++|||||.|.+.++|.+|+.. ++..+.++.+.+.+.
T Consensus         4 ~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~   82 (183)
T d1u1qa_           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   82 (183)
T ss_dssp             HHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhh
Confidence            3568999999999999999999999999999999999999999999999999999999999994 556778888887765


Q ss_pred             cCCcc----cccCCCcceeecCCCccccHHHHHhhhccCCCeeEEEEeeC-CCCCcccEEEEEEcCHHHHHHHHHHhcCc
Q 006282          107 HRDPS----IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGM  181 (652)
Q Consensus       107 ~~~~~----~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG~I~~~~v~~~-~~g~skG~afV~F~t~e~A~~Ai~~lng~  181 (652)
                      .....    .......+|||+|||.++++++|+++|+.||.|..+.+..+ .+|.++|||||+|.+.++|.+|++ +++.
T Consensus        83 ~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~  161 (183)
T d1u1qa_          83 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYH  161 (183)
T ss_dssp             CCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCE
T ss_pred             hhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCC
Confidence            54332    23345678999999999999999999999999999999998 568999999999999999999996 6888


Q ss_pred             eecCeeeeecccccchhhH
Q 006282          182 LINDKQVFVGHFLRKQERE  200 (652)
Q Consensus       182 ~l~g~~~~v~~~~~~~~~~  200 (652)
                      .++|+.+.|.++.++.++.
T Consensus       162 ~~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         162 TVNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             EETTEEEEEEECCCHHHHH
T ss_pred             eECCEEEEEEecCCccccc
Confidence            9999999999887766554

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.95  E-value=2.3e-29  Score=198.28  Aligned_cols=80  Identities=33%  Similarity=0.436  Sum_probs=74.6

Q ss_pred             ccchhhhhcCChHHHHHHhhhhchhhhhhc--cCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHHHHhh
Q 006282          556 TALSTALANASPEQQRTLLGESLYPLVEQL--ERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQ  633 (652)
Q Consensus       556 ~~~~~~l~~~~~~~~~~~~g~~~~~~~~~~--~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~~~~~  633 (652)
                      +.+++.++.+++++||++|||+|||+|+++  +|++||||||||||||++||++||+|+++|+.||+||++||++|++++
T Consensus         6 p~~~~~~~~~~~~~qk~~LGe~Lyp~V~~~~~~pe~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~~~~~~   85 (92)
T d1ifwa_           6 PRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQ   85 (92)
T ss_dssp             SSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCChHHHhhcCHHHHHHHHHHHHHHHHHHhccCccccccchhhhcCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            356778888999999999999999999998  689999999999999999999999999999999999999999999876


Q ss_pred             cC
Q 006282          634 AN  635 (652)
Q Consensus       634 ~~  635 (652)
                      ..
T Consensus        86 ~~   87 (92)
T d1ifwa_          86 EQ   87 (92)
T ss_dssp             TT
T ss_pred             cc
Confidence            44

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=3e-29  Score=181.59  Aligned_cols=60  Identities=45%  Similarity=0.720  Sum_probs=59.1

Q ss_pred             HHHHhhhhchhhhhhccCCcchhhhhhhcCCChHHHHHhcCChHHHHHHHHHHHHHHHHH
Q 006282          570 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV  629 (652)
Q Consensus       570 ~~~~~g~~~~~~~~~~~~~~a~kitgmll~~~~~~~~~~~~~~~~l~~~~~~a~~~l~~~  629 (652)
                      ||++|||+|||+|++++|++||||||||||||++||++||+|+++|++||+||++||++|
T Consensus         1 qk~~LGE~Ly~~V~~~~p~~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~h   60 (61)
T d1i2ta_           1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH   60 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHhHHHHHHHChhhhcchhHHHhcCCHHHHHHHHCCHHHHHHHHHHHHHHHHHc
Confidence            799999999999999999999999999999999999999999999999999999999987

>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=99.95  E-value=1.2e-26  Score=218.56  Aligned_cols=173  Identities=24%  Similarity=0.456  Sum_probs=149.8

Q ss_pred             cceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeeC-CCCCcceeEEEeeCCHHHHHHHHHHHCCCccCCceEEEEcccc
Q 006282          208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  286 (652)
Q Consensus       208 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~i~~~-~~g~~~g~~fV~f~~~~~A~~Ai~~l~~~~~~g~~l~v~~a~~  286 (652)
                      .++|||+|||+++++++|+++|++||.|.++.++++ .++.++|||||.|.+.++|..|+. +++..+.++.+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            368999999999999999999999999999999987 579999999999999999999996 566777777777776654


Q ss_pred             chHHHHHHhHHHHHhhhhcccccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHH
Q 006282          287 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA  365 (652)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A  365 (652)
                      .....            ........++|||+|||..+|+++|+++|+.||.|..+.|+.+. +|.++|||||+|.+.++|
T Consensus        85 ~~~~~------------~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A  152 (183)
T d1u1qa_          85 REDSQ------------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV  152 (183)
T ss_dssp             TTGGG------------STTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHH
T ss_pred             ccccc------------ccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHH
Confidence            43211            11123345689999999999999999999999999999999875 689999999999999999


Q ss_pred             HHHHHHhcCcEecCeeEEEEecccHHHHH
Q 006282          366 SRALAEMNGKMIVSKPLYVAVAQRKEERR  394 (652)
Q Consensus       366 ~~A~~~lng~~~~g~~l~v~~~~~~~~r~  394 (652)
                      .+|++ +++..++|+.|.|.+|.+++++.
T Consensus       153 ~~Al~-~~~~~~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         153 DKIVI-QKYHTVNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             HHHHT-SSCEEETTEEEEEEECCCHHHHH
T ss_pred             HHHHH-hCCCeECCEEEEEEecCCccccc
Confidence            99997 79999999999999999887764

>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=99.84  E-value=3.8e-21  Score=153.60  Aligned_cols=80  Identities=60%  Similarity=1.041  Sum_probs=77.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      ++|||+|||+++||++|+++|+.||+|.+|+|++|+.+++++|||||+|.+.++|.+|++.||+..+.|++|+|.|+++|
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~d   80 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD   80 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999864

>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=99.81  E-value=2.2e-20  Score=150.17  Aligned_cols=80  Identities=35%  Similarity=0.626  Sum_probs=77.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      +++|||+|||+++|+++|+++|++||+|.++++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|.|++.
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            57899999999999999999999999999999999999999999999999999999999999999999999999999863

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.5e-20  Score=151.19  Aligned_cols=86  Identities=29%  Similarity=0.539  Sum_probs=81.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      .....++|||+|||.++|+++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCc
Q 006282          105 YSHRDP  110 (652)
Q Consensus       105 ~s~~~~  110 (652)
                      |+....
T Consensus        85 ~A~~~~   90 (93)
T d1x5ua1          85 KASAHN   90 (93)
T ss_dssp             ETTTTS
T ss_pred             EcCCCC
Confidence            987653

>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=99.80  E-value=1e-19  Score=149.50  Aligned_cols=83  Identities=31%  Similarity=0.524  Sum_probs=79.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ..+++|||+|||+++||++|+++|+.||+|.+|++.+|+.+++++|||||+|.+.++|.+|++.||+..|.|++|+|.|+
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            35789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 006282          107 HRD  109 (652)
Q Consensus       107 ~~~  109 (652)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.80  E-value=1.8e-19  Score=160.31  Aligned_cols=83  Identities=29%  Similarity=0.431  Sum_probs=79.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      +...++|||+|||+++||++|+++|+.||+|.+|+|++|+.|++++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      +..
T Consensus       119 a~~  121 (139)
T d1u6fa1         119 AAS  121 (139)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            864

>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=99.80  E-value=8.8e-20  Score=148.34  Aligned_cols=82  Identities=20%  Similarity=0.302  Sum_probs=78.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .++++|||+|||+++|+++|+++|+.||+|.+|++.+|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|.|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 006282          107 HR  108 (652)
Q Consensus       107 ~~  108 (652)
                      ..
T Consensus        85 ~~   86 (88)
T d1rk8a_          85 FV   86 (88)
T ss_dssp             EE
T ss_pred             cC
Confidence            64

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.4e-19  Score=151.54  Aligned_cols=85  Identities=25%  Similarity=0.386  Sum_probs=80.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++++|||+|||+++||++|+++|+.||.|.++++..|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34578899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCc
Q 006282          106 SHRDP  110 (652)
Q Consensus       106 s~~~~  110 (652)
                      +....
T Consensus        95 a~~k~   99 (102)
T d2cpza1          95 KRSKN   99 (102)
T ss_dssp             CCCSC
T ss_pred             eCCCC
Confidence            87654

>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=99.80  E-value=9.8e-20  Score=146.53  Aligned_cols=80  Identities=30%  Similarity=0.426  Sum_probs=76.3

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ..+.++++|||+|||+++||++|+++|++||+|.+|+|.+|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus         4 ~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           4 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.79  E-value=2e-19  Score=149.85  Aligned_cols=85  Identities=19%  Similarity=0.349  Sum_probs=80.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .+++|||+|||+++|+++|+++|++||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|+|++|+|.|+.
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            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCccc
Q 006282          108 RDPSI  112 (652)
Q Consensus       108 ~~~~~  112 (652)
                      .....
T Consensus        87 ~~~~~   91 (99)
T d1whwa_          87 IKKEA   91 (99)
T ss_dssp             CCSTT
T ss_pred             CCCcc
Confidence            76543

>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=99.79  E-value=1.7e-19  Score=144.89  Aligned_cols=80  Identities=39%  Similarity=0.662  Sum_probs=76.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      .++|||+|||+++||++|+++|++||+|.+|++.+|..+++++|||||+|.+.++|++|++.||+..|.|++|+|.|++.
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

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2e-19  Score=146.99  Aligned_cols=84  Identities=18%  Similarity=0.349  Sum_probs=79.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ...+++|||+|||.++|+++|+++|+.||+|.+|++.+|+.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 006282          106 SHRD  109 (652)
Q Consensus       106 s~~~  109 (652)
                      ++..
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            8753

>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=99.78  E-value=1e-19  Score=148.38  Aligned_cols=82  Identities=28%  Similarity=0.451  Sum_probs=78.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++|+++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|.|+
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 006282          107 HR  108 (652)
Q Consensus       107 ~~  108 (652)
                      ..
T Consensus        83 ~p   84 (89)
T d2cqba1          83 KP   84 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=99.78  E-value=5.3e-19  Score=142.81  Aligned_cols=80  Identities=28%  Similarity=0.449  Sum_probs=75.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC--ceeEee
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN--KSIRIM  104 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G--~~i~i~  104 (652)
                      ...++|||+|||+++||++|+++|++||+|.++++++|+.+++++|||||+|.+.++|.+|++.||+..+.|  ++|+|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            356789999999999999999999999999999999999999999999999999999999999999999977  889998


Q ss_pred             cc
Q 006282          105 YS  106 (652)
Q Consensus       105 ~s  106 (652)
                      |+
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            85

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=4.4e-19  Score=140.62  Aligned_cols=76  Identities=32%  Similarity=0.537  Sum_probs=74.1

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .|||+|||.++++++|+++|++||.|++++|..+.+|+++|||||+|.+.++|.+|++.|||..++|++|.|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            4999999999999999999999999999999999999999999999999999999999999999999999999986

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=4.4e-19  Score=146.02  Aligned_cols=85  Identities=22%  Similarity=0.501  Sum_probs=78.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHhhc-CCcccCCceeEee
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS-TRRSLGYGYVNYANPADAARALDVL-NFTPLNNKSIRIM  104 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~-t~~s~g~AfV~F~~~e~A~~Al~~l-n~~~i~G~~i~i~  104 (652)
                      ..+++|||+|||.+++|++|+++|+.||.|.+|++.+|.. +++++|||||+|.+.++|.+|++.| |+..|.|++|+|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            4568899999999999999999999999999999998854 7899999999999999999999998 8899999999999


Q ss_pred             cccCCcc
Q 006282          105 YSHRDPS  111 (652)
Q Consensus       105 ~s~~~~~  111 (652)
                      |++.+..
T Consensus        86 ~A~~~~~   92 (94)
T d2cpha1          86 WADSEVT   92 (94)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9987653

>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=99.77  E-value=5.8e-19  Score=142.40  Aligned_cols=79  Identities=28%  Similarity=0.450  Sum_probs=74.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC--ceeEeec
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN--KSIRIMY  105 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G--~~i~i~~  105 (652)
                      .+++|||+|||+++||++|+++|++||+|.++++++|+.+++++|||||+|.+.++|++|++.||+..+.|  ++|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            35789999999999999999999999999999999999999999999999999999999999999999988  5688888


Q ss_pred             c
Q 006282          106 S  106 (652)
Q Consensus       106 s  106 (652)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.77  E-value=3.2e-19  Score=143.21  Aligned_cols=79  Identities=34%  Similarity=0.594  Sum_probs=75.1

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      +++|||+|||.++++++|+++|++||.|.+++|.++. +|+++|||||+|.+.++|.+|++.|||..++|+.|+|+|+++
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            4689999999999999999999999999999999864 789999999999999999999999999999999999999975

>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=99.77  E-value=6.9e-19  Score=143.18  Aligned_cols=81  Identities=25%  Similarity=0.399  Sum_probs=75.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ..+++|||+|||+++||++|+++|+.||+|.+|+|.+|+.+++++|||||.|.+.++|++||+..  ..|+|+.|+|.|+
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEeC
Confidence            45689999999999999999999999999999999999999999999999999999999999954  4789999999998


Q ss_pred             cCC
Q 006282          107 HRD  109 (652)
Q Consensus       107 ~~~  109 (652)
                      ...
T Consensus        84 ~~k   86 (90)
T d2cqga1          84 NSK   86 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            764

>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=99.77  E-value=6e-19  Score=143.36  Aligned_cols=82  Identities=24%  Similarity=0.472  Sum_probs=76.8

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|++++|. +|+++|||||+|.+.++|.+|+..|||..++|+.|.|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            357899999999999999999999999999999999874 7999999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      ..+
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            764

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4.6e-19  Score=142.94  Aligned_cols=79  Identities=23%  Similarity=0.396  Sum_probs=76.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      +|||+|||+++||++|+++|+.||+|.++++.+|+.|++++|||||+|.+.++|.+|++.||+..|.|++|+|.|+...
T Consensus         3 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_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999998753

>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=99.76  E-value=9.6e-19  Score=140.42  Aligned_cols=79  Identities=34%  Similarity=0.641  Sum_probs=74.8

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .++|||+|||.++++++|+++|++||.|.+|+++++. .|.++|||||+|.+.++|.+|++.|||..++|+.|.|.|+++
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            3579999999999999999999999999999999874 689999999999999999999999999999999999999975

>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=99.76  E-value=1.3e-18  Score=145.85  Aligned_cols=83  Identities=28%  Similarity=0.408  Sum_probs=77.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++||++|+++|+.||+|.+|++++|+.|++++|||||+|.+.++|++|++.+|+ .|.|++|+|.|+.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            357899999999999999999999999999999999999999999999999999999999998876 6899999999987


Q ss_pred             CCcc
Q 006282          108 RDPS  111 (652)
Q Consensus       108 ~~~~  111 (652)
                      ....
T Consensus        88 ~~~~   91 (103)
T d2cqda1          88 LGAK   91 (103)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            6543

>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=99.76  E-value=2.7e-19  Score=149.70  Aligned_cols=85  Identities=35%  Similarity=0.550  Sum_probs=79.2

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ..++++|||+|||+++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..|+|+.|+|.|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999998874 789999999999999999999999999999999999999


Q ss_pred             cccHHH
Q 006282          387 AQRKEE  392 (652)
Q Consensus       387 ~~~~~~  392 (652)
                      ++++.+
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             eCCCCC
Confidence            987754

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=7.8e-19  Score=139.96  Aligned_cols=77  Identities=38%  Similarity=0.543  Sum_probs=73.8

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      +|||+|||.++|+++|+++|++||.|.+|+|++|. +|+++|||||+|.+.++|.+|++.|||..++|++|+|.|+++
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            69999999999999999999999999999999976 689999999999999999999999999999999999999864

>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=99.76  E-value=1.4e-18  Score=139.63  Aligned_cols=81  Identities=27%  Similarity=0.448  Sum_probs=75.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      +...++|||+|||+++||++|+++|+.||+|.+++|++|+.+++++|||||.|.+.++|++|++ +++..|+|+.|+|..
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKR   81 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            3456899999999999999999999999999999999999999999999999999999999998 688899999999976


Q ss_pred             cc
Q 006282          106 SH  107 (652)
Q Consensus       106 s~  107 (652)
                      +.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            53

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=8.8e-19  Score=147.38  Aligned_cols=82  Identities=30%  Similarity=0.569  Sum_probs=78.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++||++|+++|++||+|.+|++++|+.+++++|||||+|.+.++|++|++.||+..|.|++|+|.|+.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 006282          108 RD  109 (652)
Q Consensus       108 ~~  109 (652)
                      .+
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>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=99.76  E-value=1.1e-18  Score=140.94  Aligned_cols=78  Identities=28%  Similarity=0.589  Sum_probs=73.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCC---CcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR---RSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        32 L~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~---~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      |||+|||+++|+++|+++|++||+|.+++|.+|+.++   +++|||||+|.+.++|++|++.||+..|+|++|+|.|+.+
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   5789999999999999999999999999999999999865


Q ss_pred             C
Q 006282          109 D  109 (652)
Q Consensus       109 ~  109 (652)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.75  E-value=8.9e-19  Score=138.80  Aligned_cols=76  Identities=33%  Similarity=0.540  Sum_probs=72.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      +|||+|||+++|+++|+++|++||+|.+++|++|+ +++++|||||+|.+.++|.+|++.||+..+.|++|+|.++.
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            69999999999999999999999999999999986 78999999999999999999999999999999999998864

>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=99.75  E-value=1.2e-18  Score=142.51  Aligned_cols=84  Identities=31%  Similarity=0.542  Sum_probs=79.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++|+++|+++|++||+|..+.+.++..+++++|||||+|.+.++|++|++.||+..|.|+.|+|.|+.
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            46789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCcc
Q 006282          108 RDPS  111 (652)
Q Consensus       108 ~~~~  111 (652)
                      ...+
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=139.97  Aligned_cols=78  Identities=32%  Similarity=0.671  Sum_probs=73.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecC--eeEEEEe
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVAV  386 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g--~~l~v~~  386 (652)
                      .+++|||+|||.++|+++|+++|++||.|.+++|++|. +|+++|||||+|.+.++|.+|++.|||..+.|  ++|.|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45789999999999999999999999999999999875 68999999999999999999999999999997  5699998


Q ss_pred             c
Q 006282          387 A  387 (652)
Q Consensus       387 ~  387 (652)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.75  E-value=1.1e-18  Score=142.24  Aligned_cols=81  Identities=28%  Similarity=0.467  Sum_probs=76.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.|++
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            34689999999999999999999999999999999876 68999999999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.75  E-value=2.1e-18  Score=141.56  Aligned_cols=81  Identities=23%  Similarity=0.300  Sum_probs=76.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .+++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|.+|++.|||..++|++|.|.|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            46799999999999999999999999999999999875 68899999999999999999999999999999999999986


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ..
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=5.8e-19  Score=139.20  Aligned_cols=76  Identities=29%  Similarity=0.519  Sum_probs=72.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ++|||+|||+++||++|+++|++||+|.+++|.+|+.|++++|||||.|.+.++|++|++ +|+..++|+.|+|.++
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            579999999999999999999999999999999999999999999999999999999998 7999999999999764

>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=99.75  E-value=9.3e-19  Score=140.74  Aligned_cols=78  Identities=31%  Similarity=0.612  Sum_probs=74.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCC
Q 006282           32 LYVGDLDFNVTDSQLYDLFSQVGQVLS-VRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRD  109 (652)
Q Consensus        32 L~V~nLp~~vte~~L~~~Fs~~G~V~~-i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~  109 (652)
                      |||+|||+++||++|+++|++||.|.+ ++|.+|..+++++|||||+|.+.++|++|++.||+..|.|++|+|.|+...
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            899999999999999999999999866 589999999999999999999999999999999999999999999998754

>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=99.75  E-value=1.5e-18  Score=141.67  Aligned_cols=81  Identities=31%  Similarity=0.484  Sum_probs=76.8

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.|. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.|++
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            45689999999999999999999999999999999875 68999999999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.74  E-value=3.3e-18  Score=139.56  Aligned_cols=82  Identities=27%  Similarity=0.434  Sum_probs=75.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .+.++|||+|||.++||++|+++|+.||+|.+|++++|..++  +|||||+|.+.++|++|++.+|+..|.|+.|+|.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            446799999999999999999999999999999999997765  689999999999999999999999999999999999


Q ss_pred             cCCc
Q 006282          107 HRDP  110 (652)
Q Consensus       107 ~~~~  110 (652)
                      ....
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7643

>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=99.74  E-value=1.6e-18  Score=142.31  Aligned_cols=82  Identities=28%  Similarity=0.474  Sum_probs=77.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++|+++|+++|++||.|.+|+|+++. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|.||.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999875 78999999999999999999999999999999999999998


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      .+.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            653

>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=99.74  E-value=7.9e-19  Score=143.04  Aligned_cols=81  Identities=44%  Similarity=0.703  Sum_probs=75.4

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ..+|||+|||.++++++|+++|+.||.|.+++|+.+.. .++|||||+|.+.++|.+|++.|||..++|+.|.|.+++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            35799999999999999999999999999999998864 47999999999999999999999999999999999999876


Q ss_pred             HH
Q 006282          391 EE  392 (652)
Q Consensus       391 ~~  392 (652)
                      .+
T Consensus        87 ~~   88 (89)
T d1cvja2          87 KE   88 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.74  E-value=6.1e-18  Score=138.82  Aligned_cols=86  Identities=28%  Similarity=0.449  Sum_probs=77.8

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .......++|||+|||+++|+++|+++|+.||+|.+|++++|..+  ++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus         5 ~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   82 (93)
T d2cq3a1           5 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIE   82 (93)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            334455778999999999999999999999999999999998653  689999999999999999999999999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.|+....
T Consensus        83 V~~A~~r~   90 (93)
T d2cq3a1          83 VNNATARV   90 (93)
T ss_dssp             EEECCSSC
T ss_pred             EEecCcCC
Confidence            99998653

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.1e-18  Score=135.40  Aligned_cols=74  Identities=28%  Similarity=0.496  Sum_probs=70.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      .|||+|||+++||++|+++|++||+|.++++++|+.+++++|||||+|.+.++|++|++ +++..|+|+.|+|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            48999999999999999999999999999999999999999999999999999999998 788899999999854

>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=99.74  E-value=2.4e-18  Score=138.90  Aligned_cols=78  Identities=33%  Similarity=0.657  Sum_probs=73.4

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecC--eeEEEEe
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVAV  386 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g--~~l~v~~  386 (652)
                      ..++|||+|||.++++++|+++|++||.|.+++++++. +|+++|||||+|.+.++|.+|++.|||..+.|  ++|.|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45789999999999999999999999999999999875 78999999999999999999999999999976  8899998


Q ss_pred             c
Q 006282          387 A  387 (652)
Q Consensus       387 ~  387 (652)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=2.3e-18  Score=141.63  Aligned_cols=81  Identities=22%  Similarity=0.488  Sum_probs=75.9

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC--CCCCccEEEEEeCCHHHHHHHHHHh-cCcEecCeeEEEEe
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYVAV  386 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~--~g~s~g~afV~F~s~~~A~~A~~~l-ng~~~~g~~l~v~~  386 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+++.  +|+++|||||+|.+.++|.+|++.| ||..++|++|.|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            45789999999999999999999999999999998764  6899999999999999999999998 89999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +..+
T Consensus        87 A~~~   90 (94)
T d2cpha1          87 ADSE   90 (94)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.74  E-value=1.4e-18  Score=139.01  Aligned_cols=79  Identities=16%  Similarity=0.222  Sum_probs=69.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      ++|||+|||+++|+++|+++|+.||+|..+.+..+..+++++|||||+|.+.++|.+|++.||+..|+|++|+|.+++.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999999999988888999999999999999999999999999999999999998863

>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=99.74  E-value=4.8e-18  Score=139.47  Aligned_cols=82  Identities=28%  Similarity=0.508  Sum_probs=76.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+|+++.+..+ ++|||||+|.+.++|.+|+..|||..++|+.|.|.|+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345678999999999999999999999999999999998655 7999999999999999999999999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      .++
T Consensus        87 ~~r   89 (93)
T d2cq3a1          87 TAR   89 (93)
T ss_dssp             CSS
T ss_pred             CcC
Confidence            865

>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=2.7e-18  Score=137.30  Aligned_cols=78  Identities=15%  Similarity=0.303  Sum_probs=68.8

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      |+|||+|||.++|+++|+++|+.||.|..++++.+ ..|+++|||||+|.+.++|.+|++.|||..++|++|.|+++++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            68999999999999999999999999998877655 4789999999999999999999999999999999999999875

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.7e-18  Score=144.13  Aligned_cols=80  Identities=28%  Similarity=0.377  Sum_probs=76.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++||++|+++|+.||.|.+|++++|+.+++++|||||+|.+.++|.+|++ ||+..|.|+.|+|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            46799999999999999999999999999999999999999999999999999999999996 99999999999999875


Q ss_pred             C
Q 006282          108 R  108 (652)
Q Consensus       108 ~  108 (652)
                      .
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3e-18  Score=146.80  Aligned_cols=105  Identities=23%  Similarity=0.430  Sum_probs=87.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ++..+++|||+|||.++|+++|+++|+.||+|.+|++..+   ++++|||||+|.+.++|.+|++.||+..|.|++|+|.
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   79 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL   79 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999999765   5667999999999999999999999999999999999


Q ss_pred             cccCCcccccCCCcceeecCCCccccHHHHHhhhccCC
Q 006282          105 YSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG  142 (652)
Q Consensus       105 ~s~~~~~~~~~~~~~lfV~nLp~~~t~~~L~~~Fs~fG  142 (652)
                      |+......          ........++.+..+...+|
T Consensus        80 ~a~~~~~~----------~~~~~~~~~~~~~~~~~~~g  107 (114)
T d2f9da1          80 YYNANRAF----------QKMDTKKKEEQLKLLKEKYG  107 (114)
T ss_dssp             ECCHHHHT----------TTSCHHHHHHHHHHHHHHHC
T ss_pred             EcCCCchh----------hhhHHHHHHHHHHHHHHHhC
Confidence            98754322          12333455677777777776

>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=99.73  E-value=2.3e-18  Score=134.79  Aligned_cols=74  Identities=15%  Similarity=0.384  Sum_probs=70.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      .|||+|||+++||++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++||+ .++..|.|+.|+|..
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEE
Confidence            59999999999999999999999999999999999999999999999999999999998 466789999998864

>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=5.9e-18  Score=135.91  Aligned_cols=75  Identities=27%  Similarity=0.399  Sum_probs=71.3

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ++++|||+|||.++|+++|+++|++||.|.+|+|+.+. +|+++|||||+|.+.++|.+|+..|||..|+|+.|+|
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            46789999999999999999999999999999999875 5899999999999999999999999999999999987

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=3.7e-18  Score=137.91  Aligned_cols=82  Identities=17%  Similarity=0.315  Sum_probs=72.2

Q ss_pred             CccEEEEcCCCCCCC-HHHHHHHHhccCCeEEEEEEee-CCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           28 LTTSLYVGDLDFNVT-DSQLYDLFSQVGQVLSVRVCRD-LSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        28 ~~~sL~V~nLp~~vt-e~~L~~~Fs~~G~V~~i~v~~d-~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++|||+|||+++| |++|+++|++||.|.+|+|+++ ..+++++|||||+|.+.++|++|++ +|+..|.|+.|+|.|
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            578999999999986 6679999999999999999764 5688999999999999999999997 999999999999999


Q ss_pred             ccCCc
Q 006282          106 SHRDP  110 (652)
Q Consensus       106 s~~~~  110 (652)
                      +...|
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98654

>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=99.73  E-value=2.7e-18  Score=138.37  Aligned_cols=78  Identities=29%  Similarity=0.563  Sum_probs=74.5

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .|||+|||.++|+++|+++|+.||.|++|+|++|. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++...
T Consensus         3 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_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            69999999999999999999999999999999985 6999999999999999999999999999999999999999753

>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=1.6e-18  Score=136.61  Aligned_cols=75  Identities=35%  Similarity=0.571  Sum_probs=71.4

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      |+|||+|||+++|+++|+++|++||.|++++|++|+ +|++||||||+|.+.++|.+|++ +|+..++|+.|.|++|
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            679999999999999999999999999999999886 59999999999999999999997 7999999999999876

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=5.5e-18  Score=139.75  Aligned_cols=78  Identities=24%  Similarity=0.515  Sum_probs=73.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||.+++|++|+++|++||+|.+|++++|      +|||||+|.+.++|++|++.||+..|.|+.|+|.|++
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            4679999999999999999999999999999999976      4799999999999999999999999999999999998


Q ss_pred             CCcc
Q 006282          108 RDPS  111 (652)
Q Consensus       108 ~~~~  111 (652)
                      .+++
T Consensus        91 ~~p~   94 (96)
T d1x4ga1          91 ESPD   94 (96)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8765

>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=99.73  E-value=8.1e-18  Score=133.80  Aligned_cols=77  Identities=14%  Similarity=0.409  Sum_probs=73.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .++|||+|||+++|+++|+++|+.||.|.+++++.|+.+++++|||||.|.+.++|.+|++ +|+..|+|+.|+|.++
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            5799999999999999999999999999999999999999999999999999999999997 8999999999999754

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=4.5e-18  Score=141.52  Aligned_cols=81  Identities=23%  Similarity=0.486  Sum_probs=75.4

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ++|||+|||.++++++|+++|+.||.|.+|+|+++. +|+++|||||+|.+.++|.+|+. |||..|+|+.|.|.++..+
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCC
Confidence            579999999999999999999999999999999985 69999999999999999999995 9999999999999998766


Q ss_pred             HHH
Q 006282          391 EER  393 (652)
Q Consensus       391 ~~r  393 (652)
                      ..|
T Consensus        98 ~nr  100 (101)
T d2cq4a1          98 KNR  100 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>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=8.3e-18  Score=139.88  Aligned_cols=84  Identities=17%  Similarity=0.316  Sum_probs=77.8

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC------CcccCCc
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN------FTPLNNK   99 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln------~~~i~G~   99 (652)
                      ...+++|||+|||+++||++|+++|++||+|.++++..+..+++++|||||+|.+.++|.+|++.+|      +..|.|+
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            3457899999999999999999999999999999999999999999999999999999999999887      5678999


Q ss_pred             eeEeecccCC
Q 006282          100 SIRIMYSHRD  109 (652)
Q Consensus       100 ~i~i~~s~~~  109 (652)
                      .|+|.|+...
T Consensus        85 ~l~v~~a~~k   94 (98)
T d1x4ha1          85 QLKVDLAVTR   94 (98)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999998754

>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=99.72  E-value=4.3e-18  Score=138.40  Aligned_cols=80  Identities=29%  Similarity=0.426  Sum_probs=73.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||+++|+++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|.+|++.+  ..++|+.|.|+++.
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 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEeCC
Confidence            45689999999999999999999999999999999985 6999999999999999999999854  48999999999998


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      +++
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            764

>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=99.72  E-value=6.2e-18  Score=140.67  Aligned_cols=81  Identities=31%  Similarity=0.492  Sum_probs=76.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|.+|++.|||..|+|+.|+|.++.
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            35679999999999999999999999999999999875 79999999999999999999999999999999999999998


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        87 ~~   88 (99)
T d1whwa_          87 IK   88 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=5.3e-18  Score=136.93  Aligned_cols=77  Identities=38%  Similarity=0.663  Sum_probs=71.3

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC----CCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS----GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~----g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      |||+|||.++|+++|+++|++||.|++++|+.+..    +.++|||||+|.+.++|.+|++.|||..++|+.|.|.|+++
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            79999999999999999999999999999987753    24799999999999999999999999999999999999865


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1e-17  Score=134.86  Aligned_cols=78  Identities=17%  Similarity=0.304  Sum_probs=73.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      .++|||+|||.++|+++|+++|+.||+|.+|++.++. +++++|||||+|.+.++|.+|++ +++..|.|+.|+|+|...
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcCC
Confidence            5799999999999999999999999999999998875 78999999999999999999997 799999999999998653

>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=99.72  E-value=4.7e-18  Score=142.84  Aligned_cols=83  Identities=28%  Similarity=0.534  Sum_probs=77.3

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ++|||+|||.++++++|+++|++||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..|+|+.|.|.++..+
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            479999999999999999999999999999999875 6899999999999999999999999999999999999999876


Q ss_pred             HHHH
Q 006282          391 EERR  394 (652)
Q Consensus       391 ~~r~  394 (652)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T d1p1ta_          89 KNKE   92 (104)
T ss_dssp             THHH
T ss_pred             CCcc
Confidence            5443

>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=99.72  E-value=8.8e-18  Score=140.14  Aligned_cols=81  Identities=22%  Similarity=0.450  Sum_probs=76.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++|+++|+++|++||.|.+++|.+|+.+++++|||||+|.+.++|++|++ +++..|+|+.|.|.++.
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            45899999999999999999999999999999999999999999999999999999999997 78889999999999877


Q ss_pred             CC
Q 006282          108 RD  109 (652)
Q Consensus       108 ~~  109 (652)
                      ..
T Consensus        98 ~k   99 (103)
T d1x4ba1          98 AR   99 (103)
T ss_dssp             SC
T ss_pred             cc
Confidence            54

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=7.2e-18  Score=137.24  Aligned_cols=79  Identities=29%  Similarity=0.530  Sum_probs=73.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      .++|||+|||+++|+++|+++|+.||.|.+++|+.|..  .++|||||+|.+.++|++|++.||+..|.|+.|+|.|+..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            45799999999999999999999999999999999864  4779999999999999999999999999999999999875


Q ss_pred             C
Q 006282          109 D  109 (652)
Q Consensus       109 ~  109 (652)
                      .
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.71  E-value=7.1e-18  Score=137.57  Aligned_cols=81  Identities=32%  Similarity=0.509  Sum_probs=75.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+++.+..+ .+|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.+
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            4568999999999999999999999999999999988644 489999999999999999999999999999999999986


Q ss_pred             HH
Q 006282          390 KE  391 (652)
Q Consensus       390 ~~  391 (652)
                      +.
T Consensus        86 ~~   87 (90)
T d2cqia1          86 PS   87 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.4e-17  Score=138.91  Aligned_cols=81  Identities=20%  Similarity=0.326  Sum_probs=75.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ....++|||+|||+++|+++|+++|+.||+|.++++.++. +++++|||||+|.+.++|.+|++.||+..|+|+++++.|
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3446899999999999999999999999999999999884 789999999999999999999999999999999999987


Q ss_pred             cc
Q 006282          106 SH  107 (652)
Q Consensus       106 s~  107 (652)
                      +.
T Consensus        94 ~~   95 (101)
T d1x5oa1          94 TE   95 (101)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.71  E-value=3.4e-18  Score=137.42  Aligned_cols=78  Identities=38%  Similarity=0.718  Sum_probs=72.5

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcCCeeEE-EEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccHH
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  391 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG~I~~v-~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~~  391 (652)
                      |||+|||.++|+++|+++|++||.|.++ +++++. +|+++|||||+|.+.++|.+|++.|||..++|++|.|.|+.+++
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            7999999999999999999999999775 677764 68999999999999999999999999999999999999998764

>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=99.70  E-value=1.3e-17  Score=139.58  Aligned_cols=85  Identities=24%  Similarity=0.395  Sum_probs=78.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCe--------EEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQV--------LSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V--------~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      ....++|||+|||.++||++|+++|+.||+|        ..+.+.+|..+++++|||||+|.+.++|.+|++.||+..|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            3457899999999999999999999999987        46788888899999999999999999999999999999999


Q ss_pred             CceeEeecccCCc
Q 006282           98 NKSIRIMYSHRDP  110 (652)
Q Consensus        98 G~~i~i~~s~~~~  110 (652)
                      |+.|+|.|++..+
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998653

>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=99.70  E-value=1e-17  Score=136.82  Aligned_cols=81  Identities=28%  Similarity=0.530  Sum_probs=75.5

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecC-CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~-~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..+|||+|||.++++++|+++|+.||.|..+.++.+ .+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|+++.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            457999999999999999999999999999998876 4788999999999999999999999999999999999999986


Q ss_pred             HH
Q 006282          390 KE  391 (652)
Q Consensus       390 ~~  391 (652)
                      +.
T Consensus        85 ~~   86 (90)
T d1x5sa1          85 SS   86 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.70  E-value=9.7e-18  Score=135.43  Aligned_cols=80  Identities=26%  Similarity=0.504  Sum_probs=70.2

Q ss_pred             ccceeeecCCCCCCC-HHHHHHHhhhcCCeeEEEEecC--CCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          310 QGLNLYIKNLGDSID-DEKLKELFSEFGTITSCKVMRD--PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       310 ~~~~l~V~nlp~~~t-e~~L~~~F~~fG~I~~v~i~~~--~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      .+++|||+|||.+++ +++|+++|++||.|++|+|..+  .+|+++|||||+|.+.++|.+|++ |||..++|+.|.|++
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            467899999999986 5569999999999999998764  478999999999999999999996 999999999999999


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>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=99.70  E-value=1.5e-17  Score=139.14  Aligned_cols=80  Identities=28%  Similarity=0.416  Sum_probs=73.9

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|.+|++.+|+ .|+|+.|.|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            34679999999999999999999999999999999886 689999999999999999999998876 7999999999987


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      .+
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=4.4e-18  Score=142.62  Aligned_cols=85  Identities=22%  Similarity=0.273  Sum_probs=80.1

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      +..++++|||+|||.++|+++|+++|+.||.|.++++..+..+++++|||||.|.+.++|.+|++.||+..|.|++|+|.
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34468899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             cccCC
Q 006282          105 YSHRD  109 (652)
Q Consensus       105 ~s~~~  109 (652)
                      |++..
T Consensus        94 ~ak~k   98 (102)
T d2cpxa1          94 FGKNK   98 (102)
T ss_dssp             ECCCC
T ss_pred             eCCCc
Confidence            99864

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=1.1e-17  Score=131.67  Aligned_cols=75  Identities=25%  Similarity=0.471  Sum_probs=72.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .|||+|||+++||++|+++|+.||.|.++.+..++.+++++|||||+|.+.++|++|++ +|+..|+|++|+|.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            49999999999999999999999999999999999999999999999999999999997 9999999999999864

>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=99.70  E-value=1.9e-18  Score=141.00  Aligned_cols=82  Identities=22%  Similarity=0.348  Sum_probs=76.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ....++|||+|||.++++++|+++|+.||.|.+++|+.+.+|+++|||||+|.+.++|.+|++ |||..++|+.|.|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            335678999999999999999999999999999999888889999999999999999999996 9999999999999999


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=99.70  E-value=3.5e-17  Score=137.50  Aligned_cols=85  Identities=25%  Similarity=0.477  Sum_probs=75.3

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeC-CCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDL-STRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~-~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      +..+.++|||+|||+++||++|+++|+.|| |.+++++++. .+++++|||||+|.+.++|++|++ ||+..|.|+.|+|
T Consensus        11 p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V   88 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEE
Confidence            345678999999999999999999999999 7788888776 478899999999999999998876 9999999999999


Q ss_pred             ecccCCcc
Q 006282          104 MYSHRDPS  111 (652)
Q Consensus       104 ~~s~~~~~  111 (652)
                      .|+.....
T Consensus        89 ~~a~~~~~   96 (104)
T d1wi8a_          89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99886543

>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=99.70  E-value=3.6e-17  Score=139.93  Aligned_cols=79  Identities=23%  Similarity=0.382  Sum_probs=73.8

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .+++|||+|||.++++++|+++|+.||.|.+|++..+  +.++|||||+|.+.++|.+|++.|||..|+|+.|.|.++..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4578999999999999999999999999999999865  66799999999999999999999999999999999999875


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.69  E-value=1.3e-17  Score=148.11  Aligned_cols=80  Identities=35%  Similarity=0.559  Sum_probs=75.6

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .++|||+|||.++|+++|+++|+.||.|++|+|+++. +|+++|||||+|.+.++|.+|++.|||..|+|+.|+|.+++.
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4679999999999999999999999999999999875 689999999999999999999999999999999999999985


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus       122 ~  122 (139)
T d1u6fa1         122 G  122 (139)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.69  E-value=3.8e-17  Score=131.13  Aligned_cols=77  Identities=34%  Similarity=0.517  Sum_probs=72.1

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .++|||+|||.++|+++|+++|+.||.|.+++|+.|. +|+++|||||+|.+.++|.+|++ +++..|+|+.|.|+.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            3579999999999999999999999999999999886 59999999999999999999997 69999999999998774

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=9.8e-18  Score=139.87  Aligned_cols=80  Identities=35%  Similarity=0.548  Sum_probs=74.6

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      ++|||+|||+++++++|+++|++||.|.+++|..|. ++.++|||||+|.+.++|.+|++ ++|..|+|+.|.|.++.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            579999999999999999999999999999999875 67899999999999999999996 8999999999999999876


Q ss_pred             HH
Q 006282          391 EE  392 (652)
Q Consensus       391 ~~  392 (652)
                      ++
T Consensus       100 e~  101 (103)
T d1x4ba1         100 EE  101 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.69  E-value=4.3e-17  Score=134.34  Aligned_cols=81  Identities=17%  Similarity=0.346  Sum_probs=73.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ..++++|||+|||+++|+++|+++|+.||.|..+++.++   ..++|||||+|.+.++|++|++.||+..|.|++|+|.|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            455789999999999999999999999999999988654   45679999999999999999999999999999999999


Q ss_pred             ccCC
Q 006282          106 SHRD  109 (652)
Q Consensus       106 s~~~  109 (652)
                      ++..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8753

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.9e-17  Score=135.31  Aligned_cols=77  Identities=27%  Similarity=0.472  Sum_probs=72.5

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+++     +|||||+|.+.++|.+|+..|||..|+|+.|+|.|++
T Consensus        16 ~~~~~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          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34578999999999999999999999999999999987     8899999999999999999999999999999999997


Q ss_pred             cH
Q 006282          389 RK  390 (652)
Q Consensus       389 ~~  390 (652)
                      ++
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.69  E-value=3.2e-17  Score=135.44  Aligned_cols=84  Identities=19%  Similarity=0.304  Sum_probs=74.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEEeeC-CCCCcccEEEEEeCCHHHHHHHHhhcCCc--ccCCceeEee
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQ-VLSVRVCRDL-STRRSLGYGYVNYANPADAARALDVLNFT--PLNNKSIRIM  104 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~-V~~i~v~~d~-~t~~s~g~AfV~F~~~e~A~~Al~~ln~~--~i~G~~i~i~  104 (652)
                      +++|||+|||.++|+++|+++|+.||+ |.++++++|. .+++++|||||+|.+.++|.+|++.|++.  .+.|++|+|.
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            468999999999999999999999996 9999999985 46899999999999999999999998754  4579999999


Q ss_pred             cccCCccc
Q 006282          105 YSHRDPSI  112 (652)
Q Consensus       105 ~s~~~~~~  112 (652)
                      |+......
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99765443

>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=99.69  E-value=7.8e-18  Score=131.27  Aligned_cols=71  Identities=27%  Similarity=0.532  Sum_probs=69.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        32 L~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      |||+|||+++|+++|+++|+.||+|.++++.+++.+++++|||||+|.+.++|++|++.||+..|+|+.++
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            89999999999999999999999999999999999999999999999999999999999999999999874

>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=99.69  E-value=1e-17  Score=139.77  Aligned_cols=80  Identities=34%  Similarity=0.620  Sum_probs=75.0

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||.++++++|+++|+.||.|.++++..+.++.++|||||+|.+.++|.+|++.|||+.|.|+++.|.++++
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            45789999999999999999999999999999999998999999999999999999999999999999999988877653

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.69  E-value=4.4e-17  Score=130.60  Aligned_cols=78  Identities=17%  Similarity=0.258  Sum_probs=70.7

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc-CCceeEe
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL-NNKSIRI  103 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i-~G~~i~i  103 (652)
                      ..+++++|||+|||.++|+++|+++|+.||+|.+|++++++     +|||||+|.+.++|.+|++.||+..| .|++|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            34568899999999999999999999999999999997653     47999999999999999999999888 5799999


Q ss_pred             eccc
Q 006282          104 MYSH  107 (652)
Q Consensus       104 ~~s~  107 (652)
                      .|++
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.69  E-value=2.1e-17  Score=129.67  Aligned_cols=74  Identities=28%  Similarity=0.536  Sum_probs=69.1

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      .|||+|||+++++++|+++|++||.|.+++|+.+. +|+++|||||+|.+.++|.+|++ +++..|+|+.|.|+.|
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            38999999999999999999999999999999875 68999999999999999999997 7999999999998643

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=8.4e-17  Score=134.94  Aligned_cols=87  Identities=21%  Similarity=0.210  Sum_probs=78.5

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      ........+|||+|||+++||++|+++|+.+|.|..+.++.+..+++++|||||+|.+.++|++|++ +|+..|.||.|+
T Consensus         9 ~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~   87 (104)
T d1wg5a_           9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIE   87 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEE
Confidence            3344456789999999999999999999999999987788888889999999999999999999997 899999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.++....
T Consensus        88 V~~~~~~~   95 (104)
T d1wg5a_          88 IFKSSRAE   95 (104)
T ss_dssp             EEEECTTT
T ss_pred             EEECCHHH
Confidence            99988764

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.9e-17  Score=130.78  Aligned_cols=77  Identities=22%  Similarity=0.326  Sum_probs=73.3

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .++|||+|||.++|+++|+++|+.||.|.+|++..+.+|+++|||||+|.+.++|.+|++ ++|..+.|+.|.|.|+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            458999999999999999999999999999999999999999999999999999999996 79999999999999864

>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=99.68  E-value=2.9e-17  Score=132.85  Aligned_cols=80  Identities=16%  Similarity=0.227  Sum_probs=71.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      +..++|||+|||+++++++|+++|+.||.|....++.+..+++++|||||+|.+.++|.+|+++||+..+.|++|+|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999877444444578999999999999999999999999999999999999763

>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=6e-18  Score=138.02  Aligned_cols=83  Identities=19%  Similarity=0.276  Sum_probs=75.5

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      ..+....+|||+|||+++|+++|+++|+.||.|.+++|+.+ .+++++|||||+|.+.++|++||+ ||+..|.|+.|+|
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V   85 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEE
Confidence            34455779999999999999999999999999999998755 678999999999999999999996 9999999999999


Q ss_pred             ecccC
Q 006282          104 MYSHR  108 (652)
Q Consensus       104 ~~s~~  108 (652)
                      .|++.
T Consensus        86 ~~ak~   90 (91)
T d1fjeb1          86 EKPKG   90 (91)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99864

>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=99.67  E-value=1.8e-17  Score=129.54  Aligned_cols=74  Identities=20%  Similarity=0.380  Sum_probs=68.9

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      .|||+|||+++|+++|+++|++||.|.+|+|+.|. +|+++|||||+|.+.++|.+|++ +++..++|+.|.|+.|
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            48999999999999999999999999999999885 79999999999999999999997 5778899999999865

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=3.9e-17  Score=139.12  Aligned_cols=81  Identities=14%  Similarity=0.206  Sum_probs=72.9

Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      .....+++|||+|||+++|+++|+++|+.||+|.+|+|.      +++|||||+|.+.++|.+|++.||+..|.|++|+|
T Consensus         5 ~~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v   78 (111)
T d1whxa_           5 SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYL   78 (111)
T ss_dssp             GTSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEE
Confidence            344567899999999999999999999999999999873      35689999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|+..+.
T Consensus        79 ~~a~~~~   85 (111)
T d1whxa_          79 EWAPIGV   85 (111)
T ss_dssp             EEEETTT
T ss_pred             EECCCCc
Confidence            9987653

>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=99.67  E-value=7.1e-17  Score=129.36  Aligned_cols=79  Identities=19%  Similarity=0.383  Sum_probs=72.0

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec-CeeEEEE
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVA  385 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~-g~~l~v~  385 (652)
                      +.+++++|||+|||.++++++|+++|+.||.|.+|+++++    .+|||||+|.+.++|.+|++.|||..+. |++|.|.
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            3456789999999999999999999999999999999876    3689999999999999999999999885 7999999


Q ss_pred             eccc
Q 006282          386 VAQR  389 (652)
Q Consensus       386 ~~~~  389 (652)
                      |++.
T Consensus        80 ~akk   83 (83)
T d2b0ga1          80 FAKK   83 (83)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9873

>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=7.4e-17  Score=133.33  Aligned_cols=79  Identities=19%  Similarity=0.396  Sum_probs=70.2

Q ss_pred             CCCCCccEEEEcCCC-CCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           24 GNQFLTTSLYVGDLD-FNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        24 ~~~~~~~sL~V~nLp-~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .+...+++|||+||+ ..+++++|+++|++||+|.+|+|.        +|||||+|.+.++|++|++.||+..|.|++|+
T Consensus        10 ~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (98)
T d1wf2a_          10 DPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLD   81 (98)
T ss_dssp             CCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344556789999997 568899999999999999999983        47999999999999999999999999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.|+....
T Consensus        82 V~~a~~~~   89 (98)
T d1wf2a_          82 INLAAEPK   89 (98)
T ss_dssp             EEETTSCC
T ss_pred             EEECCCCC
Confidence            99997543

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=9.1e-17  Score=134.15  Aligned_cols=89  Identities=16%  Similarity=0.268  Sum_probs=77.7

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      +......+.+|||+|||+++||++|+++|+.||. .+|+++.+. +++++|||||+|.+.++|++|++ +|+..|.||.|
T Consensus         8 ~~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I   84 (102)
T d1weza_           8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYV   84 (102)
T ss_dssp             SSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCC
T ss_pred             CCCcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEE
Confidence            4445566789999999999999999999999985 478888875 47899999999999999999997 89999999999


Q ss_pred             EeecccCCcccc
Q 006282          102 RIMYSHRDPSIR  113 (652)
Q Consensus       102 ~i~~s~~~~~~~  113 (652)
                      +|.|+.+.+..+
T Consensus        85 ~V~~s~~~~~~~   96 (102)
T d1weza_          85 ELFLNSTAGTSG   96 (102)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEcCCCCCCC
Confidence            999998776543

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.1e-16  Score=129.98  Aligned_cols=78  Identities=21%  Similarity=0.251  Sum_probs=70.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc-CCceeEeec
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL-NNKSIRIMY  105 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i-~G~~i~i~~  105 (652)
                      +++++|||+|||+++||++|+++|+.||.|.++++..+    +++|||||+|.+.++|.+|+..||+..+ +|++|+|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            35789999999999999999999999999988876553    4568999999999999999999999888 699999999


Q ss_pred             ccC
Q 006282          106 SHR  108 (652)
Q Consensus       106 s~~  108 (652)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            875

>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=99.67  E-value=9.8e-17  Score=127.40  Aligned_cols=75  Identities=19%  Similarity=0.434  Sum_probs=70.2

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ++|||+|||+++|+++|+++|+.||.|..+++..+. ++.++|||||+|.+.++|.+|++ +||..|+|+.|.|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            579999999999999999999999999999998875 78899999999999999999986 8999999999999875

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=6.5e-17  Score=130.35  Aligned_cols=77  Identities=26%  Similarity=0.489  Sum_probs=71.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      .++|||+|||.++++++|+++|++||+|.+|++.++      +|||||+|.+.++|++|++.||+..|.|+.|+|.|+..
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999999865      47999999999999999999999999999999999987


Q ss_pred             Ccc
Q 006282          109 DPS  111 (652)
Q Consensus       109 ~~~  111 (652)
                      ...
T Consensus        82 ~~~   84 (86)
T d2cpja1          82 SAS   84 (86)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            653

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.2e-16  Score=131.52  Aligned_cols=79  Identities=20%  Similarity=0.326  Sum_probs=73.0

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...++|||+|||.++++++|+++|+.||.|..+++..+  +.++|||||+|.+.++|.+|++.|||..|.|++|.|.|++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            35678999999999999999999999999999998765  4568999999999999999999999999999999999987


Q ss_pred             c
Q 006282          389 R  389 (652)
Q Consensus       389 ~  389 (652)
                      .
T Consensus        90 ~   90 (95)
T d1x4aa1          90 S   90 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.66  E-value=5.2e-17  Score=130.92  Aligned_cols=75  Identities=28%  Similarity=0.449  Sum_probs=71.0

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .++|||+|||.++++++|+++|++||.|.+|++.++     +|||||+|.+.++|.+|++.|||..|+|+.|.|+|+..+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            467999999999999999999999999999999876     789999999999999999999999999999999999754

>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=99.66  E-value=3.9e-17  Score=133.41  Aligned_cols=80  Identities=26%  Similarity=0.517  Sum_probs=72.5

Q ss_pred             CccEEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEe
Q 006282           28 LTTSLYVGDLDFNVTDSQLY----DLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRI  103 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~----~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i  103 (652)
                      |+++|||+|||+++|+++|+    ++|++||+|.+|++.+   +++++|||||+|.+.++|.+|++.+|+..|.|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            57899999999999999985    4689999999988755   4678899999999999999999999999999999999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|++.++
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998754

>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=99.66  E-value=1.1e-16  Score=125.29  Aligned_cols=73  Identities=18%  Similarity=0.352  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      ++|||+|||+++++++|+++|+.||+|.+|++++++..+  .+||||+|.+.++|++|+. +|+..|+|++|.|..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~--~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS--SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc--ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEE
Confidence            589999999999999999999999999999999987643  4799999999999999996 899999999999975

>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=99.66  E-value=1.2e-16  Score=135.53  Aligned_cols=76  Identities=30%  Similarity=0.360  Sum_probs=70.3

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           29 TTSLYVGDLDF-NVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        29 ~~sL~V~nLp~-~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      +++|||+||++ .+||++|+++|+.||+|.+|+|.+|+     +|||||+|.+.++|.+|++.||+..|.|+.|+|.|++
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            57999999965 59999999999999999999998874     4899999999999999999999999999999999987


Q ss_pred             CC
Q 006282          108 RD  109 (652)
Q Consensus       108 ~~  109 (652)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.66  E-value=6e-17  Score=127.33  Aligned_cols=74  Identities=22%  Similarity=0.384  Sum_probs=69.7

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      .|||+|||.++|+++|+++|+.||.|..+.++.+. +|.++|||||+|.+.++|.+|++ +||..|+|+.|.|++|
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            38999999999999999999999999999988765 68899999999999999999997 9999999999999876

>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=99.66  E-value=1.2e-16  Score=132.62  Aligned_cols=82  Identities=30%  Similarity=0.539  Sum_probs=75.1

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhc------CcEecCeeE
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN------GKMIVSKPL  382 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~ln------g~~~~g~~l  382 (652)
                      .+++|||+|||.++|+++|+++|++||.|.+++++.+. .+.++|||||+|.+.++|.+|++.+|      |..+.|+.|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            46789999999999999999999999999999998775 67899999999999999999999886      678899999


Q ss_pred             EEEecccHH
Q 006282          383 YVAVAQRKE  391 (652)
Q Consensus       383 ~v~~~~~~~  391 (652)
                      .|.|+.+++
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999998753

>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=99.66  E-value=3.7e-17  Score=132.74  Aligned_cols=77  Identities=21%  Similarity=0.367  Sum_probs=70.8

Q ss_pred             CccEEEEcCCCCCCCHHHH---HHHHhccCCeEEEEEEeeCCCCCcc---cEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           28 LTTSLYVGDLDFNVTDSQL---YDLFSQVGQVLSVRVCRDLSTRRSL---GYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L---~~~Fs~~G~V~~i~v~~d~~t~~s~---g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      ..++|||+|||+++++++|   +++|++||+|.+|++.+|+.++.+.   |||||+|.+.++|++|++.||+..|.|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3568999999999999999   7789999999999999998876554   999999999999999999999999999999


Q ss_pred             Eee
Q 006282          102 RIM  104 (652)
Q Consensus       102 ~i~  104 (652)
                      ++.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            973

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.66  E-value=8.9e-17  Score=132.67  Aligned_cols=84  Identities=21%  Similarity=0.405  Sum_probs=74.3

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .....++++|||+|||.++|+++|+++|+.||.|..++     .+++++|||||+|.+.++|++|++.||+..|.|++|+
T Consensus        10 ~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~   84 (96)
T d1fjca_          10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS   84 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEE
T ss_pred             cCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEE
Confidence            34455689999999999999999999999999876553     3678999999999999999999999999999999999


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|+.....
T Consensus        85 V~~a~~k~~   93 (96)
T d1fjca_          85 LYYTGEKGG   93 (96)
T ss_dssp             EEECSSSCC
T ss_pred             EEEeCCCCC
Confidence            999987644

>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=99.66  E-value=8.3e-17  Score=127.60  Aligned_cols=74  Identities=30%  Similarity=0.491  Sum_probs=68.9

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      .+++|||+|++  +|+++|+++|++||.|.++++.++     +|||||+|.+.++|.+|+..|||..++|+.|+|.|+++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            46789999995  899999999999999999999765     78999999999999999999999999999999999986


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        77 ~   77 (79)
T d2bz2a1          77 Q   77 (79)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=2.7e-16  Score=129.90  Aligned_cols=81  Identities=23%  Similarity=0.396  Sum_probs=73.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCC--ceeE
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNN--KSIR  102 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G--~~i~  102 (652)
                      ...++++|||+|||+++|+++|+++|++||+|.++++.++      ++||||+|.+.++|++|++.||+..|.|  ++|+
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~   86 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEE
Confidence            3456899999999999999999999999999999999765      3699999999999999999999999987  5899


Q ss_pred             eecccCCcc
Q 006282          103 IMYSHRDPS  111 (652)
Q Consensus       103 i~~s~~~~~  111 (652)
                      |.|++.++.
T Consensus        87 v~~ak~~~~   95 (97)
T d1whya_          87 VDFAKSGPS   95 (97)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999987654

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=8.4e-17  Score=130.05  Aligned_cols=78  Identities=18%  Similarity=0.360  Sum_probs=72.5

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeE-EEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~-v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ..+.|||+|||.++++++|+++|+.||.|.. +.+..+.+|+++|||||+|.+.++|.+|+..||++.++|++|+|+++
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            4567999999999999999999999999976 56777789999999999999999999999999999999999999985

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.2e-16  Score=126.59  Aligned_cols=77  Identities=22%  Similarity=0.345  Sum_probs=70.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      +..+++|||+||+  +||++|+++|++||.|.+|++.++      +|||||+|.+.++|.+|++.||+..|.|++|+|.|
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999995  999999999999999999999754      47999999999999999999999999999999999


Q ss_pred             ccCCc
Q 006282          106 SHRDP  110 (652)
Q Consensus       106 s~~~~  110 (652)
                      ++++|
T Consensus        74 a~~~P   78 (79)
T d2bz2a1          74 ARKQP   78 (79)
T ss_dssp             CCSSC
T ss_pred             ecCCC
Confidence            98765

>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=99.65  E-value=1.2e-16  Score=133.55  Aligned_cols=83  Identities=25%  Similarity=0.468  Sum_probs=73.8

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCee--------EEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTIT--------SCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~--------~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      ....++|||+|||.++|+++|+++|+.||.|.        .+.+..+. +|+++|||||+|.+.++|.+|++.|||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            34567999999999999999999999999885        34555553 6889999999999999999999999999999


Q ss_pred             CeeEEEEecccH
Q 006282          379 SKPLYVAVAQRK  390 (652)
Q Consensus       379 g~~l~v~~~~~~  390 (652)
                      |+.|+|.+++++
T Consensus        85 gr~i~V~~a~~~   96 (101)
T d2cpea1          85 GSKLKVSLARKK   96 (101)
T ss_dssp             TEECEEECSSCC
T ss_pred             CEEEEEEEcCCC
Confidence            999999999865

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.6e-17  Score=130.81  Aligned_cols=74  Identities=27%  Similarity=0.430  Sum_probs=68.7

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCc-EecCeeEEEEecccHH
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK-MIVSKPLYVAVAQRKE  391 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~-~~~g~~l~v~~~~~~~  391 (652)
                      +|||+|||.++|+++|+++|++||.|.++++...     +|||||+|.+.++|.+|++.|||. .++|++|.|.|+.++.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            6999999999999999999999999988877754     889999999999999999999996 6999999999998764

>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=99.65  E-value=1.1e-17  Score=140.05  Aligned_cols=84  Identities=26%  Similarity=0.390  Sum_probs=77.7

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      .++++|||+|||.++++++|+++|+.||.|..++++.+. +|+++|||||+|.+.++|.+|++.|||..|.|++|.|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            356789999999999999999999999999999887764 7899999999999999999999999999999999999999


Q ss_pred             ccHHH
Q 006282          388 QRKEE  392 (652)
Q Consensus       388 ~~~~~  392 (652)
                      +++++
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            98654

>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=99.65  E-value=1.1e-16  Score=132.25  Aligned_cols=81  Identities=15%  Similarity=0.180  Sum_probs=72.5

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCC-eeEEEEecCC--CCCCccEEEEEeCCHHHHHHHHHHhcC--cEecCeeEEEE
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGT-ITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYVA  385 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~-I~~v~i~~~~--~g~s~g~afV~F~s~~~A~~A~~~lng--~~~~g~~l~v~  385 (652)
                      +|.|||+|||.++++++|+++|+.||. |++++++.+.  .|+++|||||+|.+.++|.+|++.|++  ..++|++|.|.
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            367999999999999999999999995 9999999874  588999999999999999999999865  45579999999


Q ss_pred             ecccHH
Q 006282          386 VAQRKE  391 (652)
Q Consensus       386 ~~~~~~  391 (652)
                      ||.++.
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            998653

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=2.5e-16  Score=123.26  Aligned_cols=72  Identities=19%  Similarity=0.309  Sum_probs=65.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCCc
Q 006282           32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP  110 (652)
Q Consensus        32 L~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~~  110 (652)
                      |||+|||+++|+++|+++|++|| +..+++      ++++|||||.|.+.++|++|++.||+..++|++|+|.|+..+.
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 444443      4567999999999999999999999999999999999998765

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.2e-16  Score=133.38  Aligned_cols=81  Identities=25%  Similarity=0.262  Sum_probs=73.0

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc--CCceeEe
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL--NNKSIRI  103 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i--~G~~i~i  103 (652)
                      +.+..+|||+|||+++||++|+++|++||.|.+|++.+++    ++|||||+|.+.++|++|++.||+..|  .|+.|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            4467899999999999999999999999999999999874    468999999999999999999999988  5789999


Q ss_pred             ecccCCc
Q 006282          104 MYSHRDP  110 (652)
Q Consensus       104 ~~s~~~~  110 (652)
                      .|++...
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9987643

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=6.7e-17  Score=131.97  Aligned_cols=82  Identities=32%  Similarity=0.511  Sum_probs=73.4

Q ss_pred             cceeeecCCCCCCCHHHHHH----HhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          311 GLNLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~----~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      +++|||+|||.++++++|++    +|++||+|.+|++..+  ++++|||||+|.+.++|.+|++.+||..++|+.|+|.|
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~--~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH--HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee--ccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            56899999999999998864    6899999999988654  66799999999999999999999999999999999999


Q ss_pred             cccHHHHH
Q 006282          387 AQRKEERR  394 (652)
Q Consensus       387 ~~~~~~r~  394 (652)
                      ++.+.+..
T Consensus        81 ak~~~~~~   88 (91)
T d1nu4a_          81 AKTDSDII   88 (91)
T ss_dssp             CSSCCTHH
T ss_pred             eCCCchhh
Confidence            98775543

>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=99.64  E-value=2.1e-16  Score=132.27  Aligned_cols=84  Identities=18%  Similarity=0.276  Sum_probs=75.6

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeE-EEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~-v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ..+||||+|||+++|+++|+++|+.||.|.. +.+..+.+|+++|||||+|.+.++|.+|+. +|+..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            3568999999999999999999999999976 566677799999999999999999999996 99999999999999987


Q ss_pred             cHHHHH
Q 006282          389 RKEERR  394 (652)
Q Consensus       389 ~~~~r~  394 (652)
                      .++.+.
T Consensus        86 ~~~~~~   91 (103)
T d2cpya1          86 LEDMRE   91 (103)
T ss_dssp             HHHHHH
T ss_pred             HHHhhh
Confidence            766553

>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=1.7e-16  Score=135.06  Aligned_cols=76  Identities=24%  Similarity=0.304  Sum_probs=70.4

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||..+++++|+++|+.||.|..|.|..     ++|||||+|.+.++|.+|++.|||..|.|++|+|.|+..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            357899999999999999999999999999998853     589999999999999999999999999999999999865


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.2e-16  Score=127.02  Aligned_cols=74  Identities=31%  Similarity=0.468  Sum_probs=67.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCc-ccCCceeEeecccC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFT-PLNNKSIRIMYSHR  108 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~-~i~G~~i~i~~s~~  108 (652)
                      .+|||+|||+++||++|+++|++||.|.++++.+      ++|||||+|.+.++|++|++.||+. .|+|++|+|.|+..
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            5799999999999999999999999998877765      3589999999999999999999986 59999999999875


Q ss_pred             C
Q 006282          109 D  109 (652)
Q Consensus       109 ~  109 (652)
                      .
T Consensus        76 k   76 (80)
T d2cqha1          76 K   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2.1e-16  Score=128.21  Aligned_cols=76  Identities=21%  Similarity=0.371  Sum_probs=68.4

Q ss_pred             ccceeeecCCCCCCCHHHH---HHHhhhcCCeeEEEEecCC-CC---CCccEEEEEeCCHHHHHHHHHHhcCcEecCeeE
Q 006282          310 QGLNLYIKNLGDSIDDEKL---KELFSEFGTITSCKVMRDP-SG---ISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL  382 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L---~~~F~~fG~I~~v~i~~~~-~g---~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l  382 (652)
                      +...|||+|||+++++++|   +++|++||.|++|+|+++. ++   ..+|||||+|.+.++|.+|++.|||..++|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4567999999999999999   7789999999999999875 22   345999999999999999999999999999999


Q ss_pred             EEE
Q 006282          383 YVA  385 (652)
Q Consensus       383 ~v~  385 (652)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.63  E-value=4.1e-16  Score=128.77  Aligned_cols=78  Identities=24%  Similarity=0.252  Sum_probs=70.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeec
Q 006282           26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY  105 (652)
Q Consensus        26 ~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~  105 (652)
                      .....+|||+|||+++++++|+++|+.||+|.++++.++       |||||+|.+.++|++|++.||+..|+|+.|+|.|
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 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc-------ceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            345678999999999999999999999999999998643       8999999999999999999999999999999998


Q ss_pred             ccCCc
Q 006282          106 SHRDP  110 (652)
Q Consensus       106 s~~~~  110 (652)
                      ...++
T Consensus        85 ~~~~~   89 (98)
T d1wg4a_          85 IRVYP   89 (98)
T ss_dssp             EEEEC
T ss_pred             EecCC
Confidence            76544

>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=99.63  E-value=3.4e-16  Score=126.95  Aligned_cols=78  Identities=22%  Similarity=0.303  Sum_probs=70.7

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEe-cCeeEEEEec
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI-VSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~-~g~~l~v~~~  387 (652)
                      +++++|||+|||.++++++|+++|++||.|.++++..+   +++|||||+|.+.++|.+|+..|||..+ +|+.|+|.|+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            45678999999999999999999999999998877654   3578999999999999999999999988 5899999998


Q ss_pred             cc
Q 006282          388 QR  389 (652)
Q Consensus       388 ~~  389 (652)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            75

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=9.5e-17  Score=129.81  Aligned_cols=73  Identities=23%  Similarity=0.265  Sum_probs=67.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccCCc
Q 006282           31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP  110 (652)
Q Consensus        31 sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~~~  110 (652)
                      +|||+|||+++|+++|+++|++||+|.++++.+|       |||||+|.+.++|++|++.||+..|.|+.|+|.+.....
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            6999999999999999999999999999998765       799999999999999999999999999999998876443

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.5e-16  Score=128.77  Aligned_cols=77  Identities=16%  Similarity=0.244  Sum_probs=67.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecccC
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      +++|||+|||+++|+++|+++|++|| +..+.+      .+++|||||+|.+.++|++|++.||+..|+|+.|+|.|+..
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-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            67899999999999999999999999 222222      45678999999999999999999999999999999999976


Q ss_pred             Cccc
Q 006282          109 DPSI  112 (652)
Q Consensus       109 ~~~~  112 (652)
                      +...
T Consensus        78 ~~~~   81 (88)
T d1wg1a_          78 DALL   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.63  E-value=4.4e-16  Score=126.24  Aligned_cols=79  Identities=19%  Similarity=0.243  Sum_probs=71.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc--CCcccCCceeE
Q 006282           25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL--NFTPLNNKSIR  102 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l--n~~~i~G~~i~  102 (652)
                      ...++++|||+|||+++|+++|+++|++||.|.++++.++      +|||||+|.+.++|++|++.+  +...++|++|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3557999999999999999999999999999999998864      369999999999999999865  56789999999


Q ss_pred             eecccCC
Q 006282          103 IMYSHRD  109 (652)
Q Consensus       103 i~~s~~~  109 (652)
                      |.|++.+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9999764

>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=99.62  E-value=2.8e-16  Score=133.15  Aligned_cols=74  Identities=22%  Similarity=0.456  Sum_probs=69.0

Q ss_pred             cceeeecCCC-CCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          311 GLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       311 ~~~l~V~nlp-~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      +++|||+||+ ..+|+++|+++|+.||.|.+|+|+++.    +|||||+|.+.++|.+|++.|||..|.|+.|.|.|++
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            4689999995 569999999999999999999999873    7899999999999999999999999999999999976

>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=99.62  E-value=4.6e-16  Score=125.56  Aligned_cols=75  Identities=28%  Similarity=0.408  Sum_probs=69.6

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .++|||+|||.++++++|+++|+.||.|..+++..     ++|||||+|.+.++|.+|+..|||..|+|+.|.|.|++++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            45799999999999999999999999998888743     5889999999999999999999999999999999999865

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.5e-16  Score=130.07  Aligned_cols=74  Identities=28%  Similarity=0.526  Sum_probs=67.9

Q ss_pred             cccceeeecCCC-CCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          309 FQGLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       309 ~~~~~l~V~nlp-~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...++|||+||+ +.+++++|+++|++||.|++|+|       ++|||||+|.+.++|.+|++.|||+.|.|+.|+|.|+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            345689999996 57889999999999999999998       3789999999999999999999999999999999998


Q ss_pred             cc
Q 006282          388 QR  389 (652)
Q Consensus       388 ~~  389 (652)
                      ..
T Consensus        86 ~~   87 (98)
T d1wf2a_          86 AE   87 (98)
T ss_dssp             TS
T ss_pred             CC
Confidence            74

>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=1.1e-16  Score=124.59  Aligned_cols=69  Identities=30%  Similarity=0.543  Sum_probs=65.8

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeE
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL  382 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~-~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l  382 (652)
                      |||+|||.++|+++|+++|+.||.|.++++..+. ++.++|||||+|.+.++|.+|++.|||+.|.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            7999999999999999999999999999998875 78899999999999999999999999999999876

>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=99.62  E-value=4.8e-16  Score=125.45  Aligned_cols=75  Identities=23%  Similarity=0.361  Sum_probs=68.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      ..++|||+|||+++|+++|+++|+.||.|..+++.+      ++|||||+|.+.++|.+|+..||+..|.|+.|+|.|++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            357999999999999999999999999998887743      56899999999999999999999999999999999987


Q ss_pred             C
Q 006282          108 R  108 (652)
Q Consensus       108 ~  108 (652)
                      .
T Consensus        81 P   81 (86)
T d2cpda1          81 P   81 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.62  E-value=6.8e-16  Score=120.69  Aligned_cols=74  Identities=19%  Similarity=0.223  Sum_probs=68.3

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ++|||+|||.++++++|+++|+.||.|.++++..+..+. ++||||+|.+.++|.+|+. +|++.|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            479999999999999999999999999999999887654 6799999999999999996 8999999999999754

>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=99.62  E-value=1.9e-15  Score=126.43  Aligned_cols=86  Identities=14%  Similarity=0.125  Sum_probs=74.1

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC--CcccCCc
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN--FTPLNNK   99 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln--~~~i~G~   99 (652)
                      ......++++|||+|||.++||++|+++|+.||+|.+|++.++      +|||||+|.+.++|++|++.++  ...+.|+
T Consensus         8 ~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~   81 (104)
T d1wexa_           8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE
Confidence            3344567899999999999999999999999999999999764      4799999999999999999874  4567899


Q ss_pred             eeEeecccCCcccc
Q 006282          100 SIRIMYSHRDPSIR  113 (652)
Q Consensus       100 ~i~i~~s~~~~~~~  113 (652)
                      +|+|.|++.+...+
T Consensus        82 ~l~v~~s~~~~~~~   95 (104)
T d1wexa_          82 QAFFNYSTSKRITR   95 (104)
T ss_dssp             BCEEEECSSSSCCC
T ss_pred             EEEEEEcCCCccCC
Confidence            99999998765433

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.7e-16  Score=131.64  Aligned_cols=81  Identities=14%  Similarity=0.155  Sum_probs=73.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        27 ~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      ...++|||+|||+++|+++|+++|+.||.|..+.+..+..+++++|||||+|.+.++|++|++ +|+..|.|+.|+|.++
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            346789999999999999999999999999876666666789999999999999999999997 8999999999999886


Q ss_pred             cC
Q 006282          107 HR  108 (652)
Q Consensus       107 ~~  108 (652)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>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=99.62  E-value=3.1e-16  Score=127.05  Aligned_cols=76  Identities=20%  Similarity=0.308  Sum_probs=68.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        28 ~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .+++|||+|||+++||++|+++|++||+|.+|++.     +.++|||||+|.+.++|++|+.  ++..|+|+.|+|.|+.
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            47899999999999999999999999999998764     3467899999999999999997  6778999999999987


Q ss_pred             CCc
Q 006282          108 RDP  110 (652)
Q Consensus       108 ~~~  110 (652)
                      ...
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.61  E-value=6e-16  Score=129.76  Aligned_cols=79  Identities=25%  Similarity=0.450  Sum_probs=71.2

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC--CCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~--~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      +.++|||+|||.++|+++|+++|+.|| |.+++++.+.  +|+++|||||+|.+.++|++|+ .||+..|+|+.|+|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            457899999999999999999999998 8888887654  6889999999999999998766 59999999999999998


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      .++
T Consensus        92 ~~~   94 (104)
T d1wi8a_          92 DQA   94 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.60  E-value=6.1e-16  Score=125.15  Aligned_cols=74  Identities=20%  Similarity=0.350  Sum_probs=65.6

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .++|||+|||.++++++|+++|++|| +..+.+.     +++|||||+|.+.++|.+|++.|||..+.|+.|.|.|++.+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            46899999999999999999999999 3334443     35899999999999999999999999999999999998754

>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=99.60  E-value=1.3e-15  Score=119.07  Aligned_cols=71  Identities=21%  Similarity=0.443  Sum_probs=64.6

Q ss_pred             eeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       314 l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      |||+|||.++++++|+++|++|| +..+++     ++++|||||+|.+.++|.+|+..|||..+.|++|.|+|++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-----~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-----cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999998 555554     346899999999999999999999999999999999999754

>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=99.60  E-value=2.6e-16  Score=131.29  Aligned_cols=81  Identities=17%  Similarity=0.242  Sum_probs=74.3

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ...+.+|||+|||+++|+++|+++|+.|| |..+.++.+.+|.++|||||+|.+.++|.+|++ +|+..|+|+.|.|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            44567899999999999999999999997 668889999899999999999999999999986 8999999999999998


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      .++
T Consensus        90 ~~~   92 (102)
T d1weza_          90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            854

>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=99.60  E-value=1.1e-15  Score=123.84  Aligned_cols=80  Identities=21%  Similarity=0.349  Sum_probs=72.3

Q ss_pred             cccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh--cCcEecCeeEEE
Q 006282          307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYV  384 (652)
Q Consensus       307 ~~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l--ng~~~~g~~l~v  384 (652)
                      +..++++|||+|||.++++++|+++|++||.|.++++.++     +|||||+|.+.++|.+|++.+  ++..+.|++|+|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            3457789999999999999999999999999999999865     689999999999999999965  577999999999


Q ss_pred             EecccHH
Q 006282          385 AVAQRKE  391 (652)
Q Consensus       385 ~~~~~~~  391 (652)
                      .|++.++
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9998653

>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=99.60  E-value=4.2e-16  Score=128.51  Aligned_cols=78  Identities=27%  Similarity=0.396  Sum_probs=71.3

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||.++|+++|+++|+.||.|..++.    +|+++|||||+|.+.++|.+|+..|||..|+|+.|.|.|+.+
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            4578999999999999999999999999877653    467899999999999999999999999999999999999987


Q ss_pred             HH
Q 006282          390 KE  391 (652)
Q Consensus       390 ~~  391 (652)
                      +.
T Consensus        91 k~   92 (96)
T d1fjca_          91 KG   92 (96)
T ss_dssp             SC
T ss_pred             CC
Confidence            63

>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=99.60  E-value=8.9e-16  Score=127.04  Aligned_cols=81  Identities=15%  Similarity=0.217  Sum_probs=71.5

Q ss_pred             CCCCccEEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHh--hcCCcccCCcee
Q 006282           25 NQFLTTSLYVGDLDFN-VTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD--VLNFTPLNNKSI  101 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~-vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~--~ln~~~i~G~~i  101 (652)
                      ...++++|||+|||.+ +||++|+++|+.||.|.+|++.++      +|||||+|.+.++|.+|++  .++...|.|++|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3456789999999985 899999999999999999999865      3799999999999999998  467778999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+++...
T Consensus        88 ~V~~s~~~~~   97 (99)
T d1x4fa1          88 KVDLSEKYKK   97 (99)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEEcCCccc
Confidence            9999987643

>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=99.59  E-value=9.1e-16  Score=130.24  Aligned_cols=86  Identities=19%  Similarity=0.250  Sum_probs=76.5

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCcee
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSI  101 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i  101 (652)
                      +..+.....+|||+|||+++|+++|+++|+.||.|..+.++.+..+++++|||||+|.+.++|++|++ +|+..|.|+.|
T Consensus        11 ~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i   89 (112)
T d1wela1          11 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFI   89 (112)
T ss_dssp             CSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCB
T ss_pred             CCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEE
Confidence            33445567899999999999999999999999999877777777889999999999999999999997 99999999999


Q ss_pred             EeecccC
Q 006282          102 RIMYSHR  108 (652)
Q Consensus       102 ~i~~s~~  108 (652)
                      +|.++..
T Consensus        90 ~V~~~~~   96 (112)
T d1wela1          90 QVHPITK   96 (112)
T ss_dssp             EEEEECH
T ss_pred             EEEEcCh
Confidence            9987653

>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=99.59  E-value=5e-16  Score=125.78  Aligned_cols=75  Identities=16%  Similarity=0.345  Sum_probs=68.3

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||+++|+++|+++|++||.|.+|++..+    ++|||||+|.+.++|.+|+.  ++..|+|+.|.|.++.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCC
Confidence            3578999999999999999999999999999987654    68899999999999999985  88899999999999875


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        78 k   78 (88)
T d1wf0a_          78 K   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=1.8e-15  Score=124.93  Aligned_cols=76  Identities=21%  Similarity=0.349  Sum_probs=70.3

Q ss_pred             cccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecC--eeEEEEe
Q 006282          309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVAV  386 (652)
Q Consensus       309 ~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g--~~l~v~~  386 (652)
                      .+.++|||+|||.++++++|+++|++||.|+.+++.++     ++||||+|.+.++|.+|++.|||..|.|  ++|+|.|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            35678999999999999999999999999999999865     7899999999999999999999999986  5899999


Q ss_pred             ccc
Q 006282          387 AQR  389 (652)
Q Consensus       387 ~~~  389 (652)
                      ++.
T Consensus        90 ak~   92 (97)
T d1whya_          90 AKS   92 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>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=99.58  E-value=4.9e-16  Score=125.56  Aligned_cols=72  Identities=25%  Similarity=0.317  Sum_probs=67.5

Q ss_pred             eeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecccH
Q 006282          313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  390 (652)
Q Consensus       313 ~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~~  390 (652)
                      .|||+|||.++++++|+++|+.||.|.++++..+      |||||+|.+.++|.+|+..|||..|.|+.|.|.+++.+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            5999999999999999999999999999998754      79999999999999999999999999999999887654

>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=99.57  E-value=1.7e-15  Score=122.67  Aligned_cols=81  Identities=16%  Similarity=0.184  Sum_probs=71.4

Q ss_pred             CCCCccEEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhc--CCcccCCcee
Q 006282           25 NQFLTTSLYVGDLDFN-VTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL--NFTPLNNKSI  101 (652)
Q Consensus        25 ~~~~~~sL~V~nLp~~-vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~l--n~~~i~G~~i  101 (652)
                      ...++++|||+|||.. +|+++|+++|+.||.|.+|++.+++      +||||+|.+.++|..|++.+  +...+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            4567899999999986 8999999999999999999998753      58999999999999999966  5667999999


Q ss_pred             EeecccCCcc
Q 006282          102 RIMYSHRDPS  111 (652)
Q Consensus       102 ~i~~s~~~~~  111 (652)
                      +|.|+++...
T Consensus        78 ~V~~s~~~~~   87 (89)
T d1x4da1          78 RVHLSQKYKR   87 (89)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEECCCccc
Confidence            9999986543

>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=99.57  E-value=1.4e-15  Score=127.43  Aligned_cols=81  Identities=22%  Similarity=0.285  Sum_probs=72.6

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEE-EEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v-~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      ...+|||+|||+++|+++|+++|+.||.|..+ .++.+.+++++|||||+|.+.++|.+|++ +|+..|+|+.|.|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            45579999999999999999999999998875 45566789999999999999999999996 99999999999999988


Q ss_pred             cHH
Q 006282          389 RKE  391 (652)
Q Consensus       389 ~~~  391 (652)
                      +++
T Consensus        93 ~~~   95 (104)
T d1wg5a_          93 RAE   95 (104)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            654

>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=99.57  E-value=1.3e-15  Score=128.59  Aligned_cols=78  Identities=19%  Similarity=0.330  Sum_probs=70.7

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEe--cCeeEEEEec
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVAVA  387 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~--~g~~l~v~~~  387 (652)
                      ...+|||+||++++|+++|+++|++||.|.+|+|+.+.   ++|||||+|.+.++|.+|+..|||..|  .++.|.|.++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            34579999999999999999999999999999999773   589999999999999999999999998  4788999988


Q ss_pred             ccH
Q 006282          388 QRK  390 (652)
Q Consensus       388 ~~~  390 (652)
                      +.+
T Consensus        83 ~~~   85 (108)
T d2adba1          83 KLT   85 (108)
T ss_dssp             SSC
T ss_pred             CCc
Confidence            754

>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=99.57  E-value=9.9e-16  Score=126.43  Aligned_cols=75  Identities=19%  Similarity=0.242  Sum_probs=69.7

Q ss_pred             ccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEeccc
Q 006282          310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  389 (652)
Q Consensus       310 ~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~~  389 (652)
                      ..++|||+|||+++++++|+++|+.||+|++++|..      +|||||+|.+.++|.+|++.|||..|.|+.|.|.+++.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            355799999999999999999999999999999864      57999999999999999999999999999999999875


Q ss_pred             H
Q 006282          390 K  390 (652)
Q Consensus       390 ~  390 (652)
                      +
T Consensus        88 ~   88 (98)
T d1wg4a_          88 Y   88 (98)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.55  E-value=5.6e-16  Score=129.19  Aligned_cols=76  Identities=17%  Similarity=0.344  Sum_probs=72.9

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEec
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  387 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~  387 (652)
                      ++++|+++.+++++++|+++|++||.|++|+|+++.+|+++|||||+|.+.++|.+|+..|||+.++|++|.|.|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.55  E-value=2.8e-15  Score=123.99  Aligned_cols=77  Identities=21%  Similarity=0.280  Sum_probs=69.9

Q ss_pred             cccceeeecCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHH--HhcCcEecCeeEEEE
Q 006282          309 FQGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA--EMNGKMIVSKPLYVA  385 (652)
Q Consensus       309 ~~~~~l~V~nlp~~-~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~--~lng~~~~g~~l~v~  385 (652)
                      ..+++|||+|||.+ +|+++|+++|++||.|.+++++++     +|||||+|.+.++|.+|++  .+++..++|+.|.|.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            35678999999975 899999999999999999999876     7899999999999999998  578889999999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      |++++
T Consensus        91 ~s~~~   95 (99)
T d1x4fa1          91 LSEKY   95 (99)
T ss_dssp             EECSC
T ss_pred             EcCCc
Confidence            99764

>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=99.55  E-value=6.9e-15  Score=122.98  Aligned_cols=78  Identities=19%  Similarity=0.238  Sum_probs=70.4

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh--cCcEecCeeEEEE
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYVA  385 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l--ng~~~~g~~l~v~  385 (652)
                      ..++.+|||+|||.++++++|+++|++||.|+++++.++     +|+|||+|.+.++|.+|+..+  ++..++|++|+|.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            345778999999999999999999999999999999765     789999999999999999987  4567889999999


Q ss_pred             ecccH
Q 006282          386 VAQRK  390 (652)
Q Consensus       386 ~~~~~  390 (652)
                      |++.+
T Consensus        87 ~s~~~   91 (104)
T d1wexa_          87 YSTSK   91 (104)
T ss_dssp             ECSSS
T ss_pred             EcCCC
Confidence            99765

>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=99.53  E-value=7.3e-15  Score=122.30  Aligned_cols=76  Identities=20%  Similarity=0.238  Sum_probs=68.2

Q ss_pred             ccceeeecCCCCCC-CH----HHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEE
Q 006282          310 QGLNLYIKNLGDSI-DD----EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  384 (652)
Q Consensus       310 ~~~~l~V~nlp~~~-te----~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v  384 (652)
                      ..++|||+||+.++ ++    ++|+++|+.||.|+++++++     +++||||+|.+.++|.+|+..|||..|+|++|+|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            35689999999886 33    56999999999999999985     4889999999999999999999999999999999


Q ss_pred             EecccH
Q 006282          385 AVAQRK  390 (652)
Q Consensus       385 ~~~~~~  390 (652)
                      .|++.+
T Consensus        79 ~~a~~~   84 (104)
T d1weya_          79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             eecccC
Confidence            999644

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.1e-16  Score=127.76  Aligned_cols=78  Identities=15%  Similarity=0.403  Sum_probs=69.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEE-----EeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEee
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRV-----CRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIM  104 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v-----~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~  104 (652)
                      ++|||+|||.++||++|+++|+.||.|.++.+     +.+..+++++|||||+|.+.++|++|++ ||+..+.|+.|+|.
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            68999999999999999999999998766554     4566788899999999999999999996 99999999999997


Q ss_pred             cccC
Q 006282          105 YSHR  108 (652)
Q Consensus       105 ~s~~  108 (652)
                      +.+.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.1e-15  Score=126.90  Aligned_cols=87  Identities=18%  Similarity=0.354  Sum_probs=77.0

Q ss_pred             ccccceeeecCCCCCCCHHHHHHHhhhcCCeeEE-EEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEe
Q 006282          308 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       308 ~~~~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v-~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ...+++|||+|||+++|+++|+++|+.||.|..+ .+..+.+|.++|||||+|.+.++|.+|++ +||..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3356789999999999999999999999999764 55566789999999999999999999996 999999999999999


Q ss_pred             cccHHHHHH
Q 006282          387 AQRKEERRA  395 (652)
Q Consensus       387 ~~~~~~r~~  395 (652)
                      +.+++....
T Consensus        94 ~~~~~~~~~  102 (112)
T d1wela1          94 ITKKGMLEK  102 (112)
T ss_dssp             ECHHHHHHH
T ss_pred             cChHHHHHH
Confidence            988876443

>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=99.52  E-value=1.2e-14  Score=117.51  Aligned_cols=75  Identities=20%  Similarity=0.325  Sum_probs=68.5

Q ss_pred             ccceeeecCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHh--cCcEecCeeEEEEe
Q 006282          310 QGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYVAV  386 (652)
Q Consensus       310 ~~~~l~V~nlp~~-~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~l--ng~~~~g~~l~v~~  386 (652)
                      .+++|||+|||.. +|+++|+++|++||.|.+++++.+     +++|||+|.+.++|.+|++.+  ++..+.|++|+|.|
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~   81 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   81 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEE
Confidence            4678999999985 889999999999999999999876     679999999999999999965  68899999999999


Q ss_pred             ccc
Q 006282          387 AQR  389 (652)
Q Consensus       387 ~~~  389 (652)
                      +++
T Consensus        82 s~~   84 (89)
T d1x4da1          82 SQK   84 (89)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            975

>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=99.52  E-value=5e-15  Score=123.34  Aligned_cols=77  Identities=18%  Similarity=0.229  Sum_probs=68.7

Q ss_pred             CccEEEEcCCCCCC-CH----HHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeE
Q 006282           28 LTTSLYVGDLDFNV-TD----SQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIR  102 (652)
Q Consensus        28 ~~~sL~V~nLp~~v-te----~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~  102 (652)
                      .+++|||+||+.++ ++    ++|+++|+.||.|.++++.+      ++|||||+|.+.++|.+|++.||+..|.|++|+
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            46799999999886 43    56899999999999999974      457999999999999999999999999999999


Q ss_pred             eecccCCc
Q 006282          103 IMYSHRDP  110 (652)
Q Consensus       103 i~~s~~~~  110 (652)
                      |.|++...
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
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=99.47  E-value=6e-16  Score=128.98  Aligned_cols=77  Identities=19%  Similarity=0.259  Sum_probs=72.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeecc
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS  106 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s  106 (652)
                      .+.++|++++.+++|++|+++|++||+|.+|+|+++ .+++++|||||.|.+.++|.+|++.||+..|+||+|+|.|+
T Consensus        27 ~~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          27 VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             cchHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            367899999999999999999999999999999987 57899999999999999999999999999999999999875

>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=99.44  E-value=8e-14  Score=118.09  Aligned_cols=77  Identities=22%  Similarity=0.227  Sum_probs=66.8

Q ss_pred             cccce-eeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCH-HHHHHHHHHhcCcEecCeeEEEEe
Q 006282          309 FQGLN-LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP-EEASRALAEMNGKMIVSKPLYVAV  386 (652)
Q Consensus       309 ~~~~~-l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~-~~A~~A~~~lng~~~~g~~l~v~~  386 (652)
                      ..|+. +||+|||+++|+++|+++|++||.|.+|+|+++     +|||||+|.+. ++|..|+..+|+..+.++.+.|.|
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            34555 599999999999999999999999999999865     78999999995 789999999999999877777776


Q ss_pred             cccH
Q 006282          387 AQRK  390 (652)
Q Consensus       387 ~~~~  390 (652)
                      ...+
T Consensus        83 ~~~~   86 (113)
T d1owxa_          83 EVLE   86 (113)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            6544

>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=99.40  E-value=2.9e-15  Score=121.90  Aligned_cols=73  Identities=19%  Similarity=0.336  Sum_probs=65.4

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEec------CCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEE
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR------DPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  385 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~------~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~  385 (652)
                      ++|||+|||.++|+++|+++|+.||.|.++.+..      ...++++|||||+|.+.++|.+|++ |||..+.|+.|+|+
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            4699999999999999999999999988776543      2357889999999999999999985 99999999999986

>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=99.39  E-value=2.4e-13  Score=112.32  Aligned_cols=65  Identities=26%  Similarity=0.483  Sum_probs=58.7

Q ss_pred             cccceeeecC--CCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          309 FQGLNLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       309 ~~~~~l~V~n--lp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      .+..+|+|.|  |+.++|+++|+++|++||.|++++++.+     ++||||+|.+.++|.+|+..|||+.+.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            3456788855  9999999999999999999999998876     789999999999999999999999873

>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=99.33  E-value=8.7e-13  Score=108.92  Aligned_cols=66  Identities=24%  Similarity=0.346  Sum_probs=58.7

Q ss_pred             CCCCccEEEEcC--CCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCccc
Q 006282           25 NQFLTTSLYVGD--LDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPL   96 (652)
Q Consensus        25 ~~~~~~sL~V~n--Lp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i   96 (652)
                      ...++.+|+|.|  ||.++||++|+++|++||.|.+|++.++      +|||||+|.+.++|++|++.||+..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345678999955  9999999999999999999999988764      36999999999999999999998776

>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=99.33  E-value=6e-13  Score=112.57  Aligned_cols=73  Identities=19%  Similarity=0.216  Sum_probs=64.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCH-HHHHHHHhhcCCcccCCceeEeecccC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP-ADAARALDVLNFTPLNNKSIRIMYSHR  108 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~-e~A~~Al~~ln~~~i~G~~i~i~~s~~  108 (652)
                      ..+||||||.++||++|+++|++||+|.+|+|.++      .|||||.|.+. ++|..|+..+|+..+.++.++|.|...
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            45599999999999999999999999999999864      47999999996 789999999999999888888877654

>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=99.30  E-value=2.1e-12  Score=106.18  Aligned_cols=78  Identities=22%  Similarity=0.339  Sum_probs=67.3

Q ss_pred             ccceeeecCC--CCCCC---------HHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEec
Q 006282          310 QGLNLYIKNL--GDSID---------DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  378 (652)
Q Consensus       310 ~~~~l~V~nl--p~~~t---------e~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~  378 (652)
                      .+.+|+|+|+  +.++.         +++|++.|++||.|+.|++..+   ..+|||||+|.+.++|.+|+..|||+.++
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            3568999999  54331         3689999999999999998776   45799999999999999999999999999


Q ss_pred             CeeEEEEecccH
Q 006282          379 SKPLYVAVAQRK  390 (652)
Q Consensus       379 g~~l~v~~~~~~  390 (652)
                      |+.|.|.++..+
T Consensus        84 gr~i~v~~~~g~   95 (99)
T d2dita1          84 GRQITAQAWDGT   95 (99)
T ss_dssp             TEECEEEECCSC
T ss_pred             CEEEEEEEeCCc
Confidence            999999998654

>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=99.28  E-value=3.6e-12  Score=100.17  Aligned_cols=74  Identities=14%  Similarity=0.171  Sum_probs=63.5

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCee-EEEEeccc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP-LYVAVAQR  389 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~-l~v~~~~~  389 (652)
                      .+.|+|.++|++.+++.| ++|++||+|.++++.+     ++|||||+|.+.++|.+|++ +||..|+|+. |.|.....
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~-----~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC-----CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            457999999999987655 5799999999998754     47899999999999999996 9999999974 67887776


Q ss_pred             HH
Q 006282          390 KE  391 (652)
Q Consensus       390 ~~  391 (652)
                      ++
T Consensus        77 k~   78 (81)
T d1wwha1          77 KN   78 (81)
T ss_dssp             HH
T ss_pred             hh
Confidence            64

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=5.8e-12  Score=103.51  Aligned_cols=80  Identities=13%  Similarity=0.164  Sum_probs=69.1

Q ss_pred             CCCCccEEEEcCC--CCCCC---------HHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCC
Q 006282           25 NQFLTTSLYVGDL--DFNVT---------DSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNF   93 (652)
Q Consensus        25 ~~~~~~sL~V~nL--p~~vt---------e~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~   93 (652)
                      ....+++|+|.||  |.++.         +++|++.|++||.|.+|+++.+    +..|+|||.|.+.++|.+|++.||+
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            4567899999999  65432         3679999999999999998775    3558999999999999999999999


Q ss_pred             cccCCceeEeecccC
Q 006282           94 TPLNNKSIRIMYSHR  108 (652)
Q Consensus        94 ~~i~G~~i~i~~s~~  108 (652)
                      ..|.|++|+|.+...
T Consensus        80 ~~~~gr~i~v~~~~g   94 (99)
T d2dita1          80 RWFGGRQITAQAWDG   94 (99)
T ss_dssp             CEETTEECEEEECCS
T ss_pred             cEECCEEEEEEEeCC
Confidence            999999999997654

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=3.9e-12  Score=105.70  Aligned_cols=82  Identities=17%  Similarity=0.311  Sum_probs=70.2

Q ss_pred             ccceeeecCC--CCCCC--------HHHHHHHhhhcCCeeEEEEecCCCC---CCccEEEEEeCCHHHHHHHHHHhcCcE
Q 006282          310 QGLNLYIKNL--GDSID--------DEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPEEASRALAEMNGKM  376 (652)
Q Consensus       310 ~~~~l~V~nl--p~~~t--------e~~L~~~F~~fG~I~~v~i~~~~~g---~s~g~afV~F~s~~~A~~A~~~lng~~  376 (652)
                      ++.+|.|+|+  +.++.        .++|++.|++||.|++|+|.++..+   .+.|++||.|.+.++|.+|+..|||+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4668999999  55443        3579999999999999999876533   456999999999999999999999999


Q ss_pred             ecCeeEEEEecccHH
Q 006282          377 IVSKPLYVAVAQRKE  391 (652)
Q Consensus       377 ~~g~~l~v~~~~~~~  391 (652)
                      ++||.|.+.+.....
T Consensus        83 f~gR~v~v~f~~~~~   97 (104)
T d1o0pa_          83 FANRVVVTKYCDPDS   97 (104)
T ss_dssp             SSSSCCEEEEECHHH
T ss_pred             ECCeEEEEEEcCHHH
Confidence            999999999998654

>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=99.22  E-value=1e-11  Score=97.52  Aligned_cols=72  Identities=17%  Similarity=0.113  Sum_probs=60.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCce-eEeeccc
Q 006282           29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKS-IRIMYSH  107 (652)
Q Consensus        29 ~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~-i~i~~s~  107 (652)
                      .+.|+|++||++++++.| ++|++||+|.++++.+      ++|||||.|.+.++|++||+ +|+..|.|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            578999999999887655 5799999999998743      45899999999999999997 9999999985 5676654


Q ss_pred             C
Q 006282          108 R  108 (652)
Q Consensus       108 ~  108 (652)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=6.5e-12  Score=104.35  Aligned_cols=82  Identities=18%  Similarity=0.214  Sum_probs=70.5

Q ss_pred             CCccEEEEcCC--CCCCC--------HHHHHHHHhccCCeEEEEEEeeCCCC--CcccEEEEEeCCHHHHHHHHhhcCCc
Q 006282           27 FLTTSLYVGDL--DFNVT--------DSQLYDLFSQVGQVLSVRVCRDLSTR--RSLGYGYVNYANPADAARALDVLNFT   94 (652)
Q Consensus        27 ~~~~sL~V~nL--p~~vt--------e~~L~~~Fs~~G~V~~i~v~~d~~t~--~s~g~AfV~F~~~e~A~~Al~~ln~~   94 (652)
                      .++++|.|+||  +.++.        .++|++.|++||.|.+|.|.++..+.  .+.|++||.|.+.++|.+|++.||+.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46899999999  55543        35689999999999999999876653  45689999999999999999999999


Q ss_pred             ccCCceeEeecccC
Q 006282           95 PLNNKSIRIMYSHR  108 (652)
Q Consensus        95 ~i~G~~i~i~~s~~  108 (652)
                      .|.||.|++.+...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999988653

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.85  E-value=4.9e-05  Score=54.83  Aligned_cols=61  Identities=21%  Similarity=0.276  Sum_probs=54.4

Q ss_pred             HHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       326 ~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      +.|.+.|+++|.|.++.+....+|..  .|-|...+.++|.-|+..||.++|++|+|.|+++.
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 QLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34567789999999999998877765  59999999999999999999999999999999874

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.58  E-value=9.5e-05  Score=57.41  Aligned_cols=68  Identities=13%  Similarity=0.108  Sum_probs=59.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCC--cccEEEEEeCCHHHHHHHHhhcCCcccC
Q 006282           30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR--SLGYGYVNYANPADAARALDVLNFTPLN   97 (652)
Q Consensus        30 ~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~--s~g~AfV~F~~~e~A~~Al~~ln~~~i~   97 (652)
                      +.|.||.||+++||+++.+.++..|++....-+..+.+.+  ...-|||+|.+.++.....+..++..|.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            6899999999999999999999999999988888876653  2267999999999999999998877663

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.53  E-value=6.1e-05  Score=57.24  Aligned_cols=75  Identities=17%  Similarity=0.251  Sum_probs=61.3

Q ss_pred             CCCCCCCccEEEEcCCCCCCCH---------HHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC
Q 006282           22 ASGNQFLTTSLYVGDLDFNVTD---------SQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN   92 (652)
Q Consensus        22 ~~~~~~~~~sL~V~nLp~~vte---------~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln   92 (652)
                      ++-..++-.+|.|.=..++..|         .+|.+.|+.||.|.-||++.|        -.+|.|.+-++|.+|++ ++
T Consensus         8 ~~~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~   78 (95)
T d1ufwa_           8 SSFQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VD   78 (95)
T ss_dssp             SCCCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GG
T ss_pred             ccccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cC
Confidence            3344555678888666555444         357889999999999999987        67999999999999999 89


Q ss_pred             CcccCCceeEeec
Q 006282           93 FTPLNNKSIRIMY  105 (652)
Q Consensus        93 ~~~i~G~~i~i~~  105 (652)
                      +..+.|+.|+|..
T Consensus        79 g~~v~G~~l~It~   91 (95)
T d1ufwa_          79 GMKVKGRAVKISG   91 (95)
T ss_dssp             GSEETTEEEEEEC
T ss_pred             CeEEcceEEEEec
Confidence            9999999999864

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.31  E-value=0.00026  Score=53.71  Aligned_cols=55  Identities=16%  Similarity=0.348  Sum_probs=50.5

Q ss_pred             HHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhcCcEecCeeEEEEecc
Q 006282          326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  388 (652)
Q Consensus       326 ~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~lng~~~~g~~l~v~~~~  388 (652)
                      .+|.+.|+.||+|.=+|++.|       -..|+|.+-+.|.+|++ ++|..+.|+.|.|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            578889999999999999988       69999999999999998 99999999999998654

>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=96.73  E-value=0.0018  Score=46.48  Aligned_cols=65  Identities=22%  Similarity=0.269  Sum_probs=53.7

Q ss_pred             CCCHHH----HHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcCCcccCCceeEeeccc
Q 006282           40 NVTDSQ----LYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSH  107 (652)
Q Consensus        40 ~vte~~----L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln~~~i~G~~i~i~~s~  107 (652)
                      .+++++    |.+.|+++|+|.++.+..... +.  -+|-|...+.+||.-|++.|+...|.+|+|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~d-g~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTD-YQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCS-TT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccC-Cc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            445555    467889999999999976533 22  489999999999999999999999999999998754

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.23  E-value=0.0087  Score=45.99  Aligned_cols=68  Identities=12%  Similarity=0.201  Sum_probs=57.2

Q ss_pred             ceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCC--CC-CCccEEEEEeCCHHHHHHHHHHhcCcEecC
Q 006282          312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SG-ISKGSGFVAFSTPEEASRALAEMNGKMIVS  379 (652)
Q Consensus       312 ~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~--~g-~s~g~afV~F~s~~~A~~A~~~lng~~~~g  379 (652)
                      ++|.|++||...|++++.+.++..|.+........+  .+ ..-..|+|.|.+.++.....+..+|..+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            579999999999999999999999998887766543  11 223569999999999999999999998853

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.50  E-value=0.033  Score=42.75  Aligned_cols=62  Identities=21%  Similarity=0.276  Sum_probs=49.5

Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHhhcC
Q 006282           23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLN   92 (652)
Q Consensus        23 ~~~~~~~~sL~V~nLp~~vte~~L~~~Fs~~G~V~~i~v~~d~~t~~s~g~AfV~F~~~e~A~~Al~~ln   92 (652)
                      .+..+.-.-+|.-..|..+...||.++|+.||.|.=-.| .|  |     -|||...+.++|+.++..++
T Consensus         9 ~d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_           9 PDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SCCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            344555678999999999999999999999997743333 33  2     59999999999999998654

>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=91.87  E-value=0.22  Score=38.03  Aligned_cols=56  Identities=27%  Similarity=0.387  Sum_probs=45.5

Q ss_pred             cceeeecCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCccEEEEEeCCHHHHHHHHHHhc
Q 006282          311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN  373 (652)
Q Consensus       311 ~~~l~V~nlp~~~te~~L~~~F~~fG~I~~v~i~~~~~g~s~g~afV~F~s~~~A~~A~~~ln  373 (652)
                      ..-||.-..|.+|...||.++|++||.|.=--| .|.      .|||.....++|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc------eEEEEecCHHHHHHHHHHhc
Confidence            345888899999999999999999998763333 332      69999999999999887544