Citrus Sinensis ID: 004002

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780
Protein Sequence
MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNNNYYYYNTT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccHHHHHccccccEEEEEcccccHHHHHHHHHHHHccccccccEEEEcccccccccccEEEEEccccccHHHHHHHHcccccccccccccEEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccHHcccccccccccccccccEEEccccccccHHHHHHHHcccccEEEEEcccccccccEEEEEEccHHHHHHHHHHccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEccccccEEEEEEccHHHHHHHHHHHcccEccccEEEEEEcccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEcccccccEEEEEEccHHHHHHHHHHHcccEEcccEEEEEcccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccEEEEcHHHHHcccccccEEEEEcccccHHHHHHHHHHHHHccccEEEEEEEcccccccccEEEEEEcccHHHHHHHHHHHHHHHHHHEEEcccccEEEEccc
Coil and Loop (DISEMBL)
mkqffdhssgppkipqlnipkevgggscgriagsdsylasddaslfssslpvlpheklnlnamglgrqsvddissglskvhhgvasddplegvmnpaignslpddeDELLAGimddfdlrglpssledledydifgsgggmelegepqeslsmsmskisisdsasgngllhysvpngagtvagehpygehpsrtLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQnkplrrrkldihfsipkdnpsdkdlnqgtlvvfnldpsvsnedLRQIFGAYGevkeiretphkrhhkFIEFYDVRAAEAALKSLnrsdiagkriklepsrpggarRNLMLQLNQELEQDESRILqhqvgspitnsppgnwvqfsspiehnplqtiskspnfrnmspttsnhmpglasilhpqvstlekiapigkdqgrgslMEHALTntisangasfqqsnsfsepkiglyrgtvssfgpspsngsgvetlsgpqflwgspsrysehssspawqtssmghpfssngkihglpysgrqgsflgssqhhhvgsapsgvplerrfgflpespetsfmnpvafcgmgigqndgsfmvnmgsrasvnpgitvprnlsdngssfrvmssprlspvflgngpypgltpanieGLYERGrsrriennngnqldsKKQFQLELEKIrsgedtrtTLMIKNIPNKYTSKMLLAAIDEnhkgtydflylpidfknkcnVGYAFInmlsplhiipfYEVLFSCAIGILFfnnnnnyyyyntt
Flexible Loop (DISEMBL)
mkqffdhssgppkipqlniPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRalqnkplrrrKLDIhfsipkdnpsdkdlnQGTLVVFNldpsvsneDLRQIFGAYGEvkeiretphkrhhKFIEFYDVRAAEAALKslnrsdiagkriklepsrpggarrNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRriennngnqldskkqFQLELEkirsgedtrttlmiknipnkYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNNnyyyyntt
Low Complexity Region (SEG)
MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIagsdsylasddaslfssslPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEslsmsmskisisdsasGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMlqlnqeleqdeSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVssfgpspsngsgVETLSGPQFLWGspsrysehsssPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFnnnnnyyyynTT
Disordered region (IsUnstruct)
************************************************************************************************************LLAGIMDDFDLRGL********DYDIF**********************************LHYSV******************RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK*LR*RKLDIHF*************QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK**********************************************************************************************************************************************************************************************************************************************************FMNPVAFCGMGIGQNDGSFMVN**********************************VFLGNGPYPGLT***I****************************************TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFF************
Disordered Region (DISOPRED)
***************************************SDDASLFSSSLPVLPHEKLNL************************************AIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQ********************************************RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI******************LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR********************************************************************************************************************************************************************************************************************************************************************************************************************************************ELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNNNYYYYN**
Disordered Region (DISEMBL)
**********PPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMEL**********SMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGS*******************HPFSSNGKIHGLPYSGRQGSFLG************GVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNNNYYYYNTT
Disordered Region (DISPRO)
*************************************************LPVLPHEKLNLNAMGLGRQSVDDISSGLSK**HGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYS***************EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD******LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR**********************ILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILH*****LEKI***************A*TNT**ANGA***********************G***SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLY*RG*************DSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNNNYYYYNTT
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNNNYYYYNTT
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	780	2.2.26 [Sep-21-2011]
Q6ZI17	848	Protein MEI2-like 2 OS=Or	yes	no	0.887	0.816	0.595	0.0
Q8VWF5	800	Protein MEI2-like 5 OS=Ar	yes	no	0.905	0.882	0.605	0.0
Q9SVV9	759	Protein MEI2-like 3 OS=Ar	no	no	0.857	0.881	0.555	0.0
Q6EQX3	811	Protein MEI2-like 5 OS=Or	no	no	0.905	0.870	0.490	0.0
Q9SJG8	843	Protein MEI2-like 2 OS=Ar	no	no	0.875	0.810	0.480	1e-171
Q75M35	955	Protein MEI2-like 3 OS=Or	no	no	0.816	0.667	0.376	1e-100
Q64M78	1001	Protein MEI2-like 4 OS=Or	no	no	0.424	0.330	0.540	3e-79
Q8W4I9	915	Protein MEI2-like 1 OS=Ar	no	no	0.307	0.262	0.494	8e-59
Q9LYN7	907	Protein MEI2-like 4 OS=Ar	no	no	0.306	0.263	0.476	1e-54
P08965	750	Meiosis protein mei2 OS=S	yes	no	0.071	0.074	0.657	4e-21

>sp|Q6ZI17|OML2_ORYSJ Protein MEI2-like 2 OS=Oryza sativa subsp. japonica GN=ML2 PE=2 SV=1

 Score =  811 bits (2094), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 433/727 (59%), Positives = 520/727 (71%), Gaps = 35/727 (4%)

Query: 42  DASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNS 101
           +ASLFS+SLPVLPHEK+N      G   +DD S+ L ++       D         I + 
Sbjct: 47  NASLFSTSLPVLPHEKINFLDSARGTPLMDDASAKLKELDDDPEGKDYKFDFDLRQIDDL 106

Query: 102 LPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISIS 161
           LP+ ED+L AGI ++ +  G  +S+E+LE++D+FGSGGGMEL+ +P ES++  +   SI+
Sbjct: 107 LPN-EDDLFAGITNEIEPAGQTNSMEELEEFDVFGSGGGMELDTDPVESITAGLGNTSIA 165

Query: 162 DSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT 221
           D   GNG+ H+   N A TVAGEHPYGEHPSRTLFVRNINSNV+D+ELR+LFEQYGDIRT
Sbjct: 166 DGLRGNGVNHFGPSNSASTVAGEHPYGEHPSRTLFVRNINSNVDDTELRSLFEQYGDIRT 225

Query: 222 LYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLV 281
           LYTA KHRGFVMISY+DIRAAR AMR LQNKPLRRRKLDIHFSIPK+NPSDKDLNQGTLV
Sbjct: 226 LYTATKHRGFVMISYFDIRAARGAMRGLQNKPLRRRKLDIHFSIPKENPSDKDLNQGTLV 285

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           +FNLDPSVSNE++RQIFG YGEVKEIRETP+K+HHKFIEFYDVRAAEAAL+SLN+S+IAG
Sbjct: 286 IFNLDPSVSNEEVRQIFGTYGEVKEIRETPNKKHHKFIEFYDVRAAEAALRSLNKSEIAG 345

Query: 342 KRIKLEPSRPGGARRNLMLQLNQELEQDESRILQ-HQVGSPITNSPPGNWVQFSSPIEHN 400
           KRIKLEPSRPGG RRNLM QL  +++QDE R  +   VGSPI +SPPG W Q+SSP ++N
Sbjct: 346 KRIKLEPSRPGGTRRNLMQQLGHDIDQDEPRSYRIPHVGSPIASSPPGAWAQYSSPTDNN 405

Query: 401 PLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTI 460
            LQ  + SP    MSP       G+   L   +S   KIAPIGKD    S  +   +N  
Sbjct: 406 LLQAFNASPTGNGMSPI------GMPPSL---ISNAVKIAPIGKDS-NWSKYDKVFSNNN 455

Query: 461 SANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSS 520
             +GA+FQ S+S+ + K             S    S   TL+GP+FLWGSP  YSEH+ S
Sbjct: 456 QPHGAAFQHSHSYQDHK-------------SEHMSSSPGTLTGPEFLWGSPKPYSEHAQS 502

Query: 521 PAWQTSSMGHPFSSNGKI--HGLPYSGRQGSFLGSS---QHHHVGSAPSGVPLERRFGFL 575
           P W+  ++GH   SN +    GL Y GRQ S  GS     HHHVGSAPSG P E  FGFL
Sbjct: 503 PIWRPPAIGHAIPSNTRSQGQGLLYGGRQASLFGSQDQLHHHHVGSAPSGAPFESHFGFL 562

Query: 576 PESPETSFMNPVAF---CGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSD-NGSSFRVM 631
           PESPETS+MN V F     +G G+N    M+NM +RASVNP   +  N+SD N SSFR +
Sbjct: 563 PESPETSYMNQVRFGNIGNIGSGRNGTGLMLNMAARASVNPVSALSGNMSDNNSSSFRPI 622

Query: 632 SSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGE 691
            SPRL   F GN  Y G     ++   ERGR+RR++++   Q DSKKQ+QL+LEKIR G+
Sbjct: 623 LSPRLGQSFYGNPTYQGPGSFGLDNSIERGRNRRVDSSVF-QADSKKQYQLDLEKIRKGD 681

Query: 692 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHI 751
           DTRTTLMIKNIPNKYTSKMLLAAIDE HKGTYDF YLPIDFKNKCNVGYAFINM+SP+HI
Sbjct: 682 DTRTTLMIKNIPNKYTSKMLLAAIDEFHKGTYDFFYLPIDFKNKCNVGYAFINMISPVHI 741

Query: 752 IPFYEVL 758
           + FY+  
Sbjct: 742 VSFYQAF 748

Probable RNA-binding protein that may play a role in growth regulation.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8VWF5|AML5_ARATH Protein MEI2-like 5 OS=Arabidopsis thaliana GN=ML5 PE=1 SV=1

 Score =  797 bits (2058), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 455/752 (60%), Positives = 556/752 (73%), Gaps = 46/752 (6%)

Query: 17  LNIPKEVGGGSCGRIAG-SDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISS 75
           ++IP E   G+ G + G    +  S DA+LFSSSLPV P  KL L+    G   +DD  +
Sbjct: 1   MDIPHEAEAGAWGILPGFGRHHHPSSDATLFSSSLPVFPRGKLQLSDNRDGFSLIDD--T 58

Query: 76  GLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIF 135
            +S+ +    S D  E   + +IGN LPD+ED LL G+MDD DL  LP    D +DYD+F
Sbjct: 59  AVSRTNKFNESADDFE---SHSIGNLLPDEED-LLTGMMDDLDLGELP----DADDYDLF 110

Query: 136 GSGGGMELEGEPQESLSMSMS-KISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRT 194
           GSGGGMEL+ + +++LSMS   ++S+S S  GN +  +++PNGAGTVAGEHPYGEHPSRT
Sbjct: 111 GSGGGMELDADFRDNLSMSGPPRLSLS-SLGGNAIPQFNIPNGAGTVAGEHPYGEHPSRT 169

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFVRNINSNVEDSEL ALFEQYGDIRTLYT CKHRGFVMISYYDIR+AR AMR+LQNKPL
Sbjct: 170 LFVRNINSNVEDSELTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPL 229

Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR 314
           RRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDPS+SN+DL  IFGA+GE+KEIRETPHKR
Sbjct: 230 RRRKLDIHFSIPKDNPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKR 289

Query: 315 HHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRIL 374
           HHKF+EFYDVR AEAALK+LNR +IAGKRIK+EPSRPGGARR+LMLQLNQ+LE D+   L
Sbjct: 290 HHKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRPGGARRSLMLQLNQDLENDDLHYL 349

Query: 375 QHQVGSPITNSPP--GNWVQFSSPIEHNPLQTI-SKSPNFRNMSPTTSNHMPGLASILHP 431
              +GSP+ NSPP  GNW   +SP+E +PLQ++ S+SP F  +SPT + H+ GLAS L+ 
Sbjct: 350 P-MIGSPMANSPPMQGNW-PLNSPVEGSPLQSVLSRSPVF-GLSPTRNGHLSGLASALNS 406

Query: 432 QVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNS-FSEPKI-GLYRGTVSSFG 489
           Q  +  K+APIG+ Q             I +NG  FQQS+  F EPK+   Y G +S  G
Sbjct: 407 QGPS-SKLAPIGRGQ-------------IGSNG--FQQSSHLFQEPKMDNKYTGNLSPSG 450

Query: 490 PSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGS 549
           P  SNG G+ETLSG +FLWGSP+  SE SSS  W TSS G+P  S      +P+  +  +
Sbjct: 451 PLISNGGGIETLSGSEFLWGSPNARSEPSSSSVWSTSSTGNPLFSTRVDRSVPFPHQHQN 510

Query: 550 FLGSSQHHHVGSAPSGVPLERRFGFLPESPETS-FMNPVAFCGM-GIGQNDGSFMVNMGS 607
              S  H HVGSAPSGVPLE+ FGF+PES + + FMN V   GM G+G N GSF   M +
Sbjct: 511 QSRSHHHFHVGSAPSGVPLEKHFGFVPESSKDALFMNTVGLQGMSGMGLNGGSFSSKMAN 570

Query: 608 RASVNPGITVPRNLSDNG-SSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRI 666
              +N G     ++++NG SS+R+MSSPR SP+FL +G  PG   +  + LYE GR RR+
Sbjct: 571 NGIINSG-----SMAENGFSSYRMMSSPRFSPMFLSSGLNPGRFASGFDSLYENGRPRRV 625

Query: 667 ENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL 726
           ENN+ NQ++S+KQFQL+LEKI +GED+RTTLMIKNIPNKYTSKMLLAAIDE ++GTY+FL
Sbjct: 626 ENNS-NQVESRKQFQLDLEKILNGEDSRTTLMIKNIPNKYTSKMLLAAIDEKNQGTYNFL 684

Query: 727 YLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           YLPIDFKNKCNVGYAFINML+P  IIPFYE  
Sbjct: 685 YLPIDFKNKCNVGYAFINMLNPELIIPFYEAF 716

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVV9|AML3_ARATH Protein MEI2-like 3 OS=Arabidopsis thaliana GN=ML3 PE=2 SV=2

 Score =  701 bits (1810), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/749 (55%), Positives = 511/749 (68%), Gaps = 80/749 (10%)

Query: 17  LNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSG 76
           +NIP        G  + SD + AS DASLFSSSLP++ H+  N+N      QSVD+++SG
Sbjct: 1   MNIP-------SGTFSRSDHFHASSDASLFSSSLPLIQHQ--NINPRDSYHQSVDEMASG 51

Query: 77  LSKVHHGVAS--DDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDI 134
           L     G+ +  DD   G  +P IGN LPDDE+EL +G+MDD +L  LP++L+DLEDYD+
Sbjct: 52  LDHFSGGIGNMLDD---GDSHP-IGNMLPDDEEELFSGLMDDLNLSSLPATLDDLEDYDL 107

Query: 135 FGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRT 194
           FGSGGG+ELE +P +SL+   S++  +DS   N +      NG G++AGEHPYGEHPSRT
Sbjct: 108 FGSGGGLELETDPYDSLNKGFSRMGFADSNVDNVMPQNIFQNGVGSIAGEHPYGEHPSRT 167

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFVRNINSNVEDSEL+ALFEQYG IRTLYTACK RGFVM+SY DIRA+R AMRALQ K L
Sbjct: 168 LFVRNINSNVEDSELQALFEQYGHIRTLYTACKQRGFVMVSYNDIRASRAAMRALQGKLL 227

Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR 314
           ++RKLDIHFSIPKDNPS+KD+NQGTLVVFNL PSVSN DL  IFG YGE+KEIRETP+KR
Sbjct: 228 KKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPSVSNRDLENIFGVYGEIKEIRETPNKR 287

Query: 315 HHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRIL 374
           HHKF+EF+DVR+A+AALK+LNR++IAGKRIKLE SRPGGARRN+MLQ+N ELEQD+S   
Sbjct: 288 HHKFVEFFDVRSADAALKALNRTEIAGKRIKLEHSRPGGARRNMMLQMNPELEQDDSYSY 347

Query: 375 QHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVS 434
            + V SP+ +SP GNW   +SPI+H PLQ+ SKSP F N+SPT         +I +P+ S
Sbjct: 348 LNHVESPLASSPIGNWR--NSPIDH-PLQSFSKSPIFGNLSPTK--------NIRYPEFS 396

Query: 435 TLEKIAPIGKDQG--RGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSP 492
              K A +  DQ   R S ++H  +++ S N AS + S +F +P+      +  S    P
Sbjct: 397 M--KTASVNNDQEGRRFSHLDHLFSSS-SYNNASHKAS-TFQQPQSFGSVSSFGSLNSHP 452

Query: 493 SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLG 552
           S+   VETLSG +FLWGSP       SS AW  +    PFSSN + H  PYS + GS   
Sbjct: 453 SH---VETLSGSEFLWGSP-------SSSAWPVN----PFSSNRENHRFPYSAQNGSL-- 496

Query: 553 SSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVN 612
             Q HH+GSAPS        GF P SPETS M  VAF G                 AS N
Sbjct: 497 -HQLHHIGSAPS--------GFFPRSPETSSMGSVAFRG-----------------ASGN 530

Query: 613 PGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPY--PGLTPANIEGLYERGRSRRIENN 669
             +   RNL +  S +F+++S+PR S +F GNG Y  P  T  +I+   E G +++ + +
Sbjct: 531 --MNAQRNLRETSSPNFKMLSAPRRSQLFTGNGSYLWPAATMVSIDDPLEDGSNQQFD-S 587

Query: 670 NGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP 729
           NGNQ D K QFQL+L KI  GED RTTLMIKNIPNKYT  MLLAAIDE + GTYDFLYLP
Sbjct: 588 NGNQADIKIQFQLDLSKIMRGEDPRTTLMIKNIPNKYTRNMLLAAIDEKNSGTYDFLYLP 647

Query: 730 IDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           IDFKNKCNVGYAFINM+SP   I  YE  
Sbjct: 648 IDFKNKCNVGYAFINMVSPKFTIALYEAF 676

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6EQX3|OML5_ORYSJ Protein MEI2-like 5 OS=Oryza sativa subsp. japonica GN=ML5 PE=2 SV=1

 Score =  653 bits (1685), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/773 (49%), Positives = 484/773 (62%), Gaps = 67/773 (8%)

Query: 1   MKQFFDH--SSGPPKIP-----QLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLP-V 52
           M+Q  DH  SS P  IP     Q+      GG S   + GS       DA LFSSSLP V
Sbjct: 1   MEQREDHTKSSEPAFIPSKRTHQMRNIWAWGGPSSTTVNGSS------DAVLFSSSLPSV 54

Query: 53  LPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAG 112
           L   KL         Q  DD+   + +        DP++ V    IGN LPDDE ELLAG
Sbjct: 55  LQFGKLPGKEREYNAQPKDDMFPMMKQPGTNARVADPMDDVAQHLIGNLLPDDE-ELLAG 113

Query: 113 IMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHY 172
           +++DFD   L + +E+ E+YD+F + GGMEL+ +P ES++   +K S+ +  +G+    Y
Sbjct: 114 VIEDFDHVKLRTQVEESEEYDVFRNSGGMELDIDPLESITFGTAKASLVN-GTGSSTNQY 172

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFV 232
           S+ NGAGTV GEHPYGEHPSRTLFVRNINSNVEDSELR+LFE +GDIR++YTA KHRGFV
Sbjct: 173 SIQNGAGTVTGEHPYGEHPSRTLFVRNINSNVEDSELRSLFEPFGDIRSMYTATKHRGFV 232

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 292
           MISYYDIR AR A  ALQ+KPLRRRKLDIH+SIPK+NPSDKD+NQGTLV+FNL+P+VSNE
Sbjct: 233 MISYYDIRHARNAKTALQSKPLRRRKLDIHYSIPKENPSDKDMNQGTLVIFNLEPAVSNE 292

Query: 293 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
           +L QIFGA+GEV+EIRETPHKRHH+FIEFYDVRAAE+AL+SLN+SDIAGKR+KLEPSRPG
Sbjct: 293 ELLQIFGAFGEVREIRETPHKRHHRFIEFYDVRAAESALRSLNKSDIAGKRVKLEPSRPG 352

Query: 353 GARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFR 412
           GARR+ +   N E EQDE++    Q+GSP  NSPP  W Q  SP + N L  ++++    
Sbjct: 353 GARRSFIQHFNHEFEQDETKHNSFQIGSPSANSPPSLWSQLGSPTDENKLNALNETAFNG 412

Query: 413 NMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNS 472
            MSP  SNH+ G +S   P  S      P+GK     S   +   + I     +   S+S
Sbjct: 413 GMSPLGSNHLSGFSSGYPPMKS------PVGK-----SSYWNNRADNIFHGSPTLHNSHS 461

Query: 473 FSEPKIGLYRGTVSSFGPSPSNGS--GVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGH 530
           F E   G+   +      + S  +  G   L+G  FLWG+ +   +H    + Q+ ++ +
Sbjct: 462 FPEHHGGIISASPLVSSAASSASTASGFTALTGTSFLWGNNNNLRDHGQPSSIQSQALSN 521

Query: 531 PFSSNGKIHGLP--YSGRQGSFLGSSQHH---HVGSAPSGVPLERRFGFLPESPETSFMN 585
               N +       Y   +GSF G+S+H    +VGSAPS  P E  FG+  +SP+TS+M 
Sbjct: 522 SLFPNNQPQRQSNLYQNLRGSF-GASEHFSQFNVGSAPSVFPFESNFGYFSDSPDTSYMR 580

Query: 586 PVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGP 645
              F G G  +  GS M N G+                          PR++   + NG 
Sbjct: 581 QGKFGGTGPTRVSGSLMTNFGAY-------------------------PRINVASMQNGS 615

Query: 646 YPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNK 705
                    EGL +RGR++ +  N+G Q DS+ Q+QL+LEKI +G+DTRTTLMIKNIPNK
Sbjct: 616 ------VGFEGLLDRGRNQTV-GNSGCQEDSRVQYQLDLEKIIAGKDTRTTLMIKNIPNK 668

Query: 706 YTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           YTS MLL  IDE H+GTYDF YLPIDFKNKCNVGYAFINM SP +I+ F++  
Sbjct: 669 YTSNMLLEVIDETHEGTYDFFYLPIDFKNKCNVGYAFINMASPGYIVSFFKAF 721

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SJG8|AML2_ARATH Protein MEI2-like 2 OS=Arabidopsis thaliana GN=ML2 PE=2 SV=2

 Score =  603 bits (1555), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 343/714 (48%), Positives = 452/714 (63%), Gaps = 31/714 (4%)

Query: 50  LPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDEL 109
           LP L HEKLN+        S D+ S  L+K+  G +  D LE V   A+   LP+DE+EL
Sbjct: 56  LPTLFHEKLNMTDSD-SWLSFDESSPNLNKLVIGNSEKDSLEDVEPDALEILLPEDENEL 114

Query: 110 LAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGL 169
           L G++D+ +  GLP  L+DLE+ D+F +GGGMEL+ E Q++ ++  S + ISD  + N  
Sbjct: 115 LPGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVESQDNHAVDASGMQISDRGAANAF 174

Query: 170 LHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR 229
           +    PN AG V+ EHP GEHPSRTLFVRNINS+VEDSEL ALFE +G+IR+LYTACK R
Sbjct: 175 VPRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVEDSELSALFEPFGEIRSLYTACKSR 234

Query: 230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV 289
           GFVMISYYDIRAA  AMRALQN  LR+R LDIHFSIPK+NPS+KD+NQGTLV+FN+D +V
Sbjct: 235 GFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIPKENPSEKDMNQGTLVIFNVDTTV 294

Query: 290 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS 349
           SN++L Q+FGAYGE++EIRETP++R H+FIE+YDVR AE ALK+LNRS+I GK IKLE S
Sbjct: 295 SNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRDAETALKALNRSEIGGKCIKLELS 354

Query: 350 RPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSP 409
           RPGGARR  +   +Q+LE+ E     +QVGS + NSPPGNW    SP++ +P    ++  
Sbjct: 355 RPGGARRLSVPSQSQDLERTEVTNFYNQVGSHVANSPPGNW-PIGSPVKGSPSHAFTRPH 413

Query: 410 NFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQ 469
               + P  S++MPGLASIL    S+    +P+  DQG  +     + N    +  S+ Q
Sbjct: 414 GLGMVRPVNSDNMPGLASILPAHPSSFHGFSPVSNDQGLLNHSNQTILNKGLMHNISYGQ 473

Query: 470 SNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQ----- 524
            +S  E   G    ++    P   + SG  T S  ++ WGSP    +H + P +      
Sbjct: 474 PHSLPEHITGGISNSMRFIAP---HSSGFGTSSDHRYRWGSP---PQHMNYPGYTGVSSS 527

Query: 525 TSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFM 584
           +SS   PF+     HG P++ RQ S LG  Q HHVGSAPS +    +      SPE    
Sbjct: 528 SSSTERPFTVR---HGFPFAERQASLLGKYQ-HHVGSAPSSIHFNTQMNCYTGSPEI--- 580

Query: 585 NPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNG 644
            P+ F  MGI +N  S      +    N G+++P N S+   +   MSS    P     G
Sbjct: 581 -PLGFSDMGINRNYNS------AHGKANLGVSLPGNSSEQDFTGFGMSSMPTVPF----G 629

Query: 645 PYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPN 704
              GL     E   E+GR    E++N NQ     ++ ++L++I SG++ RTTL+IKNIPN
Sbjct: 630 GSRGLQSVRPEPFAEQGRIHNHESHNQNQFIDGGRYHIDLDRIASGDEIRTTLIIKNIPN 689

Query: 705 KYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           KYT KML+A IDE HKG YDFL LP DFKNKCN+G+AFINM+SPLHI+PF +  
Sbjct: 690 KYTYKMLVAEIDEKHKGDYDFLCLPTDFKNKCNMGHAFINMVSPLHIVPFQQTF 743

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q75M35|OML3_ORYSJ Protein MEI2-like 3 OS=Oryza sativa subsp. japonica GN=ML3 PE=2 SV=2

 Score =  366 bits (940), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 281/746 (37%), Positives = 381/746 (51%), Gaps = 109/746 (14%)

Query: 64  GLGRQSVDDISSGLSKVHHGV-ASDDPLE---GVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           G  R+ V  +    +  H  +  SD+PLE    +    IG+ LPDD+D+L++GI D F+ 
Sbjct: 156 GKSREIVSGVLCQSTGTHTSIYDSDEPLESMEAIEAQTIGDLLPDDDDDLISGIADGFEF 215

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
            G+ S+ +D  D DIF +GGGMELE                +DS  G+ +   S  +   
Sbjct: 216 TGM-STNQDDADEDIFCTGGGMELEN---------------NDSVKGDKVQDGSFKS--- 256

Query: 180 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 239
            ++  H   + PSRTL VRNI +N+EDS+L  LF+QYGDIR LYT+ KH GFV +SYYDI
Sbjct: 257 QISSGHSINKQPSRTLVVRNITANIEDSDLTVLFQQYGDIRMLYTSFKHHGFVTVSYYDI 316

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
           RAA+ AMRAL +KPL   KLD+ FS PK+N   KD+++G LVV N+D S+SN+DL Q+  
Sbjct: 317 RAAQNAMRALHSKPLGLMKLDVQFSFPKENVPGKDIDKGMLVVSNIDSSISNDDLLQMLS 376

Query: 300 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
            YG+VKEI  +P     KF+EFYDVRAAE AL  LN+  I+G + K+E S+ G A   L 
Sbjct: 377 VYGDVKEISSSPISCTKKFVEFYDVRAAEEALHDLNKGGISGPKFKVELSQHGEAGSCLR 436

Query: 360 LQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHN-PLQTISKSPNFRNMSPTT 418
            Q ++E +QD    L HQ      NS PG   +  +  + N  +  +    N +  SPT 
Sbjct: 437 QQHSREWKQDS---LPHQP----KNSSPGTIGKLGTKCQDNSTVHNLFSPVNQQLESPTQ 489

Query: 419 SNHMPGLASILHP-----------QVSTLEKIAPIGKDQ-GRG-------SLMEHALTNT 459
                G   +  P           Q S  +   P+G+   GRG       SL EH   N 
Sbjct: 490 CISTTGPQILSSPIRIKSTLQHNNQASVGDLSGPLGQGNFGRGIQTLHPRSLPEHH--NR 547

Query: 460 ISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVET--------------LSGPQ 505
           I  N  S   S   +  +       +   GP+   G   +               L G  
Sbjct: 548 ICNNSKSMTVSGRNASSRQDGVDHNIQKVGPAGFCGHSFDQNNEAFGFTEIGSCPLHGYH 607

Query: 506 FLWGSPSRYSEHSSSPA-WQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPS 564
           + W   + + +  S+P  W  S++ HP   +      P+    GS+      HH+GSAP 
Sbjct: 608 YTWNHTNVFPQSPSAPILW--SNLQHPMHVHSYPGVPPHMLNTGSY--PMDQHHLGSAPD 663

Query: 565 GVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDN 624
                            SF N  +F    +G        ++G   S  P +  P  LS  
Sbjct: 664 N--------------GGSFGNVHSFHPGSLG--------SIGLHGS--PQL-YPSELSAF 698

Query: 625 GSSFRVMSSPRLSPVFLG-----------NGPYPGL-TPANIEGLYERGRSRRIENNNGN 672
            SS         SPV  G           NG  P +    + +   +R RSRR  + N  
Sbjct: 699 ASSRGNFREALFSPVGGGFQSLQQMCNAINGRNPMIHVSTSYDATNDRMRSRR-HDGNPA 757

Query: 673 QLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDF 732
           Q ++K+QF+L++++I  GED+RTTLMIKNIPNKY  K+LLA IDENH+GTYDF+YLPIDF
Sbjct: 758 QSENKRQFELDIDRIAKGEDSRTTLMIKNIPNKYNCKLLLAVIDENHRGTYDFIYLPIDF 817

Query: 733 KNKCNVGYAFINMLSPLHIIPFYEVL 758
           KNKCNVGYAFINM  P HIIPFY+  
Sbjct: 818 KNKCNVGYAFINMTDPQHIIPFYKTF 843

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q64M78|OML4_ORYSJ Protein MEI2-like 4 OS=Oryza sativa subsp. japonica GN=ML4 PE=2 SV=1

 Score =  296 bits (759), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 199/368 (54%), Positives = 254/368 (69%), Gaps = 37/368 (10%)

Query: 27  SCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAM-GLGRQSVDDISSGLSKVHHGVA 85
           S GRI  + +Y   ++  LFSSS+  +  +KL L +  GL  QS++       KV     
Sbjct: 129 SDGRINPNGAY---NENGLFSSSVSDIFDKKLRLTSKNGLVGQSIE-------KVDLNHV 178

Query: 86  SDDPLE---GVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYD--IFGSGGG 140
            D+P E    +    IGN L  D+D+LL+G++D+    G P++  + +D D  IF +GGG
Sbjct: 179 DDEPFELTEEIEAQIIGNLL-PDDDDLLSGVVDEV---GYPTNANNRDDADDDIFYTGGG 234

Query: 141 MELEGEPQESLSMSMSKISISDSAS-GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRN 199
           MELE +  + L         + SA+ G GLL+       G + GEH Y E PSRTLFVRN
Sbjct: 235 MELETDENKKLQ------EFNGSANDGIGLLN-------GVLNGEHLYREQPSRTLFVRN 281

Query: 200 INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL 259
           INSNVEDSEL+ LFE +GDIR LYTACKHRGFVMISYYDIR+A  A   LQNK LRRRKL
Sbjct: 282 INSNVEDSELKLLFEHFGDIRALYTACKHRGFVMISYYDIRSALNAKMELQNKALRRRKL 341

Query: 260 DIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFI 319
           DIH+SIPKDNPS+KD+NQGT+V+FN+D S++N+DL +IFG YGE+KEIR+TP K HHK I
Sbjct: 342 DIHYSIPKDNPSEKDINQGTIVLFNVDLSLTNDDLHKIFGDYGEIKEIRDTPQKGHHKII 401

Query: 320 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVG 379
           EFYDVRAAEAAL++LNR+DIAGK+IKLE SR G ARR L   ++ EL Q+E  +   ++G
Sbjct: 402 EFYDVRAAEAALRALNRNDIAGKKIKLETSRLGAARR-LSQHMSSELCQEEFGVC--KLG 458

Query: 380 SPITNSPP 387
           SP T+SPP
Sbjct: 459 SPSTSSPP 466

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8W4I9|AML1_ARATH Protein MEI2-like 1 OS=Arabidopsis thaliana GN=ML1 PE=1 SV=1

 Score =  229 bits (583), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 128/259 (49%), Positives = 172/259 (66%), Gaps = 19/259 (7%)

Query: 97  AIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMS 156
            IGN LPD ED+L A +  +   +   ++ ++L+++D+F S GGMEL+G+   S+S    
Sbjct: 140 TIGNLLPD-EDDLFAEVTGEVGRKSRANTGDELDEFDLFSSVGGMELDGDIFSSVS---- 194

Query: 157 KISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQY 216
                         H +   G     GE   GE PSRTL V NI+SNVED EL+ LFEQ+
Sbjct: 195 --------------HRNGERGGNNSVGELNRGEIPSRTLLVGNISSNVEDYELKVLFEQF 240

Query: 217 GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN 276
           GDI+ L+TACK+RGF+M+SY DIRAA+ A RALQNK LR  KLDI +SI K+NPS KD +
Sbjct: 241 GDIQALHTACKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRYSISKENPSQKDTS 300

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +G L+V NLD S+SN++L ++  +YGEVKEIR T H     +IEF+DVRAA AAL  LN 
Sbjct: 301 KGALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFDVRAAAAALGGLNG 360

Query: 337 SDIAGKRIKLEPSRPGGAR 355
            ++AGK+++L P+ P G R
Sbjct: 361 LEVAGKKLQLVPTYPEGTR 379

Probable RNA-binding transcriptional activator that plays a role in meiosis and vegetative growth. May be a downstream effector of TOR signaling pathway and recruited by RAPTOR1 for TOR substrate.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LYN7|AML4_ARATH Protein MEI2-like 4 OS=Arabidopsis thaliana GN=ML4 PE=1 SV=1

 Score =  215 bits (548), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 123/258 (47%), Positives = 172/258 (66%), Gaps = 19/258 (7%)

Query: 97  AIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMS 156
            IGN LPD ED+L A ++ +   +   +  +DL+D D+F S GGMEL+G+         S
Sbjct: 133 TIGNLLPD-EDDLFAEVVGEGVHKSRANGGDDLDDCDLFSSVGGMELDGD-------VFS 184

Query: 157 KISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQY 216
            +S  D   G+ +          TVA EHP GE  SR LFVRN++S++ED EL  LF+Q+
Sbjct: 185 SVSQRDGKRGSNV---------STVA-EHPQGEILSRILFVRNVDSSIEDCELGVLFKQF 234

Query: 217 GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN 276
           GD+R L+TA K+RGF+M+SYYDIRAA+ A RAL  + LR RKLDI +SIPK+NP +   +
Sbjct: 235 GDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYSIPKENPKENS-S 293

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +G L V NLD S+SNE+L  IF +YGE++E+R T H+    +IEF+DVR A+ AL+ LN 
Sbjct: 294 EGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGLNG 353

Query: 337 SDIAGKRIKLEPSRPGGA 354
            ++AG+++KL P+ P G 
Sbjct: 354 LEVAGRQLKLAPTCPEGT 371

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|P08965|MEI2_SCHPO Meiosis protein mei2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mei2 PE=1 SV=1

 Score =  103 bits (258), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 48/73 (65%), Positives = 56/73 (76%)

Query: 682 LELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYA 741
           ++  +I SG DTRTT+MIKNIPNK+T +ML   ID  +KGTYDFLYL IDF NKCNVGYA
Sbjct: 584 VDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFVNKCNVGYA 643

Query: 742 FINMLSPLHIIPF 754
           FIN + P  II F
Sbjct: 644 FINFIEPQSIITF 656

Crucial for commitment to meiosis but it is not sufficient itself for the commitment. May be a splicing regulator.

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

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	780
47834701	858	AML1 [Citrus unshiu]	0.971	0.883	0.989	0.0
225463378	860	PREDICTED: protein MEI2-like 2-like [Vit	0.952	0.863	0.764	0.0
356556525	862	PREDICTED: protein MEI2-like 2-like [Gly	0.966	0.874	0.753	0.0
356530557	862	PREDICTED: protein MEI2-like 2-like [Gly	0.966	0.874	0.743	0.0
359485142	842	PREDICTED: protein MEI2-like 2-like [Vit	0.95	0.880	0.709	0.0
357450609	865	Polyadenylate-binding protein [Medicago	0.966	0.871	0.709	0.0
297740630	787	unnamed protein product [Vitis vinifera]	0.832	0.824	0.676	0.0
356567420	857	PREDICTED: protein MEI2-like 2-like [Gly	0.956	0.870	0.673	0.0
357450611	764	Polyadenylate-binding protein [Medicago	0.837	0.854	0.736	0.0
449481207	846	PREDICTED: protein MEI2-like 2-like [Cuc	0.951	0.877	0.666	0.0

>gi|47834701|gb|AAT39004.1| AML1 [Citrus unshiu]

 Score = 1541 bits (3989), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 750/758 (98%), Positives = 755/758 (99%)

Query: 1   MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNL 60
           MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNL
Sbjct: 1   MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNL 60

Query: 61  NAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLR 120
           NAMGLGRQSVD+ISSGLSKVHHGV+SDDPLEG+MNPAIGNSLPDDEDELLAGIMDDFDLR
Sbjct: 61  NAMGLGRQSVDNISSGLSKVHHGVSSDDPLEGIMNPAIGNSLPDDEDELLAGIMDDFDLR 120

Query: 121 GLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGT 180
           GLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGT
Sbjct: 121 GLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGT 180

Query: 181 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIR 240
           VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIR
Sbjct: 181 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIR 240

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA 300
           AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA
Sbjct: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA 300

Query: 301 YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360
           YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML
Sbjct: 301 YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360

Query: 361 QLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSN 420
           QLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSN
Sbjct: 361 QLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSN 420

Query: 421 HMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGL 480
           HMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGL
Sbjct: 421 HMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGL 480

Query: 481 YRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHG 540
           YRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHG
Sbjct: 481 YRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHG 540

Query: 541 LPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGS 600
           LPYSGRQGSFLGSSQHHH+GSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGS
Sbjct: 541 LPYSGRQGSFLGSSQHHHIGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGS 600

Query: 601 FMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYER 660
           FMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPAN EGLYER
Sbjct: 601 FMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANSEGLYER 660

Query: 661 GRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHK 720
           GRSRRIENNNGNQ+DSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHK
Sbjct: 661 GRSRRIENNNGNQIDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHK 720

Query: 721 GTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           GTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYE  
Sbjct: 721 GTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAF 758

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463378|ref|XP_002271605.1| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]

 Score = 1152 bits (2981), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 573/750 (76%), Positives = 647/750 (86%), Gaps = 7/750 (0%)

Query: 13  KIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDD 72
           KIP ++IPK VG G+ G   GSD Y AS+DA+LFS SLPVLPHEKLNLN      QS+DD
Sbjct: 14  KIPYVSIPKAVGSGAWGMRPGSDGYNASNDATLFSCSLPVLPHEKLNLNDTEHCCQSIDD 73

Query: 73  ISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDY 132
             +GL K+   V + + LE     AIG+ LPDDEDELLAGIMDDFDL GL + +ED+E+Y
Sbjct: 74  --AGLDKLQQDVEAGESLEDDGIHAIGSLLPDDEDELLAGIMDDFDLSGLSNPMEDVEEY 131

Query: 133 DIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPS 192
           D+FGSGGGMELE +PQESL+M M+K+S+SD   GNGL  Y +PNG+GTVAGEHPYGEHPS
Sbjct: 132 DLFGSGGGMELEIDPQESLNMGMAKVSLSDGVVGNGLAQYGLPNGSGTVAGEHPYGEHPS 191

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
           RTLFVRNINSNVEDSELR LFEQYG IRTLYTACKHRGFVMISYYDIRAARTAMRALQNK
Sbjct: 192 RTLFVRNINSNVEDSELRTLFEQYGAIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 251

Query: 253 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH 312
           PLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSN+DLRQIFGAYGEVKEIRETPH
Sbjct: 252 PLRRRKLDIHFSIPKDNPSDKDVNQGTLVVFNLDPSVSNDDLRQIFGAYGEVKEIRETPH 311

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           KRHHKFIEFYDVRAAEAAL+SLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR
Sbjct: 312 KRHHKFIEFYDVRAAEAALRSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 371

Query: 373 ILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQ 432
             +H VGSP+ NSPPG+W QFSSPIEH+PLQ++SKSP FR +SPTTSNH+PGLASIL+ Q
Sbjct: 372 SFRHHVGSPMANSPPGSWAQFSSPIEHSPLQSLSKSPGFRTVSPTTSNHLPGLASILNSQ 431

Query: 433 VSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSP 492
           +S   K+APIGKDQGRG  +E+   NT S +G +FQQS+SFSEP +G Y G  SSFG S 
Sbjct: 432 ISNSVKVAPIGKDQGRGIHVENIFNNTNSNHGTAFQQSHSFSEPNLGPYPGNGSSFGAST 491

Query: 493 SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLG 552
           SNGSG+ETLSGPQFLWGSP+ YSEH++S AWQ  SMGHPF+SNG+  G PYSGR GSFLG
Sbjct: 492 SNGSGIETLSGPQFLWGSPAPYSEHTNSSAWQPPSMGHPFASNGQGRGFPYSGRHGSFLG 551

Query: 553 SSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRA 609
           SS+   HHHVGSAPSGVPLER FG+ PESPE SFM PVAF GMG+  NDGSFM+NM +RA
Sbjct: 552 SSRHHHHHHVGSAPSGVPLERHFGYFPESPEASFMTPVAFGGMGLAHNDGSFMLNMSARA 611

Query: 610 SVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIEN 668
            +N GI++P N+S++GS+ FR++SSPRLSP+F GNGP+PGL P+NIEGL +RGRSR +E 
Sbjct: 612 GMNAGISIPANMSESGSANFRMISSPRLSPMFPGNGPFPGLAPSNIEGLADRGRSRWVE- 670

Query: 669 NNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYL 728
           NNGNQ+DSKKQFQL+L+KI +GEDTRTTLMIKNIPNKYTSKMLLAAIDE H+GTYDFLYL
Sbjct: 671 NNGNQIDSKKQFQLDLDKILNGEDTRTTLMIKNIPNKYTSKMLLAAIDEYHRGTYDFLYL 730

Query: 729 PIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           PIDFKNKCNVGYAFINMLSP HIIPFY+  
Sbjct: 731 PIDFKNKCNVGYAFINMLSPSHIIPFYQAF 760

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556525|ref|XP_003546575.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1120 bits (2896), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 575/763 (75%), Positives = 635/763 (83%), Gaps = 9/763 (1%)

Query: 1   MKQFFDHSS-GPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLN 59
           M+Q FD S  GP KIP + +P + G G+   ++GSDSY AS DASLFSSSLPVLPHEKLN
Sbjct: 1   MRQSFDPSFLGPSKIPSIKVPGKAGNGAWEALSGSDSYHASSDASLFSSSLPVLPHEKLN 60

Query: 60  LNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           LN    G QS+DDISSG  K+H     +  LE     AIG +LPDDE+ELLAGI DDFDL
Sbjct: 61  LNETANGYQSIDDISSGFKKLHQDADGNGSLEDGDTHAIGPALPDDEEELLAGITDDFDL 120

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
            GLP SLEDLE+YD+FGSGGGMELE +PQE L++ +SK+S +DS  GNGL  YS PNG G
Sbjct: 121 SGLPGSLEDLEEYDLFGSGGGMELETDPQEGLTVGLSKLSFADSTVGNGLPPYSFPNGVG 180

Query: 180 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 239
           TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI
Sbjct: 181 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 240

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
           RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSNEDLRQIFG
Sbjct: 241 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVSNEDLRQIFG 300

Query: 300 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
           AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM
Sbjct: 301 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 360

Query: 360 LQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTS 419
           LQLNQEL+QDESR  ++QVGSP+ NSPPGNW+QF+SP+E N +QTI+ SP  R +SPTT 
Sbjct: 361 LQLNQELDQDESRSFRYQVGSPVANSPPGNWLQFNSPVEQNSMQTINYSPGSRIISPTTG 420

Query: 420 NHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIG 479
           NH+PGLASIL PQVS   K A IG D  R S  EH  T   S++GA+F QS+S  EPK  
Sbjct: 421 NHLPGLASILQPQVSNTVKAAAIGNDLERSSQGEHIFTGMNSSHGATF-QSHSLPEPKFS 479

Query: 480 LYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIH 539
            YRG +SS GPS SNGS VETLSGPQFLWGSP+ YSEH+   AW  SS+GHPF+SNGK H
Sbjct: 480 QYRGALSSIGPSTSNGSSVETLSGPQFLWGSPTLYSEHTKPSAWPRSSVGHPFASNGKSH 539

Query: 540 GLPYSGRQGSFLGSSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQ 596
             PYS +  SF+GSSQ   HHHVGSAPSG+P ER FGF PES ETSFMN V + G+G G 
Sbjct: 540 AFPYSTQNSSFVGSSQHLHHHHVGSAPSGLPFERHFGFHPESSETSFMNNVGYGGIGPGH 599

Query: 597 NDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIE 655
           NDG+ MVN+G   SVNP IT+PRN+SDNGSS FR+ SSPRLSPVFLGNGP+PGL P  +E
Sbjct: 600 NDGNHMVNVG--GSVNPNITIPRNISDNGSSNFRMRSSPRLSPVFLGNGPFPGLPPTTLE 657

Query: 656 GLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAI 715
           GL +R RSR IE NNG+Q+DSKKQFQL L+KI+SGEDTRTTLMIKNIPNKYTSKMLLAAI
Sbjct: 658 GLADRARSRWIE-NNGSQVDSKKQFQLNLDKIKSGEDTRTTLMIKNIPNKYTSKMLLAAI 716

Query: 716 DENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           DENH+GTYDFLYLPIDFKNKCNVGYAFINMLSP  IIPF+E  
Sbjct: 717 DENHRGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIPFFETF 759

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530557|ref|XP_003533847.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1098 bits (2839), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 568/764 (74%), Positives = 630/764 (82%), Gaps = 10/764 (1%)

Query: 1   MKQFFDHSS-GPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLN 59
           M+Q FD SS GP KIP + IP + G G+   ++GSDSY AS DASLFSSSLPVLPHEKLN
Sbjct: 1   MRQSFDPSSLGPSKIPSIKIPGKAGNGAWEALSGSDSYHASSDASLFSSSLPVLPHEKLN 60

Query: 60  LNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           LN      QS+DDISSG  K+H     +  LE     AIG +LPDDE+ELLAGIMDDFDL
Sbjct: 61  LNETANAYQSIDDISSGFKKLHQDAEGNGSLEDGDTHAIGPALPDDEEELLAGIMDDFDL 120

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
            GLP SLEDLE+YD+FG GGGMELE +PQESL++ +SK+S +DS  G+ L  YS PNG G
Sbjct: 121 SGLPGSLEDLEEYDLFGCGGGMELETDPQESLTVGISKLSFADSTVGSVLPPYSFPNGVG 180

Query: 180 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 239
            VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI
Sbjct: 181 AVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 240

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
           RAARTAMR+LQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSNEDLRQIFG
Sbjct: 241 RAARTAMRSLQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVSNEDLRQIFG 300

Query: 300 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
           AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM
Sbjct: 301 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 360

Query: 360 LQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTS 419
           LQLNQEL+Q+ESR  ++QV SP+ NSPPGNW+QF+SP+E N +QTI+ SP  R +SPTT 
Sbjct: 361 LQLNQELDQEESRSFRYQVSSPVANSPPGNWLQFNSPVEQNSMQTINHSPGSRIISPTTG 420

Query: 420 NHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIG 479
           NH+PGLASIL PQVS   K A IG D GR S  EH  +   S++GA+F QS+S  EPK  
Sbjct: 421 NHLPGLASILQPQVSNAVKAAAIGNDLGRSSQGEHIFSGMNSSHGATF-QSHSLPEPKFS 479

Query: 480 LYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPF-SSNGKI 538
            YRG +SS GPS SNGS VETLSGPQFLWGSP+ YSEH+    W  SS+GHPF +SNGK 
Sbjct: 480 QYRGALSSIGPSTSNGSSVETLSGPQFLWGSPTLYSEHTKPSVWPRSSVGHPFAASNGKS 539

Query: 539 HGLPYSGRQGSFLGSSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIG 595
           H  PYS +  SF+GSSQ   HHHVGSAPSG+P ER FGF PES ETSFMN V + G+G+G
Sbjct: 540 HAFPYSTQNSSFVGSSQHHHHHHVGSAPSGLPFERHFGFHPESSETSFMNNVGYGGIGLG 599

Query: 596 QNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANI 654
            NDG++MVN G   SVNP  T+PRN+SDNGSS  R+ SSPRLSPVFLGNGPYPGL P  +
Sbjct: 600 HNDGNYMVNAG--GSVNPNTTIPRNISDNGSSNLRMRSSPRLSPVFLGNGPYPGLPPTTL 657

Query: 655 EGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAA 714
           E L +R RSR IE NNG+Q+DSKKQFQL+L+KIRSGEDTRTTLMIKNIPNKYTSKMLLAA
Sbjct: 658 ESLADRARSRWIE-NNGSQVDSKKQFQLDLDKIRSGEDTRTTLMIKNIPNKYTSKMLLAA 716

Query: 715 IDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           IDENH+G YDFLYLPIDFK KCNVGYAFINMLSP  IIPFYE  
Sbjct: 717 IDENHRGAYDFLYLPIDFKKKCNVGYAFINMLSPFLIIPFYETF 760

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485142|ref|XP_002279792.2| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]

 Score = 1031 bits (2667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 533/751 (70%), Positives = 612/751 (81%), Gaps = 10/751 (1%)

Query: 9   SGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQ 68
           SGP KIP LN+PK++G G+ G   G+D+Y  S D SLFSSSLPVLPHEKL+ N       
Sbjct: 10  SGPFKIPSLNVPKKIGSGAWGIPHGTDAYHTSSDVSLFSSSLPVLPHEKLHFNDSEHCGH 69

Query: 69  SVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLED 128
           SVDD S  L+K+     S DPLE V   AIG+ LPDDEDELLAGIMDDFDL GLP+ +ED
Sbjct: 70  SVDDGSPSLNKLQQDEESKDPLEDVDLNAIGSLLPDDEDELLAGIMDDFDLSGLPTQVED 129

Query: 129 LEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYG 188
           LED D+FGSGGGMEL+        + +SK+S+SD  +GNG+ HY +PNG  TVAGEHPYG
Sbjct: 130 LED-DLFGSGGGMELD------FDIGISKLSLSDGVAGNGIGHYGLPNGVATVAGEHPYG 182

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
           EHPSRTLFVRNINSNVEDSEL+ LFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA
Sbjct: 183 EHPSRTLFVRNINSNVEDSELKTLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 242

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           LQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLD SVSN+DLRQIFGAYGEVKEIR
Sbjct: 243 LQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDASVSNDDLRQIFGAYGEVKEIR 302

Query: 309 ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQ 368
           ETPHKRHHKFIEFYDVRAAEAAL++LNRSDIAGKRIKLEPSRPGGARRNLM QL+QELEQ
Sbjct: 303 ETPHKRHHKFIEFYDVRAAEAALRALNRSDIAGKRIKLEPSRPGGARRNLMQQLSQELEQ 362

Query: 369 DESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASI 428
           DE+R  +H VGSP+TNSPPGNW  F SP+EHNPLQ  S SP   N+SP  SNH+PGLASI
Sbjct: 363 DEARSFRHHVGSPVTNSPPGNWAAF-SPVEHNPLQAYSHSPGLGNISPINSNHLPGLASI 421

Query: 429 LHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSF 488
           L P +S   KIAPIGKDQGR + +    TN     GA++Q S+S  E K+    G +SS 
Sbjct: 422 LPPHISNSVKIAPIGKDQGRVNHVNQVFTNAKPTQGAAYQISHSVPEQKLSASPGPISSL 481

Query: 489 GPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQG 548
           G S SN SG+ TLSGPQFLWGSP+ YSE  +S AW TSS+GHPF S+G+  G PYS + G
Sbjct: 482 GESNSNSSGIGTLSGPQFLWGSPTPYSERPNSSAWPTSSVGHPFVSSGQGQGFPYSNQHG 541

Query: 549 SFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSR 608
           SFLGS QHHHVGSAPSGVPL+R FG+ PESPETSFM+PV F GMG+ +++G+F +N+G+R
Sbjct: 542 SFLGSHQHHHVGSAPSGVPLDRHFGYFPESPETSFMSPVTFGGMGLSRSNGNFAMNVGAR 601

Query: 609 ASVNPGITVPRNLSDNG-SSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIE 667
           A++N G+ +P N+++NG  SFR++S PR  P FLGNG YP     + E L ERGR+RR+E
Sbjct: 602 AAINTGVALPGNMTENGLPSFRMLSLPRHGPPFLGNGTYPVSGVTSNEVLAERGRTRRVE 661

Query: 668 NNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLY 727
            N+GNQ+DSKKQ+QL+L+KI SGEDTRTTLMIKNIPNKYTSKMLLAAIDENH+GTYDFLY
Sbjct: 662 -NSGNQIDSKKQYQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLY 720

Query: 728 LPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           LPIDFKNKCNVGYAFINM+SP HIIPFYE  
Sbjct: 721 LPIDFKNKCNVGYAFINMVSPSHIIPFYEAF 751

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357450609|ref|XP_003595581.1| Polyadenylate-binding protein [Medicago truncatula] gi|47834691|gb|AAT38999.1| AML5 [Medicago truncatula] gi|87241360|gb|ABD33218.1| RNA-binding region RNP-1 (RNA recognition motif); RNA recognition motif 2 [Medicago truncatula] gi|355484629|gb|AES65832.1| Polyadenylate-binding protein [Medicago truncatula]

 Score = 1016 bits (2626), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 544/767 (70%), Positives = 612/767 (79%), Gaps = 13/767 (1%)

Query: 1   MKQFFDHS-SGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLN 59
           MKQ FD S   P KIP +N   ++  G+    +GSDSY AS DASLFSSSLPVLPHEKLN
Sbjct: 1   MKQSFDPSFIAPSKIPPINTAGKLRHGALEVSSGSDSYHASSDASLFSSSLPVLPHEKLN 60

Query: 60  LNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           LN    G QSVDDIS+   K H     +  L+   N AIG  LPDD++ELLAGIMDDFDL
Sbjct: 61  LNETENGFQSVDDISTNFKKHHQEAELNGSLDNGNNHAIGTMLPDDDEELLAGIMDDFDL 120

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
           RGLP SLEDLE+YD+F S GG+ELE +PQESLS+ +SK+S+SDS+ GN +  YS+PNG G
Sbjct: 121 RGLPGSLEDLEEYDLFDSSGGLELETDPQESLSVGISKLSLSDSSVGNSMPPYSLPNGVG 180

Query: 180 TVAG--EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY 237
             A   EHPYGEHPSRTLFVRNINSNVED+ELR LFEQYGDIRTLYTACKHRGFVMISYY
Sbjct: 181 GGAVAGEHPYGEHPSRTLFVRNINSNVEDTELRTLFEQYGDIRTLYTACKHRGFVMISYY 240

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQI 297
           DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSNEDLRQI
Sbjct: 241 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVSNEDLRQI 300

Query: 298 FGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           FGAYGEVKEIRETPHKRHHKFIE+YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN
Sbjct: 301 FGAYGEVKEIRETPHKRHHKFIEYYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 360

Query: 358 LMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPT 417
           LMLQLNQEL+QDESR  ++QVGSP+  SPPGNW+QF+SPIE + L  ++ SP  + MSPT
Sbjct: 361 LMLQLNQELDQDESRSFRYQVGSPLAGSPPGNWLQFNSPIEQSSLPNLNHSPGSKIMSPT 420

Query: 418 TSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPK 477
           TSNH+PGLASIL PQ+S   K A IG+D GR S  +H   N IS+ G++F  S+S  EPK
Sbjct: 421 TSNHLPGLASILQPQLSNTVKAATIGQDIGRSSHGDHIFPNKISSAGSNF-NSHSLPEPK 479

Query: 478 IGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFS-SNG 536
              YRG +SSFG S SNGS VETL+ PQFLWGSP+  SE +   AW   S+GH  S SNG
Sbjct: 480 FSPYRGALSSFGASTSNGSSVETLTAPQFLWGSPNLSSEPTKPSAWPRPSVGHQLSTSNG 539

Query: 537 KIHGLPYSGRQGSFL----GSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGM 592
             H  PYS +  SF+        HHHVGSAPSG+P ER FGF P+S ETS MN V + GM
Sbjct: 540 TSHAFPYSSQNNSFVSSSQQQHHHHHVGSAPSGLPFERHFGFFPKSSETSLMNNVGYRGM 599

Query: 593 GIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTP 651
           G+G NDG++M+N G   S N GI++PRN+ DNGSS FR+ SSP LSPVFLGNGPYPGL P
Sbjct: 600 GLGHNDGNYMLNSG--ISGNVGISIPRNMPDNGSSNFRMRSSPILSPVFLGNGPYPGLLP 657

Query: 652 ANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKML 711
             +E   +R RSR I+ NNG+Q+D+KK FQL+L+KIRSGEDTRTTLMIKNIPNKYTSKML
Sbjct: 658 TAMESFTDRVRSRWID-NNGSQVDNKKLFQLDLDKIRSGEDTRTTLMIKNIPNKYTSKML 716

Query: 712 LAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           LAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP  IIPFYE  
Sbjct: 717 LAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIPFYETF 763

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740630|emb|CBI30812.3| unnamed protein product [Vitis vinifera]

 Score =  983 bits (2541), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 505/747 (67%), Positives = 568/747 (76%), Gaps = 98/747 (13%)

Query: 13  KIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDD 72
           KIP ++IPK VG G+ G   GSD Y AS+DA+LFS SLPVLPHEKLNLN      QS+DD
Sbjct: 38  KIPYVSIPKAVGSGAWGMRPGSDGYNASNDATLFSCSLPVLPHEKLNLNDTEHCCQSIDD 97

Query: 73  ISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDY 132
             +GL K+   V + + LE     AIG+ LPDDEDELLAGIMDDFDL GL + +ED+E+Y
Sbjct: 98  --AGLDKLQQDVEAGESLEDDGIHAIGSLLPDDEDELLAGIMDDFDLSGLSNPMEDVEEY 155

Query: 133 DIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPS 192
           D+FGSGGGMELE +PQESL+M M+K+S+SD   GNGL  Y +PNG+GTVAGEHPYGEHPS
Sbjct: 156 DLFGSGGGMELEIDPQESLNMGMAKVSLSDGVVGNGLAQYGLPNGSGTVAGEHPYGEHPS 215

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
           RTLFVRNINSNVEDSELR LFEQYG IRTLYTACKHRGFVMISYYDIRAARTAMRALQNK
Sbjct: 216 RTLFVRNINSNVEDSELRTLFEQYGAIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 275

Query: 253 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH 312
           PLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSN+DLRQIFGAYGEVKEIRETPH
Sbjct: 276 PLRRRKLDIHFSIPKDNPSDKDVNQGTLVVFNLDPSVSNDDLRQIFGAYGEVKEIRETPH 335

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           KRHHKFIEFYDVRAAEAAL+SLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR
Sbjct: 336 KRHHKFIEFYDVRAAEAALRSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 395

Query: 373 ILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQ 432
             +H VGSP+ NSPPG+W QFSSPIEH+PLQ++SKSP FR +SPTTSNH+PGLASIL+ Q
Sbjct: 396 SFRHHVGSPMANSPPGSWAQFSSPIEHSPLQSLSKSPGFRTVSPTTSNHLPGLASILNSQ 455

Query: 433 VSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSP 492
           +S   K+APIGKDQGR                                     + FGP  
Sbjct: 456 ISNSVKVAPIGKDQGR-------------------------------------AKFGP-- 476

Query: 493 SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLG 552
                             P+ YSEH++S AWQ  SMGHPF+SNG+  G PYSGR      
Sbjct: 477 ---------------ISCPAPYSEHTNSSAWQPPSMGHPFASNGQGRGFPYSGRH----- 516

Query: 553 SSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVN 612
                           ER FG+ PESPE SFM PVAF GMG+  NDG+            
Sbjct: 517 ----------------ERHFGYFPESPEASFMTPVAFGGMGLAHNDGT------------ 548

Query: 613 PGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNG 671
                  N+S++GS+ FR++SSPRLSP+F GNGP+PGL P+NIEGL +RGRSR +E NNG
Sbjct: 549 -------NMSESGSANFRMISSPRLSPMFPGNGPFPGLAPSNIEGLADRGRSRWVE-NNG 600

Query: 672 NQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPID 731
           NQ+DSKKQFQL+L+KI +GEDTRTTLMIKNIPNKYTSKMLLAAIDE H+GTYDFLYLPID
Sbjct: 601 NQIDSKKQFQLDLDKILNGEDTRTTLMIKNIPNKYTSKMLLAAIDEYHRGTYDFLYLPID 660

Query: 732 FKNKCNVGYAFINMLSPLHIIPFYEVL 758
           FKNKCNVGYAFINMLSP HIIPFY+  
Sbjct: 661 FKNKCNVGYAFINMLSPSHIIPFYQAF 687

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567420|ref|XP_003551918.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score =  958 bits (2477), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 507/753 (67%), Positives = 584/753 (77%), Gaps = 7/753 (0%)

Query: 8   SSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGR 67
           ++GP  I   N+PK+ G  + G    SD +  S D SLFSSSLPVLPHEKL+L       
Sbjct: 14  AAGPSGISPHNVPKKAGSSAWGIPRASDVFHDSSDVSLFSSSLPVLPHEKLDLTDSENYG 73

Query: 68  QSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLE 127
           Q VDD    L KVH      DP +     AIGN LPDDE++LLAGIMDDFDL  LPS LE
Sbjct: 74  QPVDDNLLTLDKVHKEDEGHDPFDDFETNAIGNMLPDDEEDLLAGIMDDFDLSKLPSQLE 133

Query: 128 DLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPY 187
           DL++ D+F +GGG E++ EPQESL++SMSKI ISD  + NG+  Y++PNG GTVAGEHPY
Sbjct: 134 DLDENDLFVNGGGFEMDFEPQESLNISMSKIGISDGIASNGIGQYAIPNGVGTVAGEHPY 193

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           GEHPSRTLFVRNINSNVEDSELR LFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR
Sbjct: 194 GEHPSRTLFVRNINSNVEDSELRTLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 253

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI 307
           ALQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDPSVSN+DLRQIFGAYGEVKEI
Sbjct: 254 ALQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDPSVSNDDLRQIFGAYGEVKEI 313

Query: 308 RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELE 367
           RETPHKRHHKFIEFYDVRAAEAALK+LNRSDIAGKRIKLEPSRPGGARRNLM QL+QELE
Sbjct: 314 RETPHKRHHKFIEFYDVRAAEAALKALNRSDIAGKRIKLEPSRPGGARRNLMQQLSQELE 373

Query: 368 QDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLAS 427
           QDE+R  +HQV SP+ NSPPG+W QF SP+E NPL + SKSP     SP  +NH+ GLA+
Sbjct: 374 QDEARTFRHQVVSPVANSPPGSWAQFGSPVEQNPLASFSKSPGLGPASPINTNHLSGLAA 433

Query: 428 ILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSS 487
           IL PQ +T  KIAPIGKD GR +      +N+ S  GA+FQ S SF E  +      +S+
Sbjct: 434 ILSPQATTSTKIAPIGKDPGRAA--NQMFSNSGSTQGAAFQHSISFPEQNVKASPRPIST 491

Query: 488 FGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQ 547
           FG S S+ S + TLSGPQFLWGSP+ YSEHS++ AW +SS+G PF+S+ +  G PY+   
Sbjct: 492 FGESSSSASSIGTLSGPQFLWGSPTPYSEHSNTSAWSSSSVGLPFTSSVQRQGFPYTSNH 551

Query: 548 GSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMV-NMG 606
             FLGS  HHHVGSAPSG+PL+R F + PESPE S M+PVAF  +  G  DG+FM+ N+ 
Sbjct: 552 SPFLGSHSHHHVGSAPSGLPLDRHFSYFPESPEASLMSPVAFGNLNHG--DGNFMMNNIS 609

Query: 607 SRASVNPGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRR 665
           +RASV  G+ +  N  +  S +FR+MS PR   +F GN  Y G    NIEGL ERGRSRR
Sbjct: 610 ARASVGAGVGLSGNTPEISSPNFRMMSLPRHGSLFHGNSLYSGPGATNIEGLAERGRSRR 669

Query: 666 IENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDF 725
            E N GNQ+DSKK +QL+L+KI  GEDTRTTLMIKNIPNKYTSKMLLAAIDENH+GTYDF
Sbjct: 670 PE-NGGNQIDSKKLYQLDLDKIVCGEDTRTTLMIKNIPNKYTSKMLLAAIDENHQGTYDF 728

Query: 726 LYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           LYLPIDFKNKCNVGYAFINM+SP HII FY+  
Sbjct: 729 LYLPIDFKNKCNVGYAFINMVSPSHIIAFYKAF 761

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357450611|ref|XP_003595582.1| Polyadenylate-binding protein [Medicago truncatula] gi|355484630|gb|AES65833.1| Polyadenylate-binding protein [Medicago truncatula]

 Score =  956 bits (2471), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 490/665 (73%), Positives = 550/665 (82%), Gaps = 12/665 (1%)

Query: 102 LPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISIS 161
           LPDD++ELLAGIMDDFDLRGLP SLEDLE+YD+F S GG+ELE +PQESLS+ +SK+S+S
Sbjct: 2   LPDDDEELLAGIMDDFDLRGLPGSLEDLEEYDLFDSSGGLELETDPQESLSVGISKLSLS 61

Query: 162 DSASGNGLLHYSVPNGAGTVAG--EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI 219
           DS+ GN +  YS+PNG G  A   EHPYGEHPSRTLFVRNINSNVED+ELR LFEQYGDI
Sbjct: 62  DSSVGNSMPPYSLPNGVGGGAVAGEHPYGEHPSRTLFVRNINSNVEDTELRTLFEQYGDI 121

Query: 220 RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
           RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGT
Sbjct: 122 RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGT 181

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE+YDVRAAEAALKSLNRSDI
Sbjct: 182 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEYYDVRAAEAALKSLNRSDI 241

Query: 340 AGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEH 399
           AGKRIKLEPSRPGGARRNLMLQLNQEL+QDESR  ++QVGSP+  SPPGNW+QF+SPIE 
Sbjct: 242 AGKRIKLEPSRPGGARRNLMLQLNQELDQDESRSFRYQVGSPLAGSPPGNWLQFNSPIEQ 301

Query: 400 NPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNT 459
           + L  ++ SP  + MSPTTSNH+PGLASIL PQ+S   K A IG+D GR S  +H   N 
Sbjct: 302 SSLPNLNHSPGSKIMSPTTSNHLPGLASILQPQLSNTVKAATIGQDIGRSSHGDHIFPNK 361

Query: 460 ISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSS 519
           IS+ G++F  S+S  EPK   YRG +SSFG S SNGS VETL+ PQFLWGSP+  SE + 
Sbjct: 362 ISSAGSNF-NSHSLPEPKFSPYRGALSSFGASTSNGSSVETLTAPQFLWGSPNLSSEPTK 420

Query: 520 SPAWQTSSMGHPFS-SNGKIHGLPYSGRQGSFL----GSSQHHHVGSAPSGVPLERRFGF 574
             AW   S+GH  S SNG  H  PYS +  SF+        HHHVGSAPSG+P ER FGF
Sbjct: 421 PSAWPRPSVGHQLSTSNGTSHAFPYSSQNNSFVSSSQQQHHHHHVGSAPSGLPFERHFGF 480

Query: 575 LPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSS 633
            P+S ETS MN V + GMG+G NDG++M+N G   S N GI++PRN+ DNGSS FR+ SS
Sbjct: 481 FPKSSETSLMNNVGYRGMGLGHNDGNYMLNSG--ISGNVGISIPRNMPDNGSSNFRMRSS 538

Query: 634 PRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDT 693
           P LSPVFLGNGPYPGL P  +E   +R RSR I+ NNG+Q+D+KK FQL+L+KIRSGEDT
Sbjct: 539 PILSPVFLGNGPYPGLLPTAMESFTDRVRSRWID-NNGSQVDNKKLFQLDLDKIRSGEDT 597

Query: 694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 753
           RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP  IIP
Sbjct: 598 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIP 657

Query: 754 FYEVL 758
           FYE  
Sbjct: 658 FYETF 662

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449481207|ref|XP_004156114.1| PREDICTED: protein MEI2-like 2-like [Cucumis sativus]

 Score =  953 bits (2464), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 504/756 (66%), Positives = 592/756 (78%), Gaps = 14/756 (1%)

Query: 6   DHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGL 65
           D  SG  K   +N+P++ G  + G    SDS+ AS D SLFSSSLPVLPHEKL+ ++  L
Sbjct: 7   DSMSGQAKNLLVNVPRKAGSSAWGIPCASDSFHASSDVSLFSSSLPVLPHEKLDFDSE-L 65

Query: 66  GRQSVDDISSGLSKVHHGVASDDPLEGVMNP--AIGNSLPDDEDELLAGIMDDFDLRGLP 123
            +    D+S+ L          DPLE V     AIGN LPDD DEL +G+MDDFDL GLP
Sbjct: 66  CQSDGADLSNELDP---KTDIKDPLEDVEVEVDAIGNLLPDD-DELFSGLMDDFDLSGLP 121

Query: 124 SSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAG 183
           S LEDLE+YD+FGSGGGMEL+ EPQE+LSM MSK+++SDS +G+ + HY++PNG GTVAG
Sbjct: 122 SQLEDLEEYDLFGSGGGMELDFEPQENLSMGMSKLNLSDSVTGSMVSHYALPNGVGTVAG 181

Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR 243
           EHPYGEHPSRTLFVRNINSNVED+ELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR
Sbjct: 182 EHPYGEHPSRTLFVRNINSNVEDAELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR 241

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
           TAMRALQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLD SVSN+DLR+IFGAYGE
Sbjct: 242 TAMRALQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDASVSNDDLRRIFGAYGE 301

Query: 304 VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLN 363
           VKEIRETPHKRHHKFIEFYDVRAAEAAL++LNRSDIAGKRIKLEPSRPGGARRNLM QL+
Sbjct: 302 VKEIRETPHKRHHKFIEFYDVRAAEAALRALNRSDIAGKRIKLEPSRPGGARRNLMQQLS 361

Query: 364 QELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMP 423
           QELEQD++R  +HQVGSP TNSPPGNW    SP+EHN   + SKSP   ++SP  S+H+ 
Sbjct: 362 QELEQDDARTFRHQVGSPATNSPPGNWSHIGSPVEHN---SFSKSPGLGSLSPINSSHLS 418

Query: 424 GLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRG 483
           GLASIL P +S   +IAPIGKDQGR +     LTN+    G ++    SF + K     G
Sbjct: 419 GLASILPPNLSNSPRIAPIGKDQGRANHASQVLTNSALMQGTAYHHHQSFPDNKFSSNGG 478

Query: 484 TVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPY 543
           + SS     SN S + TLSGPQFLWGSP+ Y+E  +S AW T S G PF+SNG+  G PY
Sbjct: 479 STSSVADLNSNSSSIGTLSGPQFLWGSPTPYAERPNSSAWPTPSAGQPFTSNGQGQGFPY 538

Query: 544 SGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMV 603
               GS LG S HHHVGSAPSGVPL+R FG+ PESPETSFM+P       + +++G+FM 
Sbjct: 539 VRHHGSLLG-SHHHHVGSAPSGVPLDRPFGYFPESPETSFMSPGTLGSTSLSRHNGNFM- 596

Query: 604 NMGSRASVNPGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGR 662
           N+ +RA++  G+ +P N+++NGS +FR+MS PR   ++ GNG +PG    + +GL ERGR
Sbjct: 597 NLSTRAAMTGGLGLPTNMAENGSPNFRLMSLPRQGSIYYGNGSFPGSGVVSADGLLERGR 656

Query: 663 SRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGT 722
           SRR+E N GNQ++SKKQ+QL+LEKI SGEDTRTTLMIKNIPNKYTSKMLLAAIDENH+G 
Sbjct: 657 SRRVE-NVGNQIESKKQYQLDLEKIVSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGA 715

Query: 723 YDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVL 758
           YDFLYLPIDFKNKCNVGYAFINM+SP  IIPFYE  
Sbjct: 716 YDFLYLPIDFKNKCNVGYAFINMVSPTQIIPFYEAF 751

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	780
TAIR|locus:2013583	800	ML5 "MEI2-like protein 5" [Ara	0.812	0.792	0.514	1.7e-162
TAIR|locus:2117706	759	ML3 "MEI2-like 3" [Arabidopsis	0.766	0.787	0.457	7.8e-126
TAIR|locus:2045605	843	ML2 "MEI2-like 2" [Arabidopsis	0.724	0.670	0.448	7.7e-119
TAIR|locus:2156166	915	ML1 "MEI2-like protein 1" [Ara	0.237	0.202	0.572	1.1e-105
TAIR|locus:2182885	907	ML4 "MEI2-like 4" [Arabidopsis	0.225	0.194	0.544	7.9e-94
TAIR|locus:2090350	615	TEL1 "terminal EAR1-like 1" [A	0.119	0.151	0.526	1e-39
TAIR|locus:2008530	527	TEL2 "terminal EAR1-like 2" [A	0.124	0.184	0.494	1.8e-36
DICTYBASE|DDB_G0279255	1698	DDB_G0279255 [Dictyostelium di	0.262	0.120	0.297	2.8e-28
POMBASE|SPAC27D7.03c	750	mei2 "RNA-binding protein invo	0.093	0.097	0.657	1.7e-24
DICTYBASE|DDB_G0268266	689	DDB_G0268266 "RNA recognition	0.217	0.246	0.359	7.5e-20

TAIR|locus:2013583 ML5 "MEI2-like protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 1582 (562.0 bits), Expect = 1.7e-162, P = 1.7e-162
 Identities = 348/676 (51%), Positives = 429/676 (63%)

Query:    17 LNIPKEVGGGSCGRIXXXXXXXX-XXXXXXXXXXXPVLPHEKLNLNAMGLGRQSVDDISS 75
             ++IP E   G+ G +                    PV P  KL L+    G   +DD  +
Sbjct:     1 MDIPHEAEAGAWGILPGFGRHHHPSSDATLFSSSLPVFPRGKLQLSDNRDGFSLIDD--T 58

Query:    76 GLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIF 135
              +S+ +    S D  E   + +IGN LPD+ED LL G+MDD DL  LP    D +DYD+F
Sbjct:    59 AVSRTNKFNESADDFE---SHSIGNLLPDEED-LLTGMMDDLDLGELP----DADDYDLF 110

Query:   136 GSGGGMELEGEPQEXXXXXXXXXXXXXXXXGNGLLHYSVPNGAGTVAGEHPYGEHPSRTL 195
             GSGGGMEL+ + ++                GN +  +++PNGAGTVAGEHPYGEHPSRTL
Sbjct:   111 GSGGGMELDADFRDNLSMSGPPRLSLSSLGGNAIPQFNIPNGAGTVAGEHPYGEHPSRTL 170

Query:   196 FVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR 255
             FVRNINSNVEDSEL ALFEQYGDIRTLYT CKHRGFVMISYYDIR+AR AMR+LQNKPLR
Sbjct:   171 FVRNINSNVEDSELTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLR 230

Query:   256 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH 315
             RRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDPS+SN+DL  IFGA+GE+KEIRETPHKRH
Sbjct:   231 RRKLDIHFSIPKDNPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRH 290

Query:   316 HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMXXXXXXXXXXXSRILQ 375
             HKF+EFYDVR AEAALK+LNR +IAGKRIK+EPSRPGGARR+LM              L 
Sbjct:   291 HKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRPGGARRSLMLQLNQDLENDDLHYLP 350

Query:   376 HQVGSPITNSPP--GNWVQFSSPIEHNPLQTI-SKSPNFRNMSPTTSNHMPGLASILHPQ 432
               +GSP+ NSPP  GNW   +SP+E +PLQ++ S+SP F  +SPT + H+ GLAS L+ Q
Sbjct:   351 -MIGSPMANSPPMQGNW-PLNSPVEGSPLQSVLSRSPVF-GLSPTRNGHLSGLASALNSQ 407

Query:   433 VSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNS-FSEPKI-GLYRGTVXXXXX 490
               +  K+APIG+ Q             I +NG  FQQS+  F EPK+   Y G +     
Sbjct:   408 GPS-SKLAPIGRGQ-------------IGSNG--FQQSSHLFQEPKMDNKYTGNLSPSGP 451

Query:   491 XXXXXXXVETLSGPQFLWGXXXXXXXXXXXPAWQTSSMGHPFSSNGKIHGLPYSGRQGSF 550
                    +ETLSG +FLWG             W TSS G+P  S      +P+  +  + 
Sbjct:   452 LISNGGGIETLSGSEFLWGSPNARSEPSSSSVWSTSSTGNPLFSTRVDRSVPFPHQHQNQ 511

Query:   551 LGSSQHHHVGSAPSGVPLERRFGFLPESPETS-FMNPVAFCGM-GIGQNDGSFMVNMGSR 608
               S  H HVGSAPSGVPLE+ FGF+PES + + FMN V   GM G+G N GSF   M + 
Sbjct:   512 SRSHHHFHVGSAPSGVPLEKHFGFVPESSKDALFMNTVGLQGMSGMGLNGGSFSSKMANN 571

Query:   609 ASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIEN 668
               +N G ++  N     SS+R+MSSPR SP+FL +G  PG   +  + LYE GR RR+EN
Sbjct:   572 GIINSG-SMAEN---GFSSYRMMSSPRFSPMFLSSGLNPGRFASGFDSLYENGRPRRVEN 627

Query:   669 NNGNQLDSKK-QFQLE 683
             N+      K+ Q  LE
Sbjct:   628 NSNQVESRKQFQLDLE 643

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR|locus:2117706 ML3 "MEI2-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 1236 (440.2 bits), Expect = 7.8e-126, P = 7.8e-126
 Identities = 294/642 (45%), Positives = 382/642 (59%)

Query:    51 PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVAS--DDPLEGVMNPAIGNSLPDDEDE 108
             P++ H+  N+N      QSVD+++SGL     G+ +  DD   G  +P IGN LPDDE+E
Sbjct:    28 PLIQHQ--NINPRDSYHQSVDEMASGLDHFSGGIGNMLDD---GDSHP-IGNMLPDDEEE 81

Query:   109 LLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEXXXXXXXXXXXXXXXXGNG 168
             L +G+MDD +L  LP++L+DLEDYD+FGSGGG+ELE +P +                 N 
Sbjct:    82 LFSGLMDDLNLSSLPATLDDLEDYDLFGSGGGLELETDPYDSLNKGFSRMGFADSNVDNV 141

Query:   169 LLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH 228
             +      NG G++AGEHPYGEHPSRTLFVRNINSNVEDSEL+ALFEQYG IRTLYTACK 
Sbjct:   142 MPQNIFQNGVGSIAGEHPYGEHPSRTLFVRNINSNVEDSELQALFEQYGHIRTLYTACKQ 201

Query:   229 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 288
             RGFVM+SY DIRA+R AMRALQ K L++RKLDIHFSIPKDNPS+KD+NQGTLVVFNL PS
Sbjct:   202 RGFVMVSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPS 261

Query:   289 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
             VSN DL  IFG YGE+KEIRETP+KRHHKF+EF+DVR+A+AALK+LNR++IAGKRIKLE 
Sbjct:   262 VSNRDLENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADAALKALNRTEIAGKRIKLEH 321

Query:   349 SRPGGARRNLMXXXXXXXXXXXSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKS 408
             SRPGGARRN+M           S    + V SP+ +SP GNW   +SPI+H PLQ+ SKS
Sbjct:   322 SRPGGARRNMMLQMNPELEQDDSYSYLNHVESPLASSPIGNWR--NSPIDH-PLQSFSKS 378

Query:   409 PNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQ-GRG-SLMEHALTNTISANGAS 466
             P F N+SPT +        I +P+ S   K A +  DQ GR  S ++H  +++ S N AS
Sbjct:   379 PIFGNLSPTKN--------IRYPEFSM--KTASVNNDQEGRRFSHLDHLFSSS-SYNNAS 427

Query:   467 FQQSNSFSEPKIGLYRGTVXXXXXXXXXXXXVETLSGPQFLWGXXXXXXXXXXXPAWQTS 526
              + S +F +P+     G+V            VETLSG +FLWG            +    
Sbjct:   428 HKAS-TFQQPQSF---GSVSSFGSLNSHPSHVETLSGSEFLWGSPSSSAWPVNPFSSNRE 483

Query:   527 SMGHPFSS-NGKIHGLPYSGR--QGSFLGSSQHHHVGS-----APSGVPLERRFGFLPES 578
             +   P+S+ NG +H L + G    G F  S +   +GS     A   +  +R    L E+
Sbjct:   484 NHRFPYSAQNGSLHQLHHIGSAPSGFFPRSPETSSMGSVAFRGASGNMNAQRN---LRET 540

Query:   579 PETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRN--LSDNGSS--FRVMSSP 634
                +F    A     +   +GS++    +  S++  +    N     NG+    ++    
Sbjct:   541 SSPNFKMLSAPRRSQLFTGNGSYLWPAATMVSIDDPLEDGSNQQFDSNGNQADIKIQFQL 600

Query:   635 RLSPVFLGNGPYPGLTPANIEGLYERGRS-RRIENNNGNQLD 675
              LS +  G  P   L   NI   Y R      I+  N    D
Sbjct:   601 DLSKIMRGEDPRTTLMIKNIPNKYTRNMLLAAIDEKNSGTYD 642

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

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

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

TAIR|locus:2045605 ML2 "MEI2-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1170 (416.9 bits), Expect = 7.7e-119, P = 7.7e-119
 Identities = 263/587 (44%), Positives = 342/587 (58%)

Query:    51 PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELL 110
             P L HEKLN+        S D+ S  L+K+  G +  D LE V   A+   LP+DE+ELL
Sbjct:    57 PTLFHEKLNMTDSD-SWLSFDESSPNLNKLVIGNSEKDSLEDVEPDALEILLPEDENELL 115

Query:   111 AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEXXXXXXXXXXXXXXXXGNGLL 170
              G++D+ +  GLP  L+DLE+ D+F +GGGMEL+ E Q+                 N  +
Sbjct:   116 PGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVESQDNHAVDASGMQISDRGAANAFV 175

Query:   171 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 230
                 PN AG V+ EHP GEHPSRTLFVRNINS+VEDSEL ALFE +G+IR+LYTACK RG
Sbjct:   176 PRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVEDSELSALFEPFGEIRSLYTACKSRG 235

Query:   231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVS 290
             FVMISYYDIRAA  AMRALQN  LR+R LDIHFSIPK+NPS+KD+NQGTLV+FN+D +VS
Sbjct:   236 FVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIPKENPSEKDMNQGTLVIFNVDTTVS 295

Query:   291 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
             N++L Q+FGAYGE++EIRETP++R H+FIE+YDVR AE ALK+LNRS+I GK IKLE SR
Sbjct:   296 NDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRDAETALKALNRSEIGGKCIKLELSR 355

Query:   351 PGGARRNLMXXXXXXXXXXXSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPN 410
             PGGARR  +                +QVGS + NSPPGNW    SP++ +P    ++   
Sbjct:   356 PGGARRLSVPSQSQDLERTEVTNFYNQVGSHVANSPPGNW-PIGSPVKGSPSHAFTRPHG 414

Query:   411 FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQS 470
                + P  S++MPGLASIL    S+    +P+  DQG  +     + N    +  S+ Q 
Sbjct:   415 LGMVRPVNSDNMPGLASILPAHPSSFHGFSPVSNDQGLLNHSNQTILNKGLMHNISYGQP 474

Query:   471 NSFSEPKIGLYRGTVXXXXXXXXXXXXVETLSGPQFLWGX--XXXXXXXXXXPAWQTSSM 528
             +S  E   G   G                T S  ++ WG              +  +SS 
Sbjct:   475 HSLPEHITG---GISNSMRFIAPHSSGFGTSSDHRYRWGSPPQHMNYPGYTGVSSSSSST 531

Query:   529 GHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVA 588
               PF+     HG P++ RQ S LG  QHH VGSAPS +    +      SPE     P+ 
Sbjct:   532 ERPFTVR---HGFPFAERQASLLGKYQHH-VGSAPSSIHFNTQMNCYTGSPEI----PLG 583

Query:   589 FCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNG-SSFRVMSSP 634
             F  MGI +N  S      +    N G+++P N S+   + F + S P
Sbjct:   584 FSDMGINRNYNS------AHGKANLGVSLPGNSSEQDFTGFGMSSMP 624

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

TAIR|locus:2156166 ML1 "MEI2-like protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 530 (191.6 bits), Expect = 1.1e-105, Sum P(4) = 1.1e-105
 Identities = 106/185 (57%), Positives = 135/185 (72%)

Query:   171 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 230
             H +   G     GE   GE PSRTL V NI+SNVED EL+ LFEQ+GDI+ L+TACK+RG
Sbjct:   195 HRNGERGGNNSVGELNRGEIPSRTLLVGNISSNVEDYELKVLFEQFGDIQALHTACKNRG 254

Query:   231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVS 290
             F+M+SY DIRAA+ A RALQNK LR  KLDI +SI K+NPS KD ++G L+V NLD S+S
Sbjct:   255 FIMVSYCDIRAAQNAARALQNKLLRGTKLDIRYSISKENPSQKDTSKGALLVNNLDSSIS 314

Query:   291 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
             N++L ++  +YGEVKEIR T H     +IEF+DVRAA AAL  LN  ++AGK+++L P+ 
Sbjct:   315 NQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFDVRAAAAALGGLNGLEVAGKKLQLVPTY 374

Query:   351 PGGAR 355
             P G R
Sbjct:   375 PEGTR 379

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0048507 "meristem development" evidence=IGI

GO:0045836 "positive regulation of meiosis" evidence=IGI

TAIR|locus:2182885 ML4 "MEI2-like 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 501 (181.4 bits), Expect = 7.9e-94, Sum P(3) = 7.9e-94
 Identities = 97/178 (54%), Positives = 133/178 (74%)

Query:   176 NGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMIS 235
             +   TVA EHP GE  SR LFVRN++S++ED EL  LF+Q+GD+R L+TA K+RGF+M+S
Sbjct:   195 SNVSTVA-EHPQGEILSRILFVRNVDSSIEDCELGVLFKQFGDVRALHTAGKNRGFIMVS 253

Query:   236 YYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLR 295
             YYDIRAA+ A RAL  + LR RKLDI +SIPK+NP +   ++G L V NLD S+SNE+L 
Sbjct:   254 YYDIRAAQKAARALHGRLLRGRKLDIRYSIPKENPKENS-SEGALWVNNLDSSISNEELH 312

Query:   296 QIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG 353
              IF +YGE++E+R T H+    +IEF+DVR A+ AL+ LN  ++AG+++KL P+ P G
Sbjct:   313 GIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLKLAPTCPEG 370

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0048507 "meristem development" evidence=IGI

TAIR|locus:2090350 TEL1 "terminal EAR1-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 1.0e-39, Sum P(4) = 1.0e-39
 Identities = 49/93 (52%), Positives = 65/93 (69%)

Query:   263 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY 322
             F +P  +      NQGTLV+FNLDP VS+  LRQIF  YG +KE+RETP+K+H +F+EFY
Sbjct:   198 FVVPATSAVPGGCNQGTLVIFNLDPEVSSITLRQIFQVYGPIKELRETPYKKHQRFVEFY 257

Query:   323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 355
             DVR A  A   +N  +I GK++ +E SRPGG +
Sbjct:   258 DVRDAARAFDRMNGKEIGGKQVVIEFSRPGGIK 290

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

TAIR|locus:2008530 TEL2 "terminal EAR1-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 246 (91.7 bits), Expect = 1.8e-36, Sum P(3) = 1.8e-36
 Identities = 48/97 (49%), Positives = 67/97 (69%)

Query:   262 HFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEF 321
             HF  P+ N   +  NQG+LV+ NL+P+VS+  LR IF  YGEVK++RETP KR  +F+EF
Sbjct:   167 HFVFPQLNAVPEGNNQGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEF 226

Query:   322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
             +DVR A  AL+ +N   I+GK + ++ SRPGG  + L
Sbjct:   227 FDVRDAAKALRVMNGKVISGKPMVIQFSRPGGLTKKL 263

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

DICTYBASE|DDB_G0279255 DDB_G0279255 [Dictyostelium discoideum (taxid:44689)]

 Score = 231 (86.4 bits), Expect = 2.8e-28, Sum P(3) = 2.8e-28
 Identities = 67/225 (29%), Positives = 114/225 (50%)

Query:   189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-FVMISYYDIRAARTAMR 247
             E PSR LF+++I   +  +  ++  E  G I ++Y + K++G F++ISY DIR +  A  
Sbjct:   911 ESPSRYLFIKSIRG-INHNLFKSKIESIGQINSVYGSIKNKGGFLIISYLDIRHSIEAFN 969

Query:   248 ALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVV-FNLDPSVSNEDLRQIFGAYGEVKE 306
              LQ       KL +++   KD   DK    GTL+  F+ D  + N  +   F  +GE+K+
Sbjct:   970 ELQKVDFGS-KLIVNYCFDKDQTVDK----GTLIATFSNDDQIKN--IVNDFSKFGEIKD 1022

Query:   307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMXXXXXXX 366
             IR++P+K   KF+EFY++ +   A+ +LN SD    +IK+  S  GG+ ++L+       
Sbjct:  1023 IRDSPNKPLQKFVEFYNINSTLKAINNLN-SD----KIKVAFSHHGGSSKDLIKLNSTEA 1077

Query:   367 XXXXSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNF 411
                   +  H        +        S+P     + +I+KSP+F
Sbjct:  1078 F----NVTTHYFNGTYLPTTTTTTATASTPTS-TQVNSITKSPSF 1117

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

POMBASE|SPAC27D7.03c mei2 "RNA-binding protein involved in meiosis Mei2" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 246 (91.7 bits), Expect = 1.7e-24, Sum P(3) = 1.7e-24
 Identities = 48/73 (65%), Positives = 56/73 (76%)

Query:   682 LELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYA 741
             ++  +I SG DTRTT+MIKNIPNK+T +ML   ID  +KGTYDFLYL IDF NKCNVGYA
Sbjct:   584 VDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFVNKCNVGYA 643

Query:   742 FINMLSPLHIIPF 754
             FIN + P  II F
Sbjct:   644 FINFIEPQSIITF 656

GO:0003723 "RNA binding" evidence=IDA

GO:0004860 "protein kinase inhibitor activity" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007127 "meiosis I" evidence=TAS

GO:0033620 "Mei2 nuclear dot" evidence=IDA

GO:0034064 "Tor2-Mei2-Ste11 complex" evidence=IDA

GO:0045836 "positive regulation of meiosis" evidence=IMP

DICTYBASE|DDB_G0268266 DDB_G0268266 "RNA recognition motif-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 272 (100.8 bits), Expect = 7.5e-20, Sum P(2) = 7.5e-20
 Identities = 64/178 (35%), Positives = 99/178 (55%)

Query:   174 VPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVM 233
             + +  G V GE    E   RTLFVRN+  ++++ ++ A+F + G+I+  ++  + RG   
Sbjct:   170 IKDNNGKVIGEK---EKLGRTLFVRNVAYSIKEVDIPAIFAKIGEIKKTFSLLESRGIAF 226

Query:   234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNED 293
             ISYYD+R A  A   +Q   L  R +DIHFSIPK+    +D N G + V N D  + NE 
Sbjct:   227 ISYYDLRDAERAKNEIQGTTLDGRSIDIHFSIPKEESGLED-NAGFIHVKNRDVPL-NE- 283

Query:   294 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
             +R  F +YG++K++ E    R    +EFYD+RA E AL   N   +  + + L+   P
Sbjct:   284 VRIFFSSYGDIKDVTE--FNRDQVLVEFYDLRACEKALAEANGVKLGDQTLDLDYYTP 339

GO:0030587 "sorocarp development" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8VWF5	AML5_ARATH	No assigned EC number	0.6050	0.9051	0.8825	yes	no
Q6ZI17	OML2_ORYSJ	No assigned EC number	0.5955	0.8871	0.8160	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

Your Input: GSVIVG00003386001 SubName- Full=Chromosome undetermined scaffold_143, whole genome shotgun sequence; (824 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	780
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-49
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	4e-44
cd12531	86	cd12531, RRM3_MEI2_like, RNA recognition motif 3 i	8e-41
pfam04059	97	pfam04059, RRM_2, RNA recognition motif 2	9e-40
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	9e-32
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-31
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	2e-28
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	6e-28
cd12532	90	cd12532, RRM3_MEI2_fungi, RNA recognition motif 3	2e-25
cd12530	101	cd12530, RRM3_EAR1_like, RNA recognition motif 3 i	4e-25
smart00360	73	smart00360, RRM, RNA recognition motif	9e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-13
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	4e-12
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	4e-12
smart00360	73	smart00360, RRM, RNA recognition motif	5e-12
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	8e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-11
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-10
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	9e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-09
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	6e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-08
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	1e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-08
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	3e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-08
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	6e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	7e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	8e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-07
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-07
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-07
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-07
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	5e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	7e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-07
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	9e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-06
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-06
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-06
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	4e-06
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	4e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	5e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	5e-06
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	5e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	7e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	8e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	1e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-05
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	1e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	3e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	4e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-05
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	5e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	5e-05
cd12288	93	cd12288, RRM_La_like_plant, RNA recognition motif	5e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	6e-05
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	6e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	7e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	8e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	8e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	8e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	9e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	1e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-04
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	2e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-04
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	2e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	2e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-04
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	3e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	4e-04
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	5e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	5e-04
cd12695	93	cd12695, RRM3_PTBP1, RNA recognition motif 3 in ve	5e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	5e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	5e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	5e-04
cd12697	76	cd12697, RRM3_ROD1, RNA recognition motif 3 in ver	5e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	6e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	6e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	7e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	7e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	7e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	7e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	7e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	8e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	8e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	9e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.001
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.001
cd12256	89	cd12256, RRM2_LKAP, RNA recognition motif 2 in Lim	0.001
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.001
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.001
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.001
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.001
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.001
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.001
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.001
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.001
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.001
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.002
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.002
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.002
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
cd12419	80	cd12419, RRM_Ssp2_like, RNA recognition motif in y	0.002
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	0.002
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.002
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	0.002
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.002
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	0.002
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.003
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	0.003
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.003
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.003
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.003
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.003
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	0.003
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.003
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	0.003
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.003
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.003
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.004
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.004
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.004
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.004
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.004
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.004
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.004
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.004
cd12752	87	cd12752, RRM1_RBM5, RNA recognition motif 1 in ver	0.004
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.004
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.004

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

 Score =  167 bits (425), Expect = 2e-49
 Identities = 66/77 (85%), Positives = 69/77 (89%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           SRTLFVRNINSNVED ELRALFEQ+GDIRTLYTACKHRGF+M+SYYDIRAAR A RALQ 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 252 KPLRRRKLDIHFSIPKD 268
             L  RKLDIHFSIPKD
Sbjct: 61  TELGGRKLDIHFSIPKD 77

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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score =  152 bits (386), Expect = 4e-44
 Identities = 64/71 (90%), Positives = 70/71 (98%)

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           QGTLVVFNLDPSVSN+DL QIFGAYGE+KEIRETP+KRHHKFIEFYDVR+AEAALK+LNR
Sbjct: 1   QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 337 SDIAGKRIKLE 347
           S+IAGKRIKLE
Sbjct: 61  SEIAGKRIKLE 71

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|240975 cd12531, RRM3_MEI2_like, RNA recognition motif 3 in plant Mei2-like proteins

 Score =  144 bits (364), Expect = 8e-41
 Identities = 51/60 (85%), Positives = 55/60 (91%)

Query: 697 LMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYE 756
           LMIKNIPNKYT KMLLAAIDE H+GTYDF YLPIDFKNKCNVGYAFINM+SP  I+PFY+
Sbjct: 1   LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYK 60

This subgroup corresponds to the RRM3 of Mei2-like proteins, representing 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 = 86

>gnl|CDD|112856 pfam04059, RRM_2, RNA recognition motif 2

 Score =  141 bits (356), Expect = 9e-40
 Identities = 54/63 (85%), Positives = 57/63 (90%)

Query: 694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 753
           RTTLMIKNIPNKYT KMLLAAIDE +KGTYDFLYLPIDFKNKCNVGYAFINM+ P  IIP
Sbjct: 1   RTTLMIKNIPNKYTQKMLLAAIDEKNKGTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIP 60

Query: 754 FYE 756
           F +
Sbjct: 61  FGK 63

Length = 97

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  117 bits (296), Expect = 9e-32
 Identities = 40/71 (56%), Positives = 55/71 (77%)

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           QGTL+VFNLD  +S+++LR +F  +GEVK+IRETP +   KF+EFYD+RAAEAAL +LN 
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 337 SDIAGKRIKLE 347
               G R+K++
Sbjct: 61  RPFLGGRLKVK 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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score =  116 bits (293), Expect = 2e-31
 Identities = 42/71 (59%), Positives = 57/71 (80%)

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           QGTLV+FNLDP+VS+E LR IF  YG+VKE+RETP KR  +F+EF+DVR A  AL+++N 
Sbjct: 1   QGTLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 337 SDIAGKRIKLE 347
            +I+GK + +E
Sbjct: 61  KEISGKPVVIE 71

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  108 bits (271), Expect = 2e-28
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           SR+LFV N+  +V +S LR LFE YGD+R + T     G V + +YDIR A+ A+R L  
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60

Query: 252 KPLRRRKLDIH 262
           + ++++ L   
Sbjct: 61  RHMQQQALGGS 71

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  107 bits (269), Expect = 6e-28
 Identities = 41/61 (67%), Positives = 50/61 (81%), Gaps = 1/61 (1%)

Query: 697 LMIKNIPNKYTSKMLLAAIDENHKG-TYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFY 755
           +MI+NIPNKYT +MLL  +DE+ KG  YDFLYLPIDFKNKCNVGYAFIN ++P +   FY
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFY 60

Query: 756 E 756
           +
Sbjct: 61  K 61

This subfamily corresponds to the RRM3 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 = 86

>gnl|CDD|240976 cd12532, RRM3_MEI2_fungi, RNA recognition motif 3 in fungal Mei2-like proteins

 Score =  100 bits (251), Expect = 2e-25
 Identities = 39/61 (63%), Positives = 48/61 (78%)

Query: 694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 753
           RTT+M+KNIPNK+T +ML   IDE + GTYDF+YL IDF N CNVGYAF+N + P+ II 
Sbjct: 1   RTTVMLKNIPNKFTQQMLRKYIDETNPGTYDFMYLRIDFNNSCNVGYAFVNFIEPISIIT 60

Query: 754 F 754
           F
Sbjct: 61  F 61

This subgroup corresponds to the RRM3 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 90

>gnl|CDD|240974 cd12530, RRM3_EAR1_like, RNA recognition motif 3 in terminal EAR1-like proteins

 Score =   99 bits (249), Expect = 4e-25
 Identities = 40/76 (52%), Positives = 50/76 (65%), Gaps = 13/76 (17%)

Query: 694 RTTLMIKNIPNKYTSKMLL-----------AAIDENH--KGTYDFLYLPIDFKNKCNVGY 740
           RTTLMIKNIPNKY+ K+LL             I+++     +YDF+YLPIDFKNKCN+GY
Sbjct: 1   RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHIEDSSQPVSSYDFVYLPIDFKNKCNLGY 60

Query: 741 AFINMLSPLHIIPFYE 756
           AF+N  SP     FY+
Sbjct: 61  AFVNFTSPEATWRFYK 76

This subgroup corresponds to the RRM3 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 = 101

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

 Score = 72.2 bits (178), Expect = 9e-16
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 5/73 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL V NL P  + E+LR++F  +G+V+ +R    K   K     F+EF     AE AL++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 334 LNRSDIAGKRIKL 346
           LN  ++ G+ +K+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 71.6 bits (176), Expect = 2e-15
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
           L V NL P  + EDLR++F  +GE++ +R    +    +   F+EF     AE AL++LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 336 RSDIAGKRIKLE 347
             ++ G+++K+ 
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
           L V NL P  + EDL+ +F  +G ++ IR    ET   +   F+EF D   AE AL++LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 336 RSDIAGKRIK 345
             ++ G+ ++
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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 61.9 bits (151), Expect = 4e-12
 Identities = 21/73 (28%), Positives = 44/73 (60%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           TL V N++ +V +E+LR +F  +G+++ +      R    + +YD+RAA  A ++L  ++
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 339 IAGKRIKLEPSRP 351
           + G+++ +  S P
Sbjct: 63  LGGRKLDIHFSIP 75

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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
           TL V N++S + D ELR+LF Q+G+++ +           + +YDIRAA  A+ AL  +P
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRP 62

Query: 254 LRRRKLDI 261
               +L +
Sbjct: 63  FLGGRLKV 70

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|214636 smart00360, RRM, RNA recognition motif

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA 248
           TLFV N+  +  + ELR LF ++G + ++         K +GF  + +     A  A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 249 LQNKPLRRRKLDI 261
           L  K L  R L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 61.0 bits (149), Expect = 8e-12
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 8/78 (10%)

Query: 194 TLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           TL++ N+N  ++  EL+    ALF Q+G   DI    T  K RG   + + D+ +A  A+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL-KMRGQAFVVFKDVESATNAL 59

Query: 247 RALQNKPLRRRKLDIHFS 264
           RALQ  P   + + I ++
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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQ 250
           LFV N+  +  + +LR LF ++G+I ++        K +GF  + +     A  A+ AL 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 251 NKPLRRRKLDIH 262
            K L  RKL + 
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V NL  +V+ EDL+ +FG +GEV        RET   R   F+E      A AA++ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN +D  G+ + +  +RP
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 = 58.8 bits (143), Expect = 6e-11
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALK 332
             L V  L    + ++L  +F  +G V+E+      ET   R   F+ F  V  A+AA++
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 333 SLNRSDIAGKRIKLEPSR 350
            LN  ++ G+ IK+E ++
Sbjct: 62  DLNGKELEGRVIKVEKAK 79

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

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

 Score = 57.7 bits (140), Expect = 1e-10
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE-AALKSLNRS 337
           TL V  L   V+ +DLR  F  +GE++ I   P ++   F+ F    AAE AA +  N+ 
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVP-RQQCAFVTFTTREAAEKAAERLFNKL 61

Query: 338 DIAGKRIKL 346
            I G+R+KL
Sbjct: 62  IINGRRLKL 70

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 55.2 bits (134), Expect = 5e-10
 Identities = 14/56 (25%), Positives = 24/56 (42%)

Query: 209 LRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
           L  LF  +G++  +    K  GF  + +    AA  A++ L       R L + +S
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 55.7 bits (135), Expect = 7e-10
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           V NL P  +  +L   F  YG ++ +   R  P      F+EF D R AE A+++L+   
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPPG---FAFVEFEDPRDAEDAVRALDGRR 60

Query: 339 IAGKRIKLEPSRP 351
           I G R+++E SR 
Sbjct: 61  ICGNRVRVELSRG 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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 55.5 bits (134), Expect = 9e-10
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAARTAMRA 248
           +L+VRN+       +LR LF +YG I  +Y          RGF  + + D+R A  A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 249 LQNKPLRRRKLDIHFS 264
           L       R+++I F+
Sbjct: 62  LDRTRFLGREIEIQFA 77

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNR 336
           L V NL PSV+ EDLR+ F  YG+V+ +R   +K   +   F+EF     AEAALK LN 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 337 SDIAGKRIK 345
             + G+ ++
Sbjct: 61  LVLDGRTLR 69

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

>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 = 54.5 bits (132), Expect = 1e-09
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HK---FIEFYDVRAAEAALKS 333
            L+V N+    + ++LR++F  +G+VK +R  P K    H+   F+EF   + A+ A+++
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 334 LNRSDIAGKRIKLEPS 349
           L  + + G+ + LE +
Sbjct: 61  LKSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           ++ V  L P V+ E+L + F  +G++ E   I+   H     FI+F   +AA  A++S N
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 336 RSDIAGKRIKLE 347
            S +  K + ++
Sbjct: 65  HSMLKNKTMHVQ 76

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQ 250
           LFV N+  +  + +L+ LF ++G I ++        + +GF  + + D   A  A+ AL 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 251 NKPLRRRKL 259
            K L  R+L
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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.9 bits (128), Expect = 4e-09
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 294 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS 349
           L ++F  +G V++I+    K    F+EF    AAE A++ LN     G+ ++++ S
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|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 = 6e-09
 Identities = 26/68 (38%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           T+ V  LDP+V+ ++LR +FG +GE+  ++  P  +   F++F    AAEAA++ L  + 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVK-IPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61

Query: 339 IAGKRIKL 346
           I G RI+L
Sbjct: 62  IGGSRIRL 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 59.1 bits (143), Expect = 6e-09
 Identities = 52/216 (24%), Positives = 92/216 (42%), Gaps = 35/216 (16%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAARTAMRAL 249
           L+V+N++ +V + +LR LF ++G+I +     K      RGF  +++     A  A+  +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSA-AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 250 -------------------QNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSV 289
                              Q +  R  +L   F   +     K   QG  L V NLD +V
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFE--ELQQERKMKAQGVNLYVKNLDDTV 297

Query: 290 SNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           ++E LR++F   GE+   +    E    R   F+ F +   A  A+  ++   + GK + 
Sbjct: 298 TDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLY 357

Query: 346 LEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 381
           +  ++    RR     L  +  Q + R+ Q  +GSP
Sbjct: 358 VALAQRKEQRRA---HLQDQFMQLQPRMRQLPMGSP 390

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

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V N+  +   +DLR++FG YG + ++       T   R   +++F DVR AE AL  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 334 LNRSDIAGKRIKLE 347
           L+R+   G+ I+++
Sbjct: 62  LDRTRFLGREIEIQ 75

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 58.0 bits (140), Expect = 1e-08
 Identities = 45/176 (25%), Positives = 87/176 (49%), Gaps = 19/176 (10%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 243
           E   RT+FV  +     + +L   F + G +R +       + + +G   + +YD+ +  
Sbjct: 86  ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVI 145

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN--QGT------LVVFNLDPSVSNEDLR 295
            A+ AL  + L  R + +  S  + N + K      G       L V NL  +++ ++LR
Sbjct: 146 KAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELR 204

Query: 296 QIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           QIF  +G++++++     ET   +   FI+F+D   A+ AL+ +N  ++AG+ IK+
Sbjct: 205 QIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 260

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

>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal EAR1-like proteins

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 17/59 (28%), Positives = 33/59 (55%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           SR L +  +  ++ +++LR   EQ+G +R +       G V + +YD+R A  A+R ++
Sbjct: 1   SRALLLSGVPPHIPETQLRRDLEQWGAVRAVQMDAMAEGIVTVHFYDLRHAEDALRDIR 59

This subgroup corresponds to the RRM1 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 57.5 bits (139), Expect = 2e-08
 Identities = 47/197 (23%), Positives = 94/197 (47%), Gaps = 15/197 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQ 250
           +FV+N++ +V++  L   F ++G+I +   A     K RG+  + +    +A+ A++ + 
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 308
              L  +++ +   I K       L + T L V NLDPSV+ + LR++F  +GE+     
Sbjct: 151 GMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV 210

Query: 309 ---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI----AGKRIKLEPSRPGGARRNLMLQ 361
               +   R   F+ F     A  A++ +N   I     GK++ +  ++    R   + +
Sbjct: 211 MKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRR 270

Query: 362 LNQELEQDESRILQHQV 378
             +EL+Q+  R ++ Q 
Sbjct: 271 KFEELQQE--RKMKAQG 285

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 334
           L+V NL    +  DL+++F  +G V E+   P K   K     F++F     AE A+K +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEV-TIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 335 NRSDIAGKRI 344
           N   I G+ +
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|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal Mei2-like proteins

 Score = 50.8 bits (122), Expect = 3e-08
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-RGFVMISYYDIRAARTAMRALQ 250
           +R L V  +  +V  S L+ +FE+ GD++ ++      +G V++S++D+R A  A + LQ
Sbjct: 1   TRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFHDLRQAIKAYKDLQ 60

Query: 251 NKPL 254
           +K  
Sbjct: 61  SKRA 64

This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 72

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

 Score = 50.6 bits (122), Expect = 4e-08
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V  L  +V+ + L++IF  YG VK++     RE    R + ++EF     AE A+K +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 335 NRSDIAGKRIKLE 347
           +   I G+ + +E
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRT----------LYTACKHRGFVMISYYDIRAA 242
            TLFV+N+N    +  L+  FE+ G +R+                  G+  + +    AA
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 243 RTAMRALQNKPLRRRKLDIHFS 264
           + A++ LQ   L    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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 9/75 (12%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHK---FIEFYDVRAAEAALKS 333
           V NLD  +  +DLR IF  +GEV+ IR     +    R +    F+ F D  +AE AL+ 
Sbjct: 5   VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ- 63

Query: 334 LNRSDIAGKRIKLEP 348
           LN +++ G++I +  
Sbjct: 64  LNGTELGGRKISVSL 78

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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 50.4 bits (121), Expect = 6e-08
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           T+ V NLDP+ + + L + F   GEVK +R    ET   R + F+EF +  +   ALK L
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR-YAFVEFAEQTSVINALK-L 63

Query: 335 NRSDIAGKRIKLEPSR 350
           N +   G+ +K+  S 
Sbjct: 64  NGAMFGGRPLKVNHSN 79

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

 Score = 49.8 bits (119), Expect = 7e-08
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR----HHKFIEFYDVRAAEAALKSLN 335
           L V NLDP V+ + L+QIF   G V+ ++  P K     ++ F+E++    AE AL++LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 336 RSDIAGKRIKL 346
              I    I++
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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 49.9 bits (120), Expect = 8e-08
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 248
           TLFVRN+  +  D +L   F + G I+  +        K RGF  +++     A+ A+  
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 249 LQNKPLRRRKLDIHFSIPK 267
            +      RK+ + F+  K
Sbjct: 61  KKKTKFGGRKIHVEFAKKK 79

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

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 49.5 bits (119), Expect = 9e-08
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V N+    + E L +IF   G V   R     +T   + + F EF D+  A +A+++LN 
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 337 SDIAGKRIKLEPS 349
            +  G+ ++++ +
Sbjct: 63  YEFNGRALRVDFA 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDIRAART 244
           R ++VRN++  +++ +LR +F ++G++ ++    K        + GF  +++ D  +A  
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 245 AMRALQNKPLRRRKLDI 261
           A+  L    L  RK+ +
Sbjct: 61  AL-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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHK--RHHKFIEFYDVRAAEAALKSLN 335
           L+V NL   +  + LR++F A+G + +  ++ T     R   F+ +     A+ ALK  N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 336 RSDIAGKRIKLEP 348
            S I   +I +E 
Sbjct: 63  NSFIDTSKITVEI 75

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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVK--EIRETPHKRHHKFIEFYDVRAAEAALK----S 333
           L V  L PSV+  DL + F  +G V   EI +       +   + D+R +EA LK    +
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 334 LNRSDIAGKRIKLEPSR 350
           LN +   G  +K+E ++
Sbjct: 62  LNGTKWKGSVLKIEEAK 78

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           T+ V NL  S++N DL +IF  YG+V ++     +ET   +   FI F D   A   +K+
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 334 LNRSDIAGKRIK 345
           LN  ++ G+ +K
Sbjct: 63  LNNKELFGRTLK 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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 19/68 (27%), Positives = 38/68 (55%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
           TL V N++ +V + +L  +F  YG+I+ +      R    I +YD+R+A  A++AL    
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 254 LRRRKLDI 261
           +  +++ +
Sbjct: 63  IAGKRIKL 70

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALK 332
           TL + NL+  +  ++L++    +F  +G V +I   +T   R   F+ F DV +A  AL+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 333 SLNRSDIAGKRIKLEPSR 350
           +L       K ++++ ++
Sbjct: 61  ALQGFPFYDKPMRIQYAK 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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           L V NLD +V+ + L ++F   G +   K IRE      + F+E+YD R+A AAL+++N 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE-HGNDPYAFVEYYDHRSAAAALQTMNG 59

Query: 337 SDIAGKRIK 345
             I G+ IK
Sbjct: 60  RLILGQEIK 68

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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL V N  PS    D+R +F  YGE+  IR  P  R +K     +++F    +A AA+  
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIR-FPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN     G ++ ++ S P
Sbjct: 61  LNGKLGEGYKLVVKISDP 78

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|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 = 48.0 bits (115), Expect = 3e-07
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           T+ V NL   ++ E+L++ F  +G ++E+R    K  + F+ F    AA  A+ ++N + 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-GYAFVRFDTHEAAATAIVAVNGTS 60

Query: 339 IAGKRIK 345
           I G+ +K
Sbjct: 61  INGQTVK 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL  +++ +DLR IF  +GE++ ++     ET   + + FI+F D   A+ AL+ L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 335 NRSDIAGKRIKL 346
           N  ++AG+ IK+
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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           TL + NL+ + +  DLR+ F  +GE+ +  I++      + FI++ D+ +   A++ ++ 
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 337 SDIAGKRIKL 346
             +   R+KL
Sbjct: 64  EYLGNNRVKL 73

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

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

 Score = 47.5 bits (114), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           L+VRN+  +V + +LR  F  YG +   R +    + RGF  + +     A  A++ L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 252 KPLRRRKL 259
             L  R L
Sbjct: 61  LVLDGRTL 68

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

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

 Score = 52.3 bits (124), Expect = 4e-07
 Identities = 32/128 (25%), Positives = 56/128 (43%), Gaps = 5/128 (3%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
             +         TL V NL   V+ EDLR++F  +G VK +     RET   R   F+EF
Sbjct: 105 PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEF 164

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 381
               +AE A++ LN  ++ G+ ++++ ++P    R+ +          +    +  +   
Sbjct: 165 ESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEK 224

Query: 382 ITNSPPGN 389
             N   GN
Sbjct: 225 SDNLYVGN 232

Length = 306

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

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKF--IEFYDVRAAEAALKS 333
           TL V NL    ++E L + F   G +K    +++   K+   F  + F     A+ AL+ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 334 LNRSDIAGKRIKLE 347
             ++   G++I +E
Sbjct: 61  KKKTKFGGRKIHVE 74

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|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 = 47.4 bits (113), Expect = 5e-07
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 279 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           TL V   DP +   ED+ ++F  +G +        ++   F+EF D   A  AL++L+ S
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCD---IRKTFAFVEFEDSEDATKALEALHGS 57

Query: 338 DIAGKRIKLE 347
            I G  + +E
Sbjct: 58  RIDGSVLTVE 67

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|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 = 47.2 bits (113), Expect = 7e-07
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACK----HRGFVMISYYDIRAARTAMRAL 249
            L VRN+       ELR LF  +G ++++    K    HRGF  + +   + A+ AM AL
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 250 QNKPLRRRKLDIHFS 264
           ++  L  R L + ++
Sbjct: 62  KSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
            L       D+ + F  YG ++EI     K    F+EF D R A+ A+  LN  ++ G+R
Sbjct: 6   RLPYRARERDVERFFKGYGRIREIN---LKNGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 344 IKLEPSRP 351
           + +E +R 
Sbjct: 63  VIVEHARG 70

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

 Score = 47.6 bits (114), Expect = 7e-07
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-----RHHKFIEFYDVRAAEAALKS 333
           TL V  L    + E LR++F  YG+++ +R          + + F+E+   R A  A + 
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 334 LNRSDIAGKRI 344
            ++  I G  I
Sbjct: 65  AHKLVIDGSEI 75

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

 Score = 52.1 bits (125), Expect = 8e-07
 Identities = 39/173 (22%), Positives = 80/173 (46%), Gaps = 11/173 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHR--GFVMISYYDIRAARTAMRA 248
           +L+V +++ +V +++L  LF+ +G    +R    +   R  G+  +++ +   A  A+  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           +  K L  + + I +S  + +PS +    G + V NLD SV N+ L   F  +G +   +
Sbjct: 62  MNFKRLGGKPIRIMWS--QRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCK 119

Query: 309 ----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
               E    R + F+ F    +A+AA++ +N   +  K + +        R  
Sbjct: 120 VATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREA 172

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|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 = 8e-07
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL    + +DLR++F  YGEV ++     R T   R   F+ FYD R AE A+ ++
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 335 NRSDIAGKRIK 345
           +  ++ G+ ++
Sbjct: 61  DGKELDGRELR 71

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

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 51.7 bits (124), Expect = 9e-07
 Identities = 40/161 (24%), Positives = 72/161 (44%), Gaps = 14/161 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           PS  + VRN+  +V +++L      +G + +       +   ++ + D  +A+  +    
Sbjct: 1   PSPVVHVRNLPQDVVEADLVEALIPFGPV-SYVMMLPGKRQALVEFEDEESAKACVNFAT 59

Query: 251 NKP--LRRRKLDIHFS----IPKDNPSDKDLNQGTLV----VFNLDPSVSNEDLRQIFGA 300
           + P  +R +    ++S    I +D  SD D      V    V N    ++ + L QIF  
Sbjct: 60  SVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNP 119

Query: 301 YGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDI 339
           YG+V  I  T  K +     +EF  V +A+ A  +LN +DI
Sbjct: 120 YGKVLRI-VTFTKNNVFQALVEFESVNSAQHAKAALNGADI 159

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

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L+V  L   ++ E+LR +F A G ++       R T     + F+++ D   A+ A+ +L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 335 NRSDIAGKRIK 345
           N  +I  KR+K
Sbjct: 63  NGFEIRNKRLK 73

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

 Score = 46.9 bits (111), Expect = 1e-06
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 248
           +LFVRNI  +    +LR  F +YG I  +Y        + RGF  + + D+R A  A+  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 249 LQNKPLRRRKLDIHFS 264
           L  K +  R+++I F+
Sbjct: 62  LDRKWICGRQIEIQFA 77

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

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L VF L    +  DLR++F  YG ++++     ++T   R   F+ F  V  A+ A + L
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 335 NRSDIAGKRIKLEPS 349
           N  +I G+RI+++ S
Sbjct: 62  NGMEIDGRRIRVDYS 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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V +L P V+   L +IF   G V  IR      T     + ++ F +   AE AL +L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 335 NRSDIAGKRIKLEPS 349
           N   I GK I++  S
Sbjct: 62  NFDVIKGKPIRIMWS 76

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 20/70 (28%), Positives = 36/70 (51%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+       EL   FE+YG +R+++ A    GF  + + D R A  A+RAL  + +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 255 RRRKLDIHFS 264
              ++ +  S
Sbjct: 62  CGNRVRVELS 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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 49.9 bits (118), Expect = 2e-06
 Identities = 40/188 (21%), Positives = 70/188 (37%), Gaps = 26/188 (13%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 243
           +  + TLFV N+  +V + +LR LF+++G ++ +         K RGF  + +    +A 
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNP--------------------SDKDLNQGTLVVF 283
            A+  L  K L  R L +  + P   P                    +        L V 
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
           NL    + E+L  +F + G++      P K   K  +       EA+  +L  +    K+
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSKD-GKIPKSRSFVGNEASKDALESNSRGNKK 290

Query: 344 IKLEPSRP 351
             L     
Sbjct: 291 KILGRGPR 298

Length = 306

>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 = 26/74 (35%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V N+     +EDLR+ FG YG + ++       T   R   +++F DVR AE AL +
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 334 LNRSDIAGKRIKLE 347
           L+R  I G++I+++
Sbjct: 62  LDRKWICGRQIEIQ 75

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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-----RHHKFIEFYDVRAAEAALK 332
             ++V NL    + +D+R +F +YG++K +R  P K     R   F+EF   + A  A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 333 SLNRSDIAGKRIKLE 347
           +L  + + G+R+ L+
Sbjct: 60  ALKDTHLLGRRLVLQ 74

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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 46.5 bits (110), Expect = 2e-06
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V N+  +   EDLR+ FG YG + ++       T   R   +I+F DVR AE AL +
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 334 LNRSDIAGKRIKLE 347
           LNR  + G++I+++
Sbjct: 62  LNRKWVCGRQIEIQ 75

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|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 = 45.8 bits (109), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLN 335
           T+ V  +D S+S +DL++ F   GEV  +R    ++H     F+EF D  +A +AL +L+
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL-NLS 60

Query: 336 RSDIAGKRIKLEPSR 350
            + + G  +++ PS+
Sbjct: 61  GTLLGGHPLRVSPSK 75

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

 Score = 51.2 bits (122), Expect = 2e-06
 Identities = 38/169 (22%), Positives = 87/169 (51%), Gaps = 17/169 (10%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I+  + +  +R  F+ +G I+++  +      KH+GF  + Y    AA+ A+  +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 250 QNKPLRRRKLDIHF--SIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
             + L  R + +    ++P+  P    + +       + V ++ P +S  D++ +F A+G
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229

Query: 303 EVK--EIRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           E+   ++   P  R HK   FIE+ ++++   A+ S+N  D+ G+ +++
Sbjct: 230 EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

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

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 5/80 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH-----HKFIEFYDVRAAEAALKS 333
            L++  L  ++++E+ R +F A G VK  +    KR        F+++     A+ A+++
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 334 LNRSDIAGKRIKLEPSRPGG 353
           LN   +  KRIK+  +RPGG
Sbjct: 62  LNGLQLQNKRIKVAYARPGG 81

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

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

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           T+ V NL      +DLR++F  +G +  +     +ET   R   F+ F+    AE A++ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 334 LNR 336
           LN 
Sbjct: 61  LNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 9/75 (12%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGE---VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           L V NL  S + E LR++F  YGE   VK+I++      + F+ F +   A  A++ +N 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD------YAFVHFEERDDAVKAMEEMNG 57

Query: 337 SDIAGKRIKLEPSRP 351
            ++ G  I++  ++P
Sbjct: 58  KELEGSPIEVSLAKP 72

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

>gnl|CDD|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 = 45.4 bits (108), Expect = 2e-06
 Identities = 20/76 (26%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           S TL++ +++  V + +L+ LFE+YG+I+++      RG   +     + A  A++ L+N
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI-DMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 252 KPLRRRKLDIHFSIPK 267
             L  +K+ + ++  K
Sbjct: 61  VKLAGKKIKVAWAPNK 76

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|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 = 45.6 bits (109), Expect = 2e-06
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSD 338
           + + NL   V+ + L Q+F  YG V++I         +  ++F  V +AE A K+LN  +
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 339 I 339
           I
Sbjct: 64  I 64

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

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

 Score = 45.3 bits (107), Expect = 3e-06
 Identities = 22/69 (31%), Positives = 37/69 (53%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            LVV NL  S S + L+++F     ++  +     + + F+EF     A+ AL S N ++
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 339 IAGKRIKLE 347
           I G+ I+LE
Sbjct: 63  IEGRSIRLE 71

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|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 = 45.2 bits (108), Expect = 3e-06
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRAL 249
           LFV  +     + ++RALFE+YG+I  +         + +G   + +     A+ A+ AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 250 QNK 252
             K
Sbjct: 62  HGK 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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 44.9 bits (106), Expect = 4e-06
 Identities = 23/62 (37%), Positives = 38/62 (61%), Gaps = 3/62 (4%)

Query: 289 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
           V  +D+++ FG YG++ EI     K  + F+EF D R A+ A+  LN  D+ G+R+ +E 
Sbjct: 11  VREKDIQRFFGGYGKLLEI---DLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEH 67

Query: 349 SR 350
           +R
Sbjct: 68  AR 69

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

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           TL+V +L P +S +D   +   +G   V+ +      ++  F  F + +AA  AL  L++
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60

Query: 337 SDIAGKRIKLE 347
             I GKR+ +E
Sbjct: 61  LKILGKRLVVE 71

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|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 = 44.9 bits (107), Expect = 5e-06
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA 248
            LFV  +++   + EL ALF ++G +  +         + RGF  +++  +  A  A+R 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 249 LQNKPLRRRKLDI 261
           L  K L  R + +
Sbjct: 63  LNGKELEGRVIKV 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 9/61 (14%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQN 251
           LFV N+       ELRALFE+YG +    T C   K+ GFV +   +   A  A++AL  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV----TECDVVKNYGFVHME--EEEDAEDAIKALNG 55

Query: 252 K 252
            
Sbjct: 56  Y 56

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH--RGFVMISYYDIRAARTAMRAL 249
           +R L+VRN+   +   EL  LF +YG IR +        RG   + Y DI  A+ A   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

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|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 45.4 bits (108), Expect = 5e-06
 Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 13/105 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYD-----VRAAE 328
            +VV+   PS S + ++  F ++GE+ EIR      T        I++Y       RAA+
Sbjct: 4   EIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAK 63

Query: 329 AALKSLNR---SDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDE 370
           AALK++ +     I G   K+E +        +  +L ++  +  
Sbjct: 64  AALKAVRKAQDCRIGGAEFKVELNPNERKLEKIKDKLIKQNRKKS 108

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

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

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 248
           L V N+       +LR +FE+YG++      R  YT  + RGF  + +YD R A  AM A
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTR-ESRGFAFVRFYDKRDAEDAMDA 59

Query: 249 LQNKPLRRRKL 259
           +  K L  R+L
Sbjct: 60  MDGKELDGREL 70

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           L+V  +      +EL   F+++G IR +      R +  I Y  I AA+ A  AL+  PL
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI-DYDPGRNYAYIEYESIEAAQAAKEALRGFPL 59

Query: 255 RR--RKLDIHFS 264
               R+L + F+
Sbjct: 60  GGPGRRLRVDFA 71

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 44.9 bits (107), Expect = 6e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMR 247
           +TLFV  +N +  +S+LR  FE+YG I+ +         K RG+  I +   R  + A +
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 248 ALQNKPL--RRRKLDI 261
               K +  RR  +D+
Sbjct: 62  YADGKKIDGRRVLVDV 77

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

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

 Score = 44.6 bits (106), Expect = 6e-06
 Identities = 18/69 (26%), Positives = 43/69 (62%), Gaps = 5/69 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRH--HKFIEFYDVRAAEAALKSLNR 336
           V ++ P +S +D++ +F A+G++K      +    +H  + FIE+ + ++A+ A+ S+N 
Sbjct: 5   VASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNL 64

Query: 337 SDIAGKRIK 345
            D+ G++++
Sbjct: 65  FDLGGQQLR 73

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

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

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRA-ARTAMRALQNKP 253
           LFV N+ +++ + E + LF +YG++  ++   K +GF  I   D R  A  A   L    
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRTNAEKAKAELDGIM 61

Query: 254 LRRRKLDIHF 263
            + R+L + F
Sbjct: 62  RKGRQLRVRF 71

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

 Score = 44.2 bits (105), Expect = 8e-06
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--------RHHKFIEFYDVRAAEAA 330
            L + NLD  ++   L ++F  YG++K+     HK        R + F+ F     AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 331 LKSLNRSDIAGKRIKLEPSR 350
           LKSLN     GK++ +  + 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 44.1 bits (105), Expect = 8e-06
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIR-----ETPHKRHHKFIEFYDVRAAEAAL 331
           TL++  LD   + ED+ Q   A     +K++R      T   R   F+EF  +  A   +
Sbjct: 4   TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63

Query: 332 KSLNRSD---IAGKRI 344
            +LN  D   I G+ +
Sbjct: 64  DALNNLDPFVIDGRVV 79

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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 248
           +LFVRN+       +LR  F +YG I  +Y        + RGF  I + D+R A  A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 249 LQNKPLRRRKLDIHFS 264
           L  K +  R+++I F+
Sbjct: 62  LNRKWVCGRQIEIQFA 77

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

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
           + L+VRN+  +  + +LR LF +YG++  +    K + +  + + +   A  AM  +  K
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK---KIKDYAFVHFEERDDAVKAMEEMNGK 58

Query: 253 PLRRRKLDIHFSIP 266
            L    +++  + P
Sbjct: 59  ELEGSPIEVSLAKP 72

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

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 285 LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI 344
           L+P+   +D+ + F  YG    IR+   KR   F+EF D R A+ A+  L+  ++  +R+
Sbjct: 7   LNPAAREKDVERFFKGYGR---IRDIDLKRGFGFVEFDDPRDADDAVYELDGKELCNERV 63

Query: 345 KLEPSR 350
            +E +R
Sbjct: 64  TIEHAR 69

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK----RHHKFIEFYDVRAAEAALKSL 334
            L V  L  SV+ E+L ++F  +G VK +R   ++    +   ++E+ +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 335 NRSDIAGKRIKLEPSRPG 352
           + ++I  K I +  S P 
Sbjct: 64  DGTEIKEKTISVAISNPP 81

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

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

 Score = 43.7 bits (104), Expect = 1e-05
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 14/84 (16%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIR----TLYTACKH---RGFVMISYYDIRAARTA 245
           RT+F+RN+  +  + EL+ LF Q+G+++           H     FV   +    +A+  
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFV--KFKTKESAQKC 58

Query: 246 MRALQNKP-----LRRRKLDIHFS 264
           + A  N       L  R+L +  +
Sbjct: 59  LEAADNAEDSGLSLDGRRLIVTLA 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|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 = 43.4 bits (103), Expect = 1e-05
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL  + + E+LR++F A+GE+ E+     +ET   +   F+ F     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 335 NRSDIAGK 342
           + S   G+
Sbjct: 62  DGSIFQGR 69

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 194 TLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           T+++ N+N  V+  EL+    A+F Q+G   DI  L T  K RG   + + DI +A  A+
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKT-LKMRGQAFVVFKDISSATNAL 59

Query: 247 RALQNKPLRRRKLDIHFS 264
           R++Q  P   + + I +S
Sbjct: 60  RSMQGFPFYDKPMRIAYS 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKF-----IEFYDVRAAEAALKSL 334
           L V NL      + + + FG YGE+  +R        +      +EF    AA+AAL +L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 335 NRSDIAGKRIKLE 347
             +D+ G+ ++L+
Sbjct: 61  GGTDLLGRPVRLD 73

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

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

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 4/61 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK-HRGFVMISYYDIRAARTAMRALQN 251
           TL + N++  V    LR++F+ YGD++ L  T CK  + FV   ++D+R A  A+RA+  
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFV--EFFDVRDAAKALRAMNG 60

Query: 252 K 252
           K
Sbjct: 61  K 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|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 = 43.0 bits (102), Expect = 2e-05
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 196 FVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQ 250
           FV NI  +  + +L  +F + G + +          K +G+    + DI  A +A+R L 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 251 NKPLRRRKLDIHFS 264
                 R L + F+
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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 9/71 (12%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           L V NL  + ++E+LR +F  YG V E   +      +++ F+   +   AE A+K+LN 
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV------KNYGFVHMEEEEDAEDAIKALNG 55

Query: 337 SDIAGKRIKLE 347
            +  GKRI +E
Sbjct: 56  YEFMGKRINVE 66

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|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 = 42.7 bits (101), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 249
           LFVRN+     + ELR LFE +G+I  ++        + +GF  +S+     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 250 QNKPLRRRKLDI 261
                + R L +
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|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 = 42.6 bits (101), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L +++L    +++DL Q+F  +G V   +      T   +   F+ + +  +A+AA+K++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 335 NRSDIAGKRIKLE 347
           N   + GKR+K++
Sbjct: 61  NGFQVGGKRLKVQ 73

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|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL 334
           +L V N+   V+   LR++F  YG+V+ ++          + FYD+R A+ A++ L
Sbjct: 3   SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVREL 58

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMR 247
           +RTLF+ N+      S+LR  FE++G+I  +    K +G    +  I Y DI +   AMR
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEI--IDIDIKKQGGNPAYAFIQYADIASVVKAMR 59

Query: 248 ALQNKPLRRRKL 259
            +  + L   ++
Sbjct: 60  KMDGEYLGNNRV 71

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

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

 Score = 43.0 bits (102), Expect = 3e-05
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V  L+   +   LR+ F  YG +K IR     +T   R + FIEF   R  +AA K 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 334 LNRSDIAGKRIKLEPSR 350
            +   I G+R+ ++  R
Sbjct: 63  ADGKKIDGRRVLVDVER 79

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

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

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 12/73 (16%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC--------KHRGFVMISYYDIRAARTAM 246
           ++V+N+  +++D +L+ LF +YG I    T+         K +GF  +++ +  AA+ A+
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKI----TSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59

Query: 247 RALQNKPLRRRKL 259
             L  K +  +KL
Sbjct: 60  EELNGKEVNGKKL 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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 192 SRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRAL 249
           SR +FV N+N++ V   +L  +F +YG I         H+G+  + + +   AR A+   
Sbjct: 1   SR-VFVGNLNTDKVSKEDLEEIFSKYGKI----LGISLHKGYGFVQFDNEEDARAAVAGE 55

Query: 250 QNKPLRRRKLDI 261
             + +  +KLDI
Sbjct: 56  NGREIAGQKLDI 67

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

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHK---FIEFYDVRAAEAALKSL 334
           T+ V NLD SV  ++LR++F   GE+ ++R    +K   K   ++EF +  + + ALK L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK-L 59

Query: 335 NRSDIAGK 342
           +R  I G+
Sbjct: 60  DRELIKGR 67

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L N PL
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIH-KDKGFGFIRLETRTLAEIAKAELDNMPL 62

Query: 255 RRRKLDIHF 263
           R ++L + F
Sbjct: 63  RGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL-YTACKHRGFVMISYYDIRAARTAMRALQN 251
            TL+V  +   V + +LR  F Q+G+IR++     +   FV  ++    AA  A   L N
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFV--TFTTREAAEKAAERLFN 59

Query: 252 K 252
           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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK--EIRETPHKRHHK---FIEFYDVRAAEAALKS 333
           T+ V  L  + ++E L+ +F  YG V    +    H    K   FIEF     A+ A K 
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 334 LNRSD 338
           LN   
Sbjct: 61  LNNPP 65

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

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK---FIEFYDVRAAEAALKSL 334
           L V  L   V  + L   F  +G++K+I+       + H+   F+EF +   A AA+ ++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 335 NRSDIAGKRIK 345
           N S++ G+ I+
Sbjct: 61  NESELFGRTIR 71

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

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           TL V NL   V+   + Q+F   G  K    I +T     + F+EF++ R A A+L ++N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 336 RSDIAGKRIKL 346
              I GK +K+
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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--------ETPHKRHHKFIEFYDVRAAEAAL 331
           L V NL+P V+ E L Q FG +G +  ++        E    R+  F+ F +   AE AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 332 KSLNRSDIAGKRIKL 346
             L+  D+ G  +KL
Sbjct: 64  DELDGKDVMGYELKL 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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAM 246
           L+V  +   V++  L A F  +GDI+ +     Y   KHRGF  + + +   A  A+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

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

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 42.3 bits (99), Expect = 5e-05
 Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F ++G I  +  +   K RG   + + ++ +A  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 245 AMRALQNKPLRRRKLDIHFS 264
           A+R++Q  P   + + I ++
Sbjct: 62  ALRSMQGFPFYDKPMRIQYA 81

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

 Score = 42.0 bits (99), Expect = 5e-05
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHKRHHK--FIEFYDVRAAEAALKSL 334
           TL V NL+ +++ E+LR+ F  YG V++  I+  P  + +   F++F ++  A  A  ++
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 335 NRSDIAGKRIKL 346
           +   I   +IK+
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|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins related to the La autoantigen

 Score = 42.1 bits (99), Expect = 5e-05
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 20/77 (25%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----------ETPHKRH----------HKF 318
           T+V  NL    S E+L +IFG  G VK +R           T  K            H  
Sbjct: 2   TVVAENLPEDHSIENLEEIFGTVGSVKNVRICDPGRVGSGSTASKAKKPDTLVSNKLHAL 61

Query: 319 IEFYDVRAAEAALKSLN 335
           +E+  V AAE A+  L+
Sbjct: 62  VEYETVEAAEKAVTELS 78

This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 41.8 bits (99), Expect = 6e-05
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           L V NL   +S+E+L  +FG YG +++IR   T   R   F+ + D+  A+ A   L+  
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64

Query: 338 DIAGK 342
           ++A +
Sbjct: 65  NVANR 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|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 280 LVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V NL+   V+ + L  +FG YG+V  ++   +K+    I+  D + A+ AL  LN   
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61

Query: 339 IAGKRIKLEPSR 350
           + GK++++  S+
Sbjct: 62  LHGKKLRVTLSK 73

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|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 = 41.6 bits (98), Expect = 7e-05
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           TL + +L   V+ EDL+ +F  YGE++ I   P  R   ++     + A  AL+ L    
Sbjct: 4   TLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-PRGCAYVCMETRQDAHRALQKLRNVK 62

Query: 339 IAGKRIKL 346
           +AGK+IK+
Sbjct: 63  LAGKKIKV 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 10/81 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAALKS 333
           T+ + NL    + E+L+++F  +GEVK  R    K   H K   F++F    +A+  L++
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 334 LNRSD-----IAGKRIKLEPS 349
            + ++     + G+R+ +  +
Sbjct: 62  ADNAEDSGLSLDGRRLIVTLA 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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 7/64 (10%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQY-G--DIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           P++ LF++N+        L  LF Q+ G  ++R +      RG   + +     A  A++
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV----PRRGIAFVEFETEEQATVALQ 56

Query: 248 ALQN 251
           ALQ 
Sbjct: 57  ALQG 60

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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEI--RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V  L  +    DL+Q+F  YG+V   K +    +P  R   F+    V  A   ++ L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 335 NRSDIAGKRIKLE 347
           +R+++ G+ I +E
Sbjct: 62  HRTELHGRVISVE 74

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 41.4 bits (98), Expect = 8e-05
 Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 9/66 (13%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHK--------FIEFYDVRAAEA 329
            L V NL   V+ EDL  IFG + +   E +     R           F+ F     A  
Sbjct: 3   RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 330 ALKSLN 335
           AL  +N
Sbjct: 63  ALNLVN 68

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

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 249
           LFVRN+  + ++ +L  LF ++G++  ++ A      K +GF  + + D   A  A + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 250 QNKPLRRRKLDI 261
             K  + R + I
Sbjct: 65  DGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|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 = 22/70 (31%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAEAALKSLNRS 337
           V NL   +   D+  +F  YG +K I      R       F+EF D R AE A++  +  
Sbjct: 4   VGNLPGDIRERDIEDLFYKYGPIKAI--DLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGY 61

Query: 338 DIAGKRIKLE 347
           D  G R+++E
Sbjct: 62  DFDGYRLRVE 71

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|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 = 40.7 bits (96), Expect = 1e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQ 250
           T+FV  ++  V + ELR+LF  +G+I  +Y      K  GFV   +    AA  A++ LQ
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEI--VYVKIPPGKGCGFV--QFVHRAAAEAAIQQLQ 58

Query: 251 NKPL 254
              +
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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN--RS 337
           L V  L P  S  +L + F  +G ++ I   P +  + +IE+  + AA+AA ++L     
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRN-YAYIEYESIEAAQAAKEALRGFPL 59

Query: 338 DIAGKRIKLE 347
              G+R++++
Sbjct: 60  GGPGRRLRVD 69

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

 Score = 40.6 bits (96), Expect = 1e-04
 Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 4/65 (6%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           NL   + +E L+++FG YG++   +    +    +   F+ F +  AA+ A++ LN  ++
Sbjct: 8   NLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEV 67

Query: 340 AGKRI 344
            GK++
Sbjct: 68  NGKKL 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V NL  SV +E L+  F  +G V        RET   R   +++F     A+ A+++
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 334 LNRSDIAGKRIKLEPS 349
           ++  ++ G+ I ++ S
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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK--EI---RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  L+P  ++EDL  IF  +G++K  E+   ++T     + FIEF      E A   
Sbjct: 5   VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

Query: 334 LNRSDIAGKRIK 345
           ++   I  +RI 
Sbjct: 65  MDNVLIDDRRIH 76

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

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRA 248
           TLFVRN+  +V   +L   F     I+     T     + RG+  +++  +  A+ A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 249 LQNKPL--RRRKLDI 261
           L+NK L  R  +LDI
Sbjct: 61  LKNKKLHGRILRLDI 75

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

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

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V NL  SV+ EDL   F     +K        ET   R + F+ F  +  A+ AL  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 334 LNRSDIAGKRIKLEPSRP 351
           L    + G+ ++L+ +  
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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 25/80 (31%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 192 SRTLFVRNINSNVED-SELRALFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTAM 246
           SR LFV  +     D S LR LF Q G       A       RGF  + Y     A  A 
Sbjct: 2   SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 247 RALQNKPLRRRKLDIHFSIP 266
           +AL    L+   + + F  P
Sbjct: 62  QALNGHSLQGSPIRVSFGNP 81

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

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK----RHHKFIEFYDVRAAEAALKSLN 335
           ++V NL   V+ + LR+ F + GEV +++    +    R   F+ F     A+ A+K  N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 336 RSDIAGKRIKLE 347
           ++ I   +I +E
Sbjct: 63  KTFIDTSKISVE 74

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

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

 Score = 40.9 bits (95), Expect = 1e-04
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           TL V NL   V+   + Q+F   G  K    I E      + F+EFY+ R A AAL ++N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 336 RSDIAGKRIKL 346
              I GK +K+
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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 292 EDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           ++L++ F  +G VK +R     +T + +H+ FI+F +   A  A KS+N   + GK ++
Sbjct: 14  KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHK------FIEFYDVRAAE 328
           TL V NL+   + E L++ F   G V+ +    ++ P            F+EF    AA+
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 329 AALKSLNRSDIAGKRIKLEPS 349
            ALK L  + + G  ++L+ S
Sbjct: 62  KALKRLQGTVLDGHALELKLS 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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTAMRALQ 250
           + V+N+       ++R LF  YG ++++    K     RGF  + +   + A  AM AL+
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 251 NKPLRRRKLDIHFS 264
           +  L  R+L + ++
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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
            L + NL    + E L  +F  +   KE+R  P +R   F+EF     A  AL++L 
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQ 59

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

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALK 332
           G L V NL  S   +DL ++F  +GE+ E+     K+  K     ++ F D   A  A K
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 333 SLNRSDIAGKRIKLEP 348
            L+     G+ I + P
Sbjct: 63  ELDGKVFQGRLIHILP 78

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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           SR +++ NI+ ++ + +LR  F QYG+I ++    + +    +++ +I  A  A+  +++
Sbjct: 3   SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNY-LREKNCAFVNFTNISNAIKAIDGVKS 61

Query: 252 KPLRRRKLDIHF 263
            PL  +K  I +
Sbjct: 62  HPL-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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L + NL   V+  DLRQ+F  +   V  +     K  + F++  D   A+ A++ LN   
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSV--LVKKGGYAFVDCPDQSWADKAIEKLNGKI 58

Query: 339 IAGKRIKLEPSRPG 352
           + GK I++E S P 
Sbjct: 59  LQGKVIEVEHSVPK 72

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

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 5/81 (6%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 330
           ++  L+V  L  +++ E+L+ +FG+ GE+   K +R+  T     + F+ + D + AE A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 331 LKSLNRSDIAGKRIKLEPSRP 351
           + +LN   +  K IK+  +RP
Sbjct: 63  INTLNGLRLQTKTIKVSYARP 83

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

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           T+       S    D++++F   G V+++   +   + H FI F ++ AA+ A+++LN +
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 338 DIAGKRIKLE 347
            + G  IK++
Sbjct: 61  SVDGNCIKVQ 70

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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 8/80 (10%)

Query: 192 SRTLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAART 244
           + T+++ N+N  ++  EL+    ALF Q+G   DI  L T  K RG   + + ++ +A  
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTM-KMRGQAFVIFKELSSATN 59

Query: 245 AMRALQNKPLRRRKLDIHFS 264
           A+R LQ  P   + + I ++
Sbjct: 60  ALRQLQGFPFYGKPMRIQYA 79

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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 42/72 (58%), Gaps = 3/72 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L V NL  +V+ E L + FG +G+++ +++    + + FI F +   A  A++ +N  ++
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 340 AGKRIKLEPSRP 351
            G+ I++  ++P
Sbjct: 61  EGENIEIVFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFV N+ +++ + E + LF +YG+   ++   K +GF  I       A  A   L + P+
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFIN-KGKGFGFIKLESRALAEIAKAELDDTPM 62

Query: 255 RRRKLDIHF 263
           R R+L + F
Sbjct: 63  RGRQLRVRF 71

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+ +N   +EL   F  YG +R+++ A    GF  + + D R A  A+R L  + L
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           T+ V NL   +   ++  +F  YG + +I  +  P    + FIEF D R AE A++  + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 337 SDIAGKRIKLE 347
            D  G+R+++E
Sbjct: 61  YDFDGQRLRVE 71

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

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           + V  +      ED+   F  +GE+K +     R T   + +  IE+   + A+AA++ L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 335 NRSDIAGKRIK 345
           N  ++ G+ I 
Sbjct: 69  NGKELLGQTIS 79

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|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 280 LVVFNLDPSVSNED-LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V+ LD    N D L  +F  YG V  I+    K     ++  D +AAE A++ LN   
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVV 61

Query: 339 IAGKRIKLEP 348
           + G+++++  
Sbjct: 62  LFGQKLEVNF 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

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

 Score = 39.4 bits (93), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 5/62 (8%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRA 248
           T+ V N++ + ++ +LR LF  +G I  +Y A      + RGF  ++++    A  A+  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 249 LQ 250
           L 
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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 43.1 bits (101), Expect = 4e-04
 Identities = 48/186 (25%), Positives = 82/186 (44%), Gaps = 20/186 (10%)

Query: 160 ISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI 219
           +++ AS N L      N  G+   +     +    L V  +  ++ D EL ALF   G I
Sbjct: 81  MANMASTNSL------NSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPI 134

Query: 220 RTL-----YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD 274
            T      Y      G+  + +     ++ A++ L    +R ++L + ++ P    S KD
Sbjct: 135 NTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP-GGESIKD 193

Query: 275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV--KEI---RETPHKRHHKFIEFYDVRAAEA 329
            N   L V NL  +++++ L  IFG YG++  K I   + T   R   F+ F     A+ 
Sbjct: 194 TN---LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQE 250

Query: 330 ALKSLN 335
           A+ +LN
Sbjct: 251 AISALN 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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
            L V NL   V+ EDL ++FG  GEVK+++   + R  +      + F     AE A+K 
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVK-INYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 334 LNRSDIAGKRIKLE 347
            N   + G+ +++E
Sbjct: 61  FNGVLLDGQPMQVE 74

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|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 = 39.7 bits (93), Expect = 4e-04
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRGFVMISYYDIRA 241
            +  +  LFV  I  N+E+ +LR LFEQ+G I  L      YT   H+G   ++Y    +
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTG-MHKGCAFLTYCARES 59

Query: 242 ARTAMRALQNK 252
           A  A  AL  +
Sbjct: 60  ALKAQSALHEQ 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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 288 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            VS EDL +IF  YGE+ +I     K  + F++F    +   A+       I G+++ LE
Sbjct: 11  RVSKEDLFRIFSTYGELAQIV---LKNAYGFVQFDSPESCANAINCEQGKMIRGRKLHLE 67

Query: 348 PSRP 351
            S+P
Sbjct: 68  VSKP 71

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 10/67 (14%)

Query: 282 VFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNRS 337
           V NL+   VS EDL +IF  YG++  I        HK   F++F +   A AA+   N  
Sbjct: 5   VGNLNTDKVSKEDLEEIFSKYGKILGI------SLHKGYGFVQFDNEEDARAAVAGENGR 58

Query: 338 DIAGKRI 344
           +IAG+++
Sbjct: 59  EIAGQKL 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 24/72 (33%), Positives = 30/72 (41%), Gaps = 12/72 (16%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMR 247
           LFV N++    + ELRA F + G IR +          CK   FV     D      A  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFV-----DFEEIEFATN 55

Query: 248 ALQNKPLRRRKL 259
           AL+ K L  R L
Sbjct: 56  ALKGKHLNGRAL 67

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|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

 Score = 39.6 bits (92), Expect = 5e-04
 Identities = 25/92 (27%), Positives = 52/92 (56%), Gaps = 7/92 (7%)

Query: 280 LVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  LN   
Sbjct: 2   LLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQK 61

Query: 339 IAGKRIKLEPSRPGGARRNLMLQLNQELEQDE 370
           + GK +++  S      ++  +QL +E ++D+
Sbjct: 62  LHGKPLRITLS------KHQTVQLPREGQEDQ 87

This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. . Length = 93

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.5 bits (92), Expect = 5e-04
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 280 LVVFNLDPSVSN-EDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           L++ NL  S+     L++IFG YG+V+E    P KR  K     F+     + AE AL++
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREA-TIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61

Query: 334 LNRSDIAGKRIKLE 347
            N  +I G+ + ++
Sbjct: 62  TNGLEIDGRPVAVD 75

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|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 = 39.5 bits (93), Expect = 5e-04
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 8/52 (15%)

Query: 292 EDLRQIFGAYGEVKEIR-ETPHKRHHK-------FIEFYDVRAAEAALKSLN 335
           ED+++  G YG+V  +    P             F+EF DV  A+ A  +L 
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALA 77

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

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 9/77 (11%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGD------IRTLYT-ACKHRGFVMISYYDIRAARTAM 246
            +FV N+  + ++S L  LF  +G       IR L T  CK  GFV ++ Y+   A +A+
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE--EAYSAI 60

Query: 247 RALQNKPLRRRKLDIHF 263
            +L    L  R L + F
Sbjct: 61  ASLNGYRLGGRVLQVSF 77

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

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V N+  + ++++LR +F  +G V E  +    + + F+       A AA+++LN  ++ G
Sbjct: 5   VGNVSATCTSDELRGLFEEFGRVVECDKV---KDYAFVHMEREEEALAAIEALNGKEVKG 61

Query: 342 KRIKLE 347
           +RI +E
Sbjct: 62  RRINVE 67

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|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator of differentiation 1 (Rod1)

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 280 LVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V NL+P +++   L  +FG YG+V  ++   +K+ +  ++  D   A+ A+  LN   
Sbjct: 3   LLVSNLNPDAITPHGLFILFGVYGDVHRVKIMFNKKENALVQMADATQAQLAMSHLNGQR 62

Query: 339 IAGKRIKLEPSR 350
           + GK I+   S+
Sbjct: 63  LYGKVIRATLSK 74

This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. . Length = 76

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

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRA-AEAALKSLNRSD 338
           L V NL   ++ E+ +++F  YGEV E+     ++   FI   D R  AE A   L+   
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRTNAEKAKAELDGIM 61

Query: 339 IAGKRIK 345
             G++++
Sbjct: 62  RKGRQLR 68

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

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

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKF--IEFYDVRAAEAALKSL 334
           TL V NL  S   +DL + F   GEV ++R  +    R   F  +EF     A+ AL+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-K 59

Query: 335 NRSDIAGKRIKLE 347
           +  ++ G+ I+++
Sbjct: 60  SGEELLGREIRVD 72

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|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 340
            LD SV+ + L + F  YG V  +   R    +R    + F  V AA+AA+  +    + 
Sbjct: 14  GLDESVTEQYLTRHFSRYGPVVHVVIDR----QRGQALVFFDKVEAAQAAVNEMKGRKLG 69

Query: 341 GKRIKL 346
           G+++++
Sbjct: 70  GRKLQV 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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 39.2 bits (92), Expect = 7e-04
 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTA 245
           P  TLFV  ++    +  LR +F +YGDIR L           +G+  + Y   R A  A
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 246 MRALQN 251
            R    
Sbjct: 62  YRDAHK 67

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|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 38.4 bits (89), Expect = 7e-04
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNK 252
           +F+ N+N+  V+ S++ A+F +YG I      C  H+GF  + Y + R AR A+     +
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKI----VGCSVHKGFAFVQYVNERNARAAVAGEDGR 59

Query: 253 PLRRRKLDIHFS 264
            +  + LDI+ +
Sbjct: 60  MIAGQVLDINLA 71

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

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V +L P +  E LR  F  +GE+ + R     +T   + + F+ F     AE A++S+N 
Sbjct: 4   VGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63

Query: 337 SDIAGKRIK 345
             + G+ I+
Sbjct: 64  QWLGGRAIR 72

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           + V N+D   S E+LR +F AYG V         R   F+      AA+ A++ LN  ++
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM---RQFAFVHLRGEAAADRAIEELNGREL 59

Query: 340 AGKRIKLEPS 349
            G+++ +E S
Sbjct: 60  HGRKLVVEHS 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|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           T+ +FN+  +V+ E ++  F   G +V++I   P       +EF     A  A  SLN S
Sbjct: 2   TIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDH-EGALVEFESPSDAGKASLSLNGS 60

Query: 338 DIAGKRIKL 346
              GK IK+
Sbjct: 61  QFGGKTIKI 69

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|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 = 7e-04
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDI 339
           V NL P +  +D+  +F  YG +++I +  ++R     F+EF D R AE A+   +  D 
Sbjct: 4   VGNLPPDIRTKDIEDLFYKYGAIRDI-DLKNRRGPPFAFVEFEDPRDAEDAVYGRDGYDY 62

Query: 340 AGKRIKLEPSR 350
            G R+++E  R
Sbjct: 63  DGYRLRVEFPR 73

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

 Score = 38.6 bits (90), Expect = 7e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIR--ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L+V  L  +++ +++R +F + GE+   K IR   T     + F+ + D   AE A+ +L
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 335 NRSDIAGKRIK 345
           N   +  K IK
Sbjct: 64  NGLRLQNKTIK 74

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

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V N+D   + E+L++ F + G +  I     + T   +   +IEF D  + E AL  LN 
Sbjct: 4   VGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNE 62

Query: 337 SDIAGKRIK 345
           S+  G++IK
Sbjct: 63  SEFRGRQIK 71

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|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.7 bits (91), Expect = 7e-04
 Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSL 334
           TL V NL P+ + E+LRQ+F      + ++   H +      F+EF DV  A  AL SL
Sbjct: 4   TLFVANLGPNTTEEELRQLFSRQPGFRRLKM--HNKGGGPVCFVEFEDVSFATQALNSL 60

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

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMR 247
           +RTLFV N+   + + ELR  FE+YG +  +      RG    +  + + ++  A  A  
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 248 ALQNKPLRRRKLDI 261
           A+  + + R ++ I
Sbjct: 62  AMSGQYIGRNQIKI 75

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

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 42.7 bits (100), Expect = 8e-04
 Identities = 33/134 (24%), Positives = 63/134 (47%), Gaps = 16/134 (11%)

Query: 227 KHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQGTLVVF- 283
           K+RGF  + Y   RAA  A R L    ++     + + ++ P++   D+D+     +++ 
Sbjct: 180 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEV-DEDVMAKVKILYV 238

Query: 284 -NLDPSVSNEDLRQIF-----GAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
            NL  + + E + + F     G    VK+IR+      + F+ F D   A  A+  LN  
Sbjct: 239 RNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD------YAFVHFEDREDAVKAMDELNGK 292

Query: 338 DIAGKRIKLEPSRP 351
           ++ G  I++  ++P
Sbjct: 293 ELEGSEIEVTLAKP 306

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

 Score = 38.4 bits (90), Expect = 9e-04
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V  L    +++ LR+ F  +GE++E      R+T   R + F+ F D  +AE A K 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 334 LNRSDIAGKRIKLE 347
            N   I G++  + 
Sbjct: 62  PNPI-IDGRKANVN 74

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

 Score = 38.6 bits (89), Expect = 9e-04
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 5/81 (6%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 330
           ++  L+V  L  +++ E+ R +FG+ GE+   K +R+  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 331 LKSLNRSDIAGKRIKLEPSRP 351
           + +LN   +  K IK+  +RP
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

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

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG---DIRTLY---TACKHRGFVMISYYDIRAARTAMR 247
            L+V N+  NV + +L+ LF Q+G     R +    T  + RGF  +       A  A+ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETG-RSRGFGFVEMETAEEANAAIE 59

Query: 248 ALQNKPLRRRKL 259
            L       R L
Sbjct: 60  KLNGTDFGGRTL 71

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

 Score = 41.8 bits (98), Expect = 0.001
 Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 15/157 (9%)

Query: 235 SYYDIRAARTAMRALQNKPLR------RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 288
            YY  R  R+  R+             RR         K+  ++ + +  T+ V  L   
Sbjct: 41  DYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALK 100

Query: 289 VSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKR 343
               DL + F   G+V++++    +   +     ++EFYDV +   AL +L    + G+ 
Sbjct: 101 ARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRP 159

Query: 344 IKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGS 380
           I ++ S+   A +N   +       D    L+  VG+
Sbjct: 160 IIVQSSQ---AEKNRAAKAATHQPGDIPNFLKLYVGN 193

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIR------TLYTACKHRGFVMISYYDIRAARTAM 246
             +FV  +  +  D  LR  F Q+G+I          T  K RG+  +++ D  +   A 
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTG-KSRGYGFVTFKDKES---AE 56

Query: 247 RALQN 251
           RA ++
Sbjct: 57  RACKD 61

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|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP) and similar proteins

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQI----FGAYGEVKEIRETPHKRHHKF--IEFYDVRAAEAALK 332
            L V NLD  +S ++L+Q     F  +G+V  +   P         +   +++ A+ A+ 
Sbjct: 6   DLQVSNLDYRLSRKELQQTLTNQFKRHGKVLSVSLRPQTDGSLVASVRVPNLQDAQYAIS 65

Query: 333 SLNRSDIAGKRIKLEPSRPGG 353
            L+R  I  KRI +  ++   
Sbjct: 66  QLHRRKIGSKRILVSYAQGSS 86

This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. Length = 89

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKF--IEFYDVRAAEAAL----K 332
           T+ V NL    +   +RQ F   GE++E+ +           IEF     A AAL    K
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREV-KIVESEGGLVAVIEFETEDEALAALTKDHK 60

Query: 333 SLNRSDIA 340
            L  ++I+
Sbjct: 61  RLGGNEIS 68

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
           + L V NI     D +LR +F Q+G   D+  ++     +GF  +++ +   A  A   L
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 250 QNKPLRRRKLDIH 262
               +  RK++++
Sbjct: 61  HGTVVEGRKIEVN 73

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

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIR-TLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           +RTLFV+N+  N+   EL+ +FE   DIR         +G   I+Y + +    A +AL+
Sbjct: 3   ARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKG---IAYIEFKTEAEAEKALE 59

Query: 251 NK 252
            K
Sbjct: 60  EK 61

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|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
             LVV NL PSV+ +D+ ++F A G +K  R
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRAR 31

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

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMI-----SYYDIRAARTAMRAL 249
           LFV N+ +++ + + + LFE+YG+   ++   + RGF  I     +  +I  A      L
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 62

Query: 250 QNKPLRRR 257
           +N+PLR R
Sbjct: 63  KNRPLRIR 70

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

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 9/63 (14%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQN 251
           LFV N+     + E+R+LFEQYG +      C   K+ GFV +   D  AA  A+R L +
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKV----LECDIIKNYGFVHMD--DKTAADEAIRNLHH 56

Query: 252 KPL 254
             L
Sbjct: 57  YKL 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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 10/80 (12%)

Query: 279 TLVVFNLDPSVSNED----LRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEA 329
           T+ V   D S+  +D    L + F + GE+  +     RET   +   +IEF  V   E 
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 330 ALKSLNRSDIAGKRIKLEPS 349
           AL+ L+ SD+ G  + ++ +
Sbjct: 61  ALE-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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLYT---ACKHRGFVMISYYDIRAART 244
           P+R +FV  I  +  + ELR  F ++G   D++ +       K  GFV  ++     A  
Sbjct: 2   PNR-IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFV--TFETQEDAEK 58

Query: 245 AMRALQNKPLRRRKLDI 261
              A+ N   R +KL+I
Sbjct: 59  I-LAMGNLNFRGKKLNI 74

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|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 15/79 (18%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           R +F  N   +   SE+  LF +YG     D+++        GF  +   D R A  A+R
Sbjct: 1   RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMKS--------GFAFVYMEDERDAEDAIR 52

Query: 248 ALQNKPL--RRRKLDIHFS 264
            L N     +RR+L + ++
Sbjct: 53  GLDNFEFGRQRRRLRVEWA 71

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|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 = 36.8 bits (86), Expect = 0.002
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           T++V N+   + + EL+  F  +G   ++R      K +G+  + +    AA TA+ A+ 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF----KDKGYAFVRFDTHEAAATAIVAVN 57

Query: 251 NKPL 254
              +
Sbjct: 58  GTSI 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 247
             L V  +  ++   ELR+LFE  G I +          +  G+  + Y D   A+ A+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 248 ALQNKPLRRRKLDIHF 263
            L    +R ++L + +
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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAARTAMRAL 249
            LFV  +  +V   EL  LF+++G ++++      + K +G   + Y +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 250 QNKPLRRRKLDIHFSIP 266
               ++ + + +  S P
Sbjct: 64  DGTEIKEKTISVAISNP 80

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

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 293 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
           D+ + F  YG++ E+     K  + F+EF D+R A+ A+  LN  D+ G+R+ +E +R  
Sbjct: 15  DVERFFKGYGKILEV---DLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHAR-- 69

Query: 353 GARRN 357
           G RR+
Sbjct: 70  GPRRD 74

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 294 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           +RQ F  +G++ EIR  P K  + FI F    +A  A+ S+N + I G  +K
Sbjct: 17  MRQTFSPFGQIMEIRVFPEK-GYSFIRFSTHESAAHAIVSVNGTTIEGHVVK 67

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

 Score = 39.3 bits (91), Expect = 0.002
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L +  L     +  LR  F  +G+V +      RET   R   F+ F D  AA AA+  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 335 NRSDIAGKRIKLEPS--RPGGAR 355
           +  ++ G+ I++ P+  RP   R
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPR 119

Length = 144

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 334
           L V NL   ++ ++L++ F  +G V E+R        +     F+ F D  A +  L + 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 335 NRSDIAGKRIKLEPSR 350
                   R+ +E  +
Sbjct: 66  PIYFRGDHRLNVEEKK 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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDIRAARTAMRA 248
           + VRNI       ELR LF  +G+++T+    K      HRGF  + +   + A+ A +A
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 249 LQ 250
           L 
Sbjct: 63  LC 64

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast sporulation-specific protein 2 (Ssp2) and similar protein

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 287 PSVSN-EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKR 343
           PS  + E+L+  F  +GE+ +I     ++    I F D+R+A  A ++L    S +  K 
Sbjct: 3   PSDFDVEELKDDFTVFGEIVDISPIISRKLCVSIFFADIRSAIRAKETLEDKGSSLNNKY 62

Query: 344 IK 345
           IK
Sbjct: 63  IK 64

This subfamily corresponds to the RRM of the lineage specific yeast sporulation-specific protein 2 (Ssp2) and similar proteins. Ssp2 is encoded by a sporulation-specific gene necessary for outer spore wall assembly in the yeast Saccharomyces cerevisiae. It localizes to the spore wall and may play an important role after meiosis II and during spore wall formation. Ssp2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 278 GTLVVFNL-DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
             L+V NL +  V+ + L  +FG YG+V+ ++   +K+    I+  D   ++ A+  LN 
Sbjct: 14  TVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNG 73

Query: 337 SDIAGKRIKLEPSR 350
             + GK I++  S+
Sbjct: 74  QKMYGKIIRVTLSK 87

This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and 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 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 107

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

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 11/62 (17%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           +  +F ++  +    +R  F  +G+ K +    H+    F+ F    AAE    +++ + 
Sbjct: 4   SFFLFGVEDDLPEYKIRDYFEQFGKSKSVI-VNHRAKCGFVRFETREAAEKFAAAISENG 62

Query: 339 IA 340
           + 
Sbjct: 63  LN 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|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 279 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           TL V N DP +    DL + F  YG++  +R    +R+  F+++     A  AL+S N S
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYGKLVNVRI---RRNFAFVQYETQEDATKALESTNMS 57

Query: 338 DIAGKRIKLE 347
            +  + I +E
Sbjct: 58  KVLDRVISVE 67

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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V NL       +L + F  YG ++ +    +     F+EF D R AE A++ L+   I G
Sbjct: 4   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 63

Query: 342 KRIKLEPSRPGGARR 356
            R+++E S  G  RR
Sbjct: 64  SRVRVELS-TGMPRR 77

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

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAEAALKSLN 335
           L V NL  +V  E + + F  YG V+ ++  P +        F++F D+++A+ A  ++N
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61

Query: 336 RSD 338
           +  
Sbjct: 62  KMG 64

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

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

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
             ++FV  ++ +V   EL   F ++G   ++  +  A     F  I +   +AA  A+ +
Sbjct: 3   KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62

Query: 249 -----LQNKPLR 255
                L+NK + 
Sbjct: 63  ENHSMLKNKTMH 74

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

>gnl|CDD|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 = 36.8 bits (86), Expect = 0.003
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 288 SVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK 342
           + + ED+R +F  YG ++E+     ++T   +   F++F     A+ A+++L+     GK
Sbjct: 10  TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH-----GK 64

Query: 343 RIKLEPSRP 351
                 SRP
Sbjct: 65  VTMPGASRP 73

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

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

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 248
           +FV +++  ++   LRA F  +G+I      + + T  K +G+  +S+     A  A+++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTG-KSKGYGFVSFVKKEDAENAIQS 60

Query: 249 LQNKPLRRRKL 259
           +  + L  R +
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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           +FV N++ +    ELRALFE YG    + +    R F  +      AA  A+  L  + L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYG---AVLSCAVMRQFAFVHLRGEAAADRAIEELNGREL 59

Query: 255 RRRKLDIHFS 264
             RKL +  S
Sbjct: 60  HGRKLVVEHS 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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 12/46 (26%), Positives = 25/46 (54%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD 238
           R +FV  +  ++ + +LR  F Q+G++  +Y     R F  +++ D
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFAD 46

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|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR----HHKFIEFYDVRAAEAALKSL 334
            L V NL P VSNE L Q F  +GEV+        R        +EF     A+AA+K  
Sbjct: 1   ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRC 60

Query: 335 N 335
           +
Sbjct: 61  S 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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V NLD  V+ E L ++F   G V  +     R T   + + F+EF     A+ A+K +N 
Sbjct: 3   VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62

Query: 337 SDIAGKRIKL 346
             + GK I++
Sbjct: 63  IKLYGKPIRV 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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 11/27 (40%), Positives = 18/27 (66%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDI 219
           RT+FV N+    +  +L+ LF+Q+G I
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPI 27

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|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 = 36.7 bits (85), Expect = 0.003
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V N+    + E L+ IF   G V        RET   + + F E+ D   A +A+++LN 
Sbjct: 3   VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62

Query: 337 SDIAGKRIKLE 347
            ++ G++++++
Sbjct: 63  YELNGRQLRVD 73

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH-RGFVMISYYDIRAARTAMRALQ 250
           +FV  I  ++ + EL  LFE+ G   ++R +       RG+  ++Y +  AA+ A++ L 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 251 NKPLRRRKL 259
           N  +R  K 
Sbjct: 64  NYEIRPGKR 72

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 21/84 (25%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMIS--------Y----YDIRA 241
            L V N+     D + R L   +G +         R F++ S        Y    Y  +A
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAV--------ERCFLVYSESTGESKGYGFVEYASKA 52

Query: 242 -ARTAMRALQNKPLRRRKLDIHFS 264
            A  A   L  K +  RKL + ++
Sbjct: 53  SALKAKNQLDGKQIGGRKLQVDWA 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|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 36.9 bits (85), Expect = 0.004
 Identities = 20/68 (29%), Positives = 36/68 (52%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V NL  + +  +L + FG YG ++ +    +     F+EF D R A  A++ L+   + G
Sbjct: 9   VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 68

Query: 342 KRIKLEPS 349
            R+++E S
Sbjct: 69  CRVRVELS 76

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG---DIRTLYTAC-KHRGFVMISYYDIRAARTAMRAL 249
           TLFV N++ + E  +L   F++ G   D+R       + +GF  + +     A+ A+   
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-K 59

Query: 250 QNKPLRRR--KLDI 261
             + L  R  ++D+
Sbjct: 60  SGEELLGREIRVDL 73

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 9/76 (11%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-------RHHKFIEFYDVRAAEAALK 332
           ++V N+    + ++LR++F  +GE+K +R  P K       R   F++F   + A+ A K
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVR-LPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 333 SLNRSD-IAGKRIKLE 347
           +L  S  + G+R+ LE
Sbjct: 62  ALCHSTHLYGRRLVLE 77

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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+ +     EL   F  YG +RT++ A    GF  + + D R A  A+R L  K +
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 255 --RRRKLDIHFSIPK 267
              R ++++   +P+
Sbjct: 62  CGSRVRVELSTGMPR 76

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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 16/44 (36%), Positives = 29/44 (65%)

Query: 290 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS 333
           S ++LR+IF  YG+V ++  +  K+    +EF   +AAEAA+++
Sbjct: 17  SEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVEN 60

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

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           ++ V       S E L   F A+G V  +     K  +  +EF      +  L     + 
Sbjct: 4   SVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSEPQHT- 62

Query: 339 IAGKRIKLEP 348
           + G R+++ P
Sbjct: 63  LNGHRLRVRP 72

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

>gnl|CDD|240867 cd12421, RRM1_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 = 15/70 (21%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
           L +RN+  +V +S+L AL   +G +   L    K++  V      + +A++ +      P
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALV--EMDSVESAKSMVDYYLTVP 59

Query: 254 LRRRKLDIHF 263
              R   ++ 
Sbjct: 60  ALIRGRRVYI 69

This subfamily corresponds to the RRM1 of the majority of family members that include 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. 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. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to 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. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

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

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAALKSL 334
           L+V  L  +++ ++LR +F + GEV   K IR+    H   + F+ + + + AE A+ +L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 335 NRSDIAGKRIKLEPSRP 351
           N   +  K IK+  +RP
Sbjct: 64  NGLRLQSKTIKVSYARP 80

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

>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 36.9 bits (85), Expect = 0.004
 Identities = 23/86 (26%), Positives = 46/86 (53%), Gaps = 7/86 (8%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFE-----QYGDIRTLYTACK-HRGFVMISYYDIRAA 242
           E  S+T+ +R +  N+ ++++R L E     Q  D+R +       RGF  + +Y ++ A
Sbjct: 2   EKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDA 61

Query: 243 RTAMRALQNK-PLRRRKLDIHFSIPK 267
            + M A Q K  ++ + + +H+S P+
Sbjct: 62  TSWMEANQKKLVIQGKTIAMHYSNPR 87

This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 87

>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 = 36.4 bits (84), Expect = 0.004
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALK 332
           G L +  L    + + L Q+F  YG++ E+     RET   R   F+ F +   A+ A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 333 SLNRSDIAGKRIKLE 347
           ++N   + G++I+++
Sbjct: 61  AMNGKSVDGRQIRVD 75

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

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE--TPHKRHHKFIEFYDVRAAEAALKS 333
           TL + +L+P +    +   F   GE   VK IR   T     + F+EF    AAE AL+S
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 334 LNRSDIAGK 342
           LN   I   
Sbjct: 61  LNGKPIPNT 69

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	780
KOG4660	549	consensus Protein Mei2, essential for commitment t	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	99.98
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.91
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.91
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.91
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.89
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.89
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.88
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.88
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.86
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.86
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.85
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.85
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.83
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.78
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.77
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.73
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.72
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.71
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.69
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.66
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.61
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.6
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.59
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.57
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.56
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.51
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.49
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.48
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.46
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.44
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.43
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.41
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.41
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.34
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.32
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.32
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.31
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.3
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.26
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.24
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.24
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.24
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.23
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.21
KOG0122	270	consensus Translation initiation factor 3, subunit	99.17
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.16
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.15
KOG0122	270	consensus Translation initiation factor 3, subunit	99.15
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.14
PLN03120	260	nucleic acid binding protein; Provisional	99.14
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.13
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.13
PLN03120	260	nucleic acid binding protein; Provisional	99.12
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.11
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.11
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.1
smart00362	72	RRM_2 RNA recognition motif.	99.09
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.09
PLN03213	759	repressor of silencing 3; Provisional	99.08
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.05
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.04
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.03
smart00362	72	RRM_2 RNA recognition motif.	99.0
smart00360	71	RRM RNA recognition motif.	98.98
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.98
PLN03213	759	repressor of silencing 3; Provisional	98.98
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.97
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.97
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.96
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.94
PLN03121	243	nucleic acid binding protein; Provisional	98.94
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.93
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.93
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.92
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.92
smart00360	71	RRM RNA recognition motif.	98.92
PLN03121	243	nucleic acid binding protein; Provisional	98.91
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.88
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.88
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.86
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.85
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.83
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.83
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.83
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.8
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.78
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.77
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.76
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.76
smart00361	70	RRM_1 RNA recognition motif.	98.75
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.67
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.65
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.63
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.62
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.6
smart00361	70	RRM_1 RNA recognition motif.	98.56
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.48
KOG4210	285	consensus Nuclear localization sequence binding pr	98.43
KOG0226	290	consensus RNA-binding proteins [General function p	98.42
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.42
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.41
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.3
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.26
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.24
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.24
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.23
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.22
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.2
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.16
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.11
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.07
KOG0151	877	consensus Predicted splicing regulator, contains R	98.02
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.01
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.95
KOG0151	877	consensus Predicted splicing regulator, contains R	97.93
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.86
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.86
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	97.83
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.79
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.79
KOG0226	290	consensus RNA-binding proteins [General function p	97.76
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.73
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.7
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.69
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.66
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.49
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.47
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.46
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.35
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.34
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.31
KOG4210	285	consensus Nuclear localization sequence binding pr	97.3
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.28
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.17
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.72
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.57
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.53
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.42
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.4
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.38
KOG1295	376	consensus Nonsense-mediated decay protein Upf3 [RN	96.36
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.27
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.22
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.15
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.05
KOG3152	278	consensus TBP-binding protein, activator of basal	96.04
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.02
KOG1995	351	consensus Conserved Zn-finger protein [General fun	95.98
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.57
KOG2314	698	consensus Translation initiation factor 3, subunit	95.53
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.18
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.91
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.89
KOG2314	698	consensus Translation initiation factor 3, subunit	94.86
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	94.58
KOG3152	278	consensus TBP-binding protein, activator of basal	94.51
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.35
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.74
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	93.56
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	93.54
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	90.7
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	90.6
KOG2135	526	consensus Proteins containing the RNA recognition	90.51
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	90.33
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	90.08
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	90.03
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	89.23
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	88.96
KOG2591	684	consensus c-Mpl binding protein, contains La domai	88.91
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	88.88
KOG2068	327	consensus MOT2 transcription factor [Transcription	88.54
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	87.26
KOG1996	378	consensus mRNA splicing factor [RNA processing and	87.15
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	86.61
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	86.17
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	86.13
KOG2068	327	consensus MOT2 transcription factor [Transcription	86.03
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	85.64
KOG2591	684	consensus c-Mpl binding protein, contains La domai	84.77
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	84.25
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	80.41

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=100.00  E-value=4.6e-59  Score=511.95  Aligned_cols=454  Identities=51%  Similarity=0.750  Sum_probs=339.6

Q ss_pred             HHHHHhcCCCcEEEeccCccCcccceEEEeecCccccCcccccccCCCCcccCCCCCCCCCCCcEEEEeCCCCCCCHHHH
Q 004002          130 EDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSEL  209 (780)
Q Consensus       130 el~dlFs~~G~i~V~~d~~esa~~g~~~v~~~~~~~a~~~~~~~l~n~~~k~~g~~~~~e~~s~tLfVgNLp~~vteeeL  209 (780)
                      +++++|...|++++..+....+..   .              ....+....+..++|..+  +++ +|         -+|
T Consensus         2 ~d~~lf~~~G~~el~~~~~~~~~~---~--------------~~~~n~~~~~~~~~P~~~--s~~-~~---------~~l   52 (549)
T KOG4660|consen    2 EDCDLFSSGGGMELDADSFDNLSV---R--------------NSDRNSAGFVFPEHPPGE--SRT-FV---------SEL   52 (549)
T ss_pred             CccccccCCCCCCcccccccchhh---c--------------ccccCCCccccCCCCCCC--CCC-Ch---------hhH
Confidence            457889999999776664433221   1              112244556677778777  666 77         788


Q ss_pred             HHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCCCCCCCCccceeecCCCCCC
Q 004002          210 RALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV  289 (780)
Q Consensus       210 r~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~v  289 (780)
                      -.+|+.|                                  ++.+           +.+++.+++.++++|+|.|||.+|
T Consensus        53 ~a~f~~~----------------------------------~~p~-----------~~~np~~~~~~~~~L~v~nl~~~V   87 (549)
T KOG4660|consen   53 SALFEPF----------------------------------NKPL-----------RPDNPSEKDMNQGTLVVFNLPRSV   87 (549)
T ss_pred             Hhhhhcc----------------------------------CCCC-----------CcCCCCcccCccceEEEEecCCcC
Confidence            8899888                                  1111           116677888999999999999999


Q ss_pred             ChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchhhhHhhhhchhccHH
Q 004002          290 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQD  369 (780)
Q Consensus       290 teedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r~~~l~ql~~~~~~~  369 (780)
                      ++++|+++|+.||+|++|+.+...+|..||+|.|+.+|++|+++||+.+|.|++|+    ++...+++.+-+..      
T Consensus        88 sn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k----~~~~~~~~~~~~~~------  157 (549)
T KOG4660|consen   88 SNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK----RPGGARRAMGLQSG------  157 (549)
T ss_pred             CHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc----CCCcccccchhccc------
Confidence            99999999999999999999999999999999999999999999999999999999    77777766554433      


Q ss_pred             HHHHHHhhhCCCCCCCCCCCcccCCCcCCCccccccCCCCCCCCCCCCCCCCCCCCccccCCCCCcccccccCCCCcccc
Q 004002          370 ESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRG  449 (780)
Q Consensus       370 ~~~~~~~~~Gsp~~~s~P~~~~~~gsp~~~~~~~~~~~s~g~g~~sp~~~~~~~~l~~~~p~~~~~~~~~~~~~~~~~~~  449 (780)
                        ..+..++++|+++++|+.|.               +..+||.++|.....+.....    ++-.+    ..+...+.-
T Consensus       158 --~~~~~~~~~p~a~s~pgg~~---------------~~~~~g~l~P~~s~~~~~~~~----~~~~~----~~~~~~~~~  212 (549)
T KOG4660|consen  158 --TSFLNHFGSPLANSPPGGWP---------------RGQLFGMLSPTRSSILLEHIS----SVDGS----SPGRETPLL  212 (549)
T ss_pred             --chhhhhccchhhcCCCCCCc---------------CCcceeeeccchhhhhhhcch----hccCc----cccccccch
Confidence              55677899999999999994               345677788876543222111    11111    111223333


Q ss_pred             chhhhhcccccccCCCcccCCCCCCCCCCCccCCccCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCcccCCCCC
Q 004002          450 SLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMG  529 (780)
Q Consensus       450 ~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~  529 (780)
                      .|  |.|..      ....-+|.++|...          |..+++..++.+++++.-+|                     
T Consensus       213 ~h--q~~~~------~~~~~s~a~~~~~~----------G~~~s~~~~v~t~S~~~g~~---------------------  253 (549)
T KOG4660|consen  213 NH--QRFVE------FADNRSYAFSEPRG----------GFLISNSSGVITFSGPGGVW---------------------  253 (549)
T ss_pred             hh--hhhhh------hccccchhhcccCC----------ceecCCCCceEEecCCCccc---------------------
Confidence            33  33332      11224446677632          66777777888888874444                     


Q ss_pred             CCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCcCCCcccccCCCCCCCCCCcccccCCCC
Q 004002          530 HPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRA  609 (780)
Q Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~hhvgsap~~~~~~~~~~~~~~s~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  609 (780)
                      +++...         +.....+.+++||||||||+                  ..++..-+++++.+..|.+.++-+.  
T Consensus       254 n~~~~~---------r~~~~~~~~~~~~hi~~~Ps------------------~~~l~~~~~~~f~~~s~~~~~~~~~--  304 (549)
T KOG4660|consen  254 NPFPSR---------RQRQNSSSSHYEHHIGSAPS------------------MHHLLSRISVGFNGGSGALEMNSNG--  304 (549)
T ss_pred             CCcccc---------ccccccCcccccCccCCCcc------------------cccccccCccccCCCCCCccccccc--
Confidence            222111         11223344578999999997                  2234445667777777777665332  


Q ss_pred             CCCCC-ccCCCCcCCCCCc-ccccCCCCCCCcccCCCCCCCCCCCCCccccc---cccccccCCCCCCCcCcccccccch
Q 004002          610 SVNPG-ITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIEGLYE---RGRSRRIENNNGNQLDSKKQFQLEL  684 (780)
Q Consensus       610 ~~~~~-~~~~~n~~~~~~~-~~~~s~~~~~~~~~g~~~~~~~~~~~~~~~~~---r~r~r~~~~~~~~~~~~~~~~~~~~  684 (780)
                      ..|-| ....+|+++..+. +++.+.++..+.|.+++.+    .+..|.+.+   ..|.||.+. ..++.+ ++++.+|+
T Consensus       305 ~~n~g~~~~t~~~~e~~s~n~~~e~~~rv~~~f~~~~~~----~~~~~~~~~~~~~~~~~Rtt~-~i~ni~-n~~~~~dl  378 (549)
T KOG4660|consen  305 QANQGFLTKTGNVTEFNSKNVGMESSPRVPKNFEGRRSY----TSQNDYPVELILNYRDRRTTV-MIKNIP-NKYGQLDL  378 (549)
T ss_pred             cCCCCccccCcccccccCCCccccccCCCCccccccccc----ccccccccccccccccchhhh-hhhccc-cchhHHHH
Confidence            34555 5589999999987 9999999999999999966    334555555   788889887 555555 99999999


Q ss_pred             hhhhcCCCcceeEEEecCCCCCCHHHHHHHHhhcCCCcceeEEeeccccCCcceeeEEeccCCccchHHHHHHhcCceeE
Q 004002          685 EKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIG  764 (780)
Q Consensus       685 ~~i~~~~d~rtt~mirniPn~~~~~~l~~~i~~~~~~~ydf~ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~~~~~~  764 (780)
                      .+|.+|++.|||+||||||||||++||++. ||.++|+|||+||||||+|+||||||||||++|++|++||++|||++|+
T Consensus       379 ~~Ildge~~rtt~~iknipNK~T~~ml~~~-d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~  457 (549)
T KOG4660|consen  379 LRILDGECPRTTLMIKNIPNKYTSKMLLAA-DEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWE  457 (549)
T ss_pred             HHHHhCcCchhhhHhhccCchhhHHhhhhh-hccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchh
Confidence            999999999999999999999999999999 9999999999999999999999999999999999999999999999988


Q ss_pred             EEE
Q 004002          765 ILF  767 (780)
Q Consensus       765 ~~~  767 (780)
                      .++
T Consensus       458 ~Fn  460 (549)
T KOG4660|consen  458 KFN  460 (549)
T ss_pred             hhc
Confidence            654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=3.6e-32  Score=298.83  Aligned_cols=240  Identities=18%  Similarity=0.294  Sum_probs=198.5

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCCCCCC
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPY  187 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~~~~  187 (780)
                      ++++|++||.+++|.+++++|+.+|.|   .|..|..++..+|++++.|.+...|.    .+++..+.+...++....+.
T Consensus         4 ~~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~~~   83 (352)
T TIGR01661         4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPS   83 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccc
Confidence            689999999999999999999999997   67778888889999999999876664    34555565554444333332


Q ss_pred             C-CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccc--ccc
Q 004002          188 G-EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKL  259 (780)
Q Consensus       188 ~-e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~I  259 (780)
                      . ....++|||+|||.++++++|+.+|++||.|..++.     ++.++|||||+|.+.++|++|++.|+|..+.+  ++|
T Consensus        84 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i  163 (352)
T TIGR01661        84 SDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPI  163 (352)
T ss_pred             ccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeE
Confidence            2 234679999999999999999999999999988762     46789999999999999999999999999876  567


Q ss_pred             ccccCCCCCCCCC----------------C--------------------------------------------------
Q 004002          260 DIHFSIPKDNPSD----------------K--------------------------------------------------  273 (780)
Q Consensus       260 ~V~~a~pk~~~s~----------------~--------------------------------------------------  273 (780)
                      .|.|+........                .                                                  
T Consensus       164 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (352)
T TIGR01661       164 TVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQR  243 (352)
T ss_pred             EEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccccccccccc
Confidence            7777643321000                0                                                  


Q ss_pred             ----------------------CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHH
Q 004002          274 ----------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRA  326 (780)
Q Consensus       274 ----------------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~  326 (780)
                                            .....+|||+|||.++++++|+++|++||.|++|++     ++.+||||||+|.+.++
T Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~  323 (352)
T TIGR01661       244 ASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDE  323 (352)
T ss_pred             CCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHH
Confidence                                  000125999999999999999999999999999986     67789999999999999


Q ss_pred             HHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          327 AEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       327 A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      |.+||.+|||..++|++|+|.|+.++..
T Consensus       324 A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       324 AAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            9999999999999999999999988764

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=99.98  E-value=3.1e-33  Score=251.03  Aligned_cols=72  Identities=58%  Similarity=1.015  Sum_probs=70.6

Q ss_pred             ceeEEEecCCCCCCHHHHHHHHhhcCCCcceeEEeeccccCCcceeeEEeccCCccchHHHHHHhcCceeEE
Q 004002          694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGI  765 (780)
Q Consensus       694 rtt~mirniPn~~~~~~l~~~i~~~~~~~ydf~ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~~~~~~~  765 (780)
                      ||||||||||||||++||+++||+.++|+||||||||||+++||+|||||||+++++|.+|+++|+|++|..
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~   72 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPN   72 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCcccc
Confidence            899999999999999999999999999999999999999999999999999999999999999999999863

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=1e-29  Score=273.23  Aligned_cols=243  Identities=20%  Similarity=0.343  Sum_probs=205.2

Q ss_pred             HHhhhcCCceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCc
Q 004002          107 DELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAG  179 (780)
Q Consensus       107 ddl~s~v~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~  179 (780)
                      +--....-+|+||++||+++.|++|+.+|...|.|   +|++|+..+.++|++||+|..+..|.    .++++.++.+  
T Consensus        76 eg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~G--  153 (506)
T KOG0117|consen   76 EGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPG--  153 (506)
T ss_pred             cCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCC--
Confidence            33334557899999999999999999999999997   89999999999999999999886664    4556666543  


Q ss_pred             ccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCC-EEEEE------eCCCcceEEEEEEecHHHHHHHHHHccC-
Q 004002          180 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLY------TACKHRGFVMISYYDIRAARTAMRALQN-  251 (780)
Q Consensus       180 k~~g~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~-I~sv~------~tgkskG~aFV~F~~~e~A~~Al~~Lng-  251 (780)
                      +.-+  ......+++|||+|||+++++++|++.+.+.++ |..|.      ...|+||||||+|+++.+|..|.++|-. 
T Consensus       154 K~ig--vc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g  231 (506)
T KOG0117|consen  154 KLLG--VCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPG  231 (506)
T ss_pred             CEeE--EEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCC
Confidence            1111  122346799999999999999999999999986 44443      3578999999999999999999998744 


Q ss_pred             -ccccccccccccCCCCCCCCCCCC-CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHH
Q 004002          252 -KPLRRRKLDIHFSIPKDNPSDKDL-NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA  329 (780)
Q Consensus       252 -~~l~gr~I~V~~a~pk~~~s~~~~-~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~  329 (780)
                       .++.|..+.|.||.|...+.+..+ ..+.|||+||+.++|+|.|+++|++||.|+.|+..   |.||||.|.++++|.+
T Consensus       232 ~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~---rDYaFVHf~eR~davk  308 (506)
T KOG0117|consen  232 KIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP---RDYAFVHFAEREDAVK  308 (506)
T ss_pred             ceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecc---cceeEEeecchHHHHH
Confidence             457899999999999887665433 34789999999999999999999999999999764   6799999999999999


Q ss_pred             HHHHhCCCccCCceEEEEecCCCchhh
Q 004002          330 ALKSLNRSDIAGKRIKLEPSRPGGARR  356 (780)
Q Consensus       330 Ai~~LnG~~i~Gr~L~V~~a~~k~~r~  356 (780)
                      |++.|||++|+|..|.|.+|+|..+++
T Consensus       309 Am~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  309 AMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             HHHHhcCceecCceEEEEecCChhhhc
Confidence            999999999999999999999976544

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

Probab=99.97  E-value=1.3e-30  Score=304.58  Aligned_cols=265  Identities=19%  Similarity=0.338  Sum_probs=215.5

Q ss_pred             eeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccC---CCC
Q 004002          116 DFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVA---GEH  185 (780)
Q Consensus       116 el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~---g~~  185 (780)
                      .++|++|+.+++|.+++++|+.+|.|   .|..|..+..++|++++.|.+...|..    ++...+.+..+++.   .+.
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            58999999999999999999999986   677788888899999999998776652    22222333332331   111


Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       186 ~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      .......++|||+|||.++++++|+++|++||+|.+|++    .++++|||||+|.+.++|++|++.|+|..+.++.|.|
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v  161 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV  161 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEE
Confidence            122234578999999999999999999999999999873    5789999999999999999999999999999999999


Q ss_pred             ccCCCCCCC-CCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCC
Q 004002          262 HFSIPKDNP-SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  336 (780)
Q Consensus       262 ~~a~pk~~~-s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG  336 (780)
                      ....++... .......++|||+||+.++|+++|+++|++||+|+++++    .++++|||||+|++.++|.+|++.|+|
T Consensus       162 ~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g  241 (562)
T TIGR01628       162 GRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNG  241 (562)
T ss_pred             eccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            776655433 223345578999999999999999999999999999875    456789999999999999999999999


Q ss_pred             CccC----CceEEEEecCCCchhhh----------------------HhhhhchhccHHHHHHHHhhhCC
Q 004002          337 SDIA----GKRIKLEPSRPGGARRN----------------------LMLQLNQELEQDESRILQHQVGS  380 (780)
Q Consensus       337 ~~i~----Gr~L~V~~a~~k~~r~~----------------------~l~ql~~~~~~~~~~~~~~~~Gs  380 (780)
                      ..+.    |+.|.|.+++++.++..                      ++.++...+++++++.+|.++|.
T Consensus       242 ~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~  311 (562)
T TIGR01628       242 KKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGE  311 (562)
T ss_pred             cEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCC
Confidence            9999    99999999887765521                      33455566778888888877653

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=7.9e-31  Score=264.74  Aligned_cols=214  Identities=25%  Similarity=0.428  Sum_probs=180.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ++..++|.|..||..+|+||||.+|...|+|++|+     ++|.+.||+||.|.++++|++|+..|||.+|..+.|+|.|
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            44568999999999999999999999999999998     5899999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       264 a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      ++|..    ..++..+|||++||+.+|..||+++|++||.|...|     +++.+||.|||+|+.+.+|++||+.|||..
T Consensus       118 ARPSs----~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  118 ARPSS----DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             ccCCh----hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            99854    456778999999999999999999999999998765     478899999999999999999999999999


Q ss_pred             cCC--ceEEEEecCCCchhhhHhhhhchhccHHHHHHHHhhhCCCCCCCCCCCcccCCCcCCCcccccc------CCCCC
Q 004002          339 IAG--KRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTI------SKSPN  410 (780)
Q Consensus       339 i~G--r~L~V~~a~~k~~r~~~l~ql~~~~~~~~~~~~~~~~Gsp~~~s~P~~~~~~gsp~~~~~~~~~------~~s~g  410 (780)
                      ..|  .+|.|+|+....++....-          +.   .-|++|      .  ++|++|+++ +.+.+      .....
T Consensus       194 P~g~tepItVKFannPsq~t~~a~----------ls---~ly~sp------~--rr~~Gp~hh-~~~r~r~~~~~~~~~~  251 (360)
T KOG0145|consen  194 PSGCTEPITVKFANNPSQKTNQAL----------LS---QLYQSP------A--RRYGGPMHH-QAQRFRLDNLLNPHAA  251 (360)
T ss_pred             CCCCCCCeEEEecCCcccccchhh----------hH---HhhcCc------c--ccCCCcccc-hhhhhccccccchhhh
Confidence            988  5899999987654432110          11   123333      2  568999998 55554      23334


Q ss_pred             CCCCCCCCCCCCCCCccc
Q 004002          411 FRNMSPTTSNHMPGLASI  428 (780)
Q Consensus       411 ~g~~sp~~~~~~~~l~~~  428 (780)
                      ..++||++.+++.+|++.
T Consensus       252 ~~rfsP~~~d~m~~l~~~  269 (360)
T KOG0145|consen  252 QARFSPMTIDGMSGLAGV  269 (360)
T ss_pred             hccCCCccccccceeeee
Confidence            568999999999998664

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

Probab=99.97  E-value=2e-29  Score=294.44  Aligned_cols=246  Identities=19%  Similarity=0.321  Sum_probs=199.6

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCC--
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEH--  185 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~--  185 (780)
                      ..++|++|+.++++.+++++|+.+|.|   .|..+ ..+..++++++.|.+.+.|..    +++..+.+....+....  
T Consensus        89 ~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628        89 GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             CceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            569999999999999999999999997   34333 355678999999998766642    22233333322221111  


Q ss_pred             ----CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcccc--
Q 004002          186 ----PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLR--  255 (780)
Q Consensus       186 ----~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~--  255 (780)
                          .......++|||+|||.++|+++|+++|++||+|.+++    ..++++|||||+|.+.++|.+|++.|+|..+.  
T Consensus       168 ~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~  247 (562)
T TIGR01628       168 HEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLA  247 (562)
T ss_pred             cccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEeccc
Confidence                11223457899999999999999999999999999887    35778999999999999999999999999999  


Q ss_pred             --ccccccccCCCCCCCCC--------------CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCccc
Q 004002          256 --RRKLDIHFSIPKDNPSD--------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRH  315 (780)
Q Consensus       256 --gr~I~V~~a~pk~~~s~--------------~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG  315 (780)
                        |+.+.|.++..+.....              ......+|||+||+.++|+++|+++|++||.|++|++    ++.++|
T Consensus       248 ~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g  327 (562)
T TIGR01628       248 KEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRG  327 (562)
T ss_pred             ccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCC
Confidence              99999988866543310              1223468999999999999999999999999999976    567899


Q ss_pred             EEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchhhhHhhh
Q 004002          316 HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQ  361 (780)
Q Consensus       316 ~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r~~~l~q  361 (780)
                      ||||+|.+.++|.+|++.|||+.+.|++|.|.+++.+..++..+++
T Consensus       328 ~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~~~  373 (562)
T TIGR01628       328 FGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQD  373 (562)
T ss_pred             eEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHHHH
Confidence            9999999999999999999999999999999999998877655443

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.96  E-value=5.5e-29  Score=286.30  Aligned_cols=233  Identities=21%  Similarity=0.306  Sum_probs=192.3

Q ss_pred             CCceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCC-CcccCCC
Q 004002          113 IMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNG-AGTVAGE  184 (780)
Q Consensus       113 v~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~-~~k~~g~  184 (780)
                      ..++++|++||.+++|++++++|+.+|.|   .|.+| .+..+++++++.|.+.+.|.    .++.+.+.++ ...+   
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V---  132 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGV---  132 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccc---
Confidence            45899999999999999999999999976   67777 77889999999999877665    2334444322 1111   


Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCC-EEEE-E-----eCCCcceEEEEEEecHHHHHHHHHHccC--cccc
Q 004002          185 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD-IRTL-Y-----TACKHRGFVMISYYDIRAARTAMRALQN--KPLR  255 (780)
Q Consensus       185 ~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~-I~sv-~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng--~~l~  255 (780)
                        ......++|||+|||.++|+++|+++|+++++ +.++ .     ..++++|||||+|.++++|++|++.|..  ..+.
T Consensus       133 --~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~  210 (578)
T TIGR01648       133 --CISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLW  210 (578)
T ss_pred             --cccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEec
Confidence              12235689999999999999999999999964 3332 2     2467899999999999999999998864  3578


Q ss_pred             ccccccccCCCCCCCCCCC-CCccceeecCCCCCCChhHHHHHhccc--CCeeEEEeCCCcccEEEEEEcCHHHHHHHHH
Q 004002          256 RRKLDIHFSIPKDNPSDKD-LNQGTLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAALK  332 (780)
Q Consensus       256 gr~I~V~~a~pk~~~s~~~-~~~~~L~V~NLp~~vteedL~~~Fs~y--G~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~  332 (780)
                      |+.|.|.|+.++....+.. ...++|||+||+.++++++|+++|++|  |+|+.|++.   ++||||+|++.++|++|++
T Consensus       211 Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~s~e~A~kAi~  287 (578)
T TIGR01648       211 GHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---RDYAFVHFEDREDAVKAMD  287 (578)
T ss_pred             CceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---cCeEEEEeCCHHHHHHHHH
Confidence            9999999998865443322 234689999999999999999999999  999999764   6899999999999999999


Q ss_pred             HhCCCccCCceEEEEecCCCch
Q 004002          333 SLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       333 ~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      .|||.+|.|+.|+|+++++...
T Consensus       288 ~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       288 ELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HhCCCEECCEEEEEEEccCCCc
Confidence            9999999999999999988643

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.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=8.2e-29  Score=252.05  Aligned_cols=216  Identities=17%  Similarity=0.316  Sum_probs=178.4

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCcccccccCCCCcccCCCCCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEH  190 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~~~~~l~n~~~k~~g~~~~~e~  190 (780)
                      -+.|||++|..+++|+.+..||...|.+   .|.+|..        +     ..++...   ....         .....
T Consensus         6 prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~--------~-----v~wa~~p---~nQs---------k~t~~   60 (321)
T KOG0148|consen    6 PRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDEL--------K-----VNWATAP---GNQS---------KPTSN   60 (321)
T ss_pred             CceEEeeccChhhHHHHHHHHHHhccccccceeehhhh--------c-----cccccCc---ccCC---------CCccc
Confidence            3679999999999999999999999987   5555510        0     1111111   0000         00011


Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..-.+||+.|..+++.++||+.|.+||+|.+++     .++|+||||||.|.+.++|++||..|+|..|++|.|+-.|+.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            134799999999999999999999999999887     479999999999999999999999999999999999999998


Q ss_pred             CCCCCCC------------CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHH
Q 004002          266 PKDNPSD------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       266 pk~~~s~------------~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                      .|....-            .....++|||+|++..++|++|++.|++||.|.+||+.+ -+||+||+|++.|+|.+||..
T Consensus       141 RKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk-~qGYaFVrF~tkEaAahAIv~  219 (321)
T KOG0148|consen  141 RKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFK-DQGYAFVRFETKEAAAHAIVQ  219 (321)
T ss_pred             cCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEec-ccceEEEEecchhhHHHHHHH
Confidence            7653211            123457999999999999999999999999999999974 479999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCCchh
Q 004002          334 LNRSDIAGKRIKLEPSRPGGAR  355 (780)
Q Consensus       334 LnG~~i~Gr~L~V~~a~~k~~r  355 (780)
                      ||+++|+|..++|.|.+.....
T Consensus       220 mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  220 MNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             hcCceeCceEEEEeccccCCCC
Confidence            9999999999999999876543

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.95  E-value=9.6e-28  Score=275.32  Aligned_cols=233  Identities=19%  Similarity=0.243  Sum_probs=179.5

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcEE-EeccCccCcccceEEEeecCccccCccc------ccccCCCCcccCCC---
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGME-LEGEPQESLSMSMSKISISDSASGNGLL------HYSVPNGAGTVAGE---  184 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i~-V~~d~~esa~~g~~~v~~~~~~~a~~~~------~~~l~n~~~k~~g~---  184 (780)
                      ..++|++||.+++|.+++++|+.+|.|. |.+-    ..++++++.|.+.+.|..+.      ...+.+....+...   
T Consensus         3 ~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~----~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMML----PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEE----CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            4689999999999999999999999982 2111    13578888888876665332      22333332222110   


Q ss_pred             ---CCC-------CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC-CCcceEEEEEEecHHHHHHHHHHccCcc
Q 004002          185 ---HPY-------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-CKHRGFVMISYYDIRAARTAMRALQNKP  253 (780)
Q Consensus       185 ---~~~-------~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t-gkskG~aFV~F~~~e~A~~Al~~Lng~~  253 (780)
                         ...       ......+|||+||+..+|+++|+++|+.||+|.+|++. .+.+|+|||+|.+.++|.+|++.|||..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~  158 (481)
T TIGR01649        79 EIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGAD  158 (481)
T ss_pred             ccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCc
Confidence               000       11122479999999999999999999999999998743 3335799999999999999999999999


Q ss_pred             ccc--cccccccCCCCCC-------CC----------C------------------------------------------
Q 004002          254 LRR--RKLDIHFSIPKDN-------PS----------D------------------------------------------  272 (780)
Q Consensus       254 l~g--r~I~V~~a~pk~~-------~s----------~------------------------------------------  272 (780)
                      |.+  +.|+|.|+.+...       .+          +                                          
T Consensus       159 i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  238 (481)
T TIGR01649       159 IYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGG  238 (481)
T ss_pred             ccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCccccc
Confidence            964  4677777654210       00          0                                          


Q ss_pred             --------------------------------CCCCccceeecCCCC-CCChhHHHHHhcccCCeeEEEeCCCcccEEEE
Q 004002          273 --------------------------------KDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFI  319 (780)
Q Consensus       273 --------------------------------~~~~~~~L~V~NLp~-~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV  319 (780)
                                                      ......+|||+|||. .+|+++|+++|+.||.|..|++...++|+|||
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV  318 (481)
T TIGR01649       239 DRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALI  318 (481)
T ss_pred             ccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEE
Confidence                                            001235899999997 69999999999999999999986667899999


Q ss_pred             EEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          320 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       320 ~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      +|.+.++|++||+.|||..|.|++|+|.+++.
T Consensus       319 ~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~  350 (481)
T TIGR01649       319 EMADPYQAQLALTHLNGVKLFGKPLRVCPSKQ  350 (481)
T ss_pred             EECCHHHHHHHHHHhCCCEECCceEEEEEccc
Confidence            99999999999999999999999999998754

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).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=1.1e-27  Score=262.84  Aligned_cols=162  Identities=23%  Similarity=0.425  Sum_probs=145.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ....++|||+|||+++|+++|+++|+.||+|++|+     .+++++|||||+|.++++|++||+.|++..|.+++|+|.|
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            34679999999999999999999999999999887     3678999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       264 a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      +.+...    .....+|||+|||.++|+++|+++|++||+|+.|++     +++++++|||+|+++++|++||+.||+..
T Consensus       184 a~p~~~----~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  259 (346)
T TIGR01659       184 ARPGGE----SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI  259 (346)
T ss_pred             cccccc----ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCc
Confidence            876432    234568999999999999999999999999999875     56778999999999999999999999999


Q ss_pred             cCC--ceEEEEecCCCch
Q 004002          339 IAG--KRIKLEPSRPGGA  354 (780)
Q Consensus       339 i~G--r~L~V~~a~~k~~  354 (780)
                      +.|  ++|+|.+++....
T Consensus       260 ~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       260 PEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             cCCCceeEEEEECCcccc
Confidence            876  6899999886543

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).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=2.5e-27  Score=239.54  Aligned_cols=245  Identities=20%  Similarity=0.308  Sum_probs=197.7

Q ss_pred             ccccccccCCCCCCchHHhhhcCCceeeeccCCCCCChHHHHHHhcCCCcEEEeccCccCcccceEEEeecCccccC---
Q 004002           91 EGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN---  167 (780)
Q Consensus        91 ee~e~~~i~nlLP~deddl~s~v~~el~V~~Lp~s~~E~el~dlFs~~G~i~V~~d~~esa~~g~~~v~~~~~~~a~---  167 (780)
                      +|..+.+|+|+||..        |++.+++.|+.+++|+|.+         .|..|..++.+.|+.|+.+.+...|.   
T Consensus        38 ~~skTNLIvNYLPQ~--------MTqdE~rSLF~SiGeiESc---------KLvRDKitGqSLGYGFVNYv~p~DAe~Ai  100 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQN--------MTQDELRSLFGSIGEIESC---------KLVRDKITGQSLGYGFVNYVRPKDAEKAI  100 (360)
T ss_pred             Ccccceeeeeecccc--------cCHHHHHHHhhcccceeee---------eeeeccccccccccceeeecChHHHHHHH
Confidence            445577788888866        4544444444444444433         45677888999999999998876553   


Q ss_pred             -cccccccCCCCcccCCCCCCCC-CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHH
Q 004002          168 -GLLHYSVPNGAGTVAGEHPYGE-HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIR  240 (780)
Q Consensus       168 -~~~~~~l~n~~~k~~g~~~~~e-~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e  240 (780)
                       .+++.++.++.+++....|..+ ....+|||.+||+.+|..||.++|++||.|...+     +++.+||.|||.|...+
T Consensus       101 ntlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~  180 (360)
T KOG0145|consen  101 NTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRI  180 (360)
T ss_pred             hhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchh
Confidence             6677888999899988877644 4568999999999999999999999999987655     57999999999999999


Q ss_pred             HHHHHHHHccCccccc--cccccccCCCCCCCCC-------------C--------------------------------
Q 004002          241 AARTAMRALQNKPLRR--RKLDIHFSIPKDNPSD-------------K--------------------------------  273 (780)
Q Consensus       241 ~A~~Al~~Lng~~l~g--r~I~V~~a~pk~~~s~-------------~--------------------------------  273 (780)
                      +|+.||+.|||..-.|  .+|.|+|+........             +                                
T Consensus       181 EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~  260 (360)
T KOG0145|consen  181 EAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTI  260 (360)
T ss_pred             HHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccc
Confidence            9999999999988655  4788888753321100             0                                


Q ss_pred             --------------CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHh
Q 004002          274 --------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL  334 (780)
Q Consensus       274 --------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~L  334 (780)
                                    .....+|||.||.++.+|.-|+++|++||.|..|++     +.+.||||||.+.+.++|..||..|
T Consensus       261 d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sL  340 (360)
T KOG0145|consen  261 DGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL  340 (360)
T ss_pred             cccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHh
Confidence                          001148999999999999999999999999999875     5788999999999999999999999


Q ss_pred             CCCccCCceEEEEecCCC
Q 004002          335 NRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       335 nG~~i~Gr~L~V~~a~~k  352 (780)
                      ||+.+++|.|.|.|...+
T Consensus       341 NGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  341 NGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             cCccccceEEEEEEecCC
Confidence            999999999999998654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.94  E-value=2.1e-26  Score=253.21  Aligned_cols=159  Identities=21%  Similarity=0.406  Sum_probs=143.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      +.++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++||+.|+|..|.|++|.|.|+.
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            4689999999999999999999999999999872     57899999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~  340 (780)
                      +...    .....+|||+|||..+++++|+++|++||.|..+++     ++.++|||||+|++.++|++||+.|||..+.
T Consensus        82 ~~~~----~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661        82 PSSD----SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             cccc----ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccC
Confidence            7543    234568999999999999999999999999988865     4567899999999999999999999999998


Q ss_pred             C--ceEEEEecCCCc
Q 004002          341 G--KRIKLEPSRPGG  353 (780)
Q Consensus       341 G--r~L~V~~a~~k~  353 (780)
                      |  .+|.|.++....
T Consensus       158 g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       158 GCTEPITVKFANNPS  172 (352)
T ss_pred             CCceeEEEEECCCCC
Confidence            7  678888886544

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=6.8e-26  Score=260.06  Aligned_cols=162  Identities=25%  Similarity=0.335  Sum_probs=139.5

Q ss_pred             CCcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          191 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       191 ~s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      ++++|||+|||+ .+|+++|+++|+.||+|.+|+.....+|||||+|.+.++|++|++.|+|..|.|++|+|.++.....
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~  353 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNV  353 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccc
Confidence            567999999998 6999999999999999999986545689999999999999999999999999999999998754311


Q ss_pred             CCC------------C---------------------CCCccceeecCCCCCCChhHHHHHhcccCC--eeEEEeCCC--
Q 004002          270 PSD------------K---------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGE--VKEIRETPH--  312 (780)
Q Consensus       270 ~s~------------~---------------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~--I~~v~~~g~--  312 (780)
                      ...            +                     .....+|||+|||.++++++|+++|+.||.  |+.|++...  
T Consensus       354 ~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~  433 (481)
T TIGR01649       354 QPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDN  433 (481)
T ss_pred             cCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCC
Confidence            000            0                     012358999999999999999999999998  888877433  


Q ss_pred             -cccEEEEEEcCHHHHHHHHHHhCCCccCCce------EEEEecCCC
Q 004002          313 -KRHHKFIEFYDVRAAEAALKSLNRSDIAGKR------IKLEPSRPG  352 (780)
Q Consensus       313 -srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~------L~V~~a~~k  352 (780)
                       ++++|||+|++.++|.+||..|||+.|.|+.      |+|.+++++
T Consensus       434 ~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       434 ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence             3789999999999999999999999999985      999999864

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.94  E-value=1.3e-25  Score=255.78  Aligned_cols=239  Identities=21%  Similarity=0.282  Sum_probs=188.1

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCcc---cccccCCCCcccCC----
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAGTVAG----  183 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~---~~~~l~n~~~k~~g----  183 (780)
                      ...++|++||..+++.+++++|+.+|.|   .|..+..+...+|++++.|.+...|..+   .+..+.+..+.+..    
T Consensus        89 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~  168 (457)
T TIGR01622        89 DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAE  168 (457)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchh
Confidence            3679999999999999999999999997   6677777888999999999987665422   22222222111100    


Q ss_pred             --------CC-CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHc
Q 004002          184 --------EH-PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRAL  249 (780)
Q Consensus       184 --------~~-~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~L  249 (780)
                              .. .......++|||+|||.++|+++|+++|++||.|..|+.     +++++|||||+|.+.++|.+|++.|
T Consensus       169 ~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l  248 (457)
T TIGR01622       169 KNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM  248 (457)
T ss_pred             hhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhc
Confidence                    00 001122589999999999999999999999999998872     4688999999999999999999999


Q ss_pred             cCccccccccccccCCCCCCCC----------------------------------C-----------------------
Q 004002          250 QNKPLRRRKLDIHFSIPKDNPS----------------------------------D-----------------------  272 (780)
Q Consensus       250 ng~~l~gr~I~V~~a~pk~~~s----------------------------------~-----------------------  272 (780)
                      +|..|.|++|.|.|+.......                                  .                       
T Consensus       249 ~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (457)
T TIGR01622       249 NGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD  328 (457)
T ss_pred             CCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccc
Confidence            9999999999999953210000                                  0                       


Q ss_pred             -----------------------------CCCCccceeecCCCCCCC----------hhHHHHHhcccCCeeEEEeC-CC
Q 004002          273 -----------------------------KDLNQGTLVVFNLDPSVS----------NEDLRQIFGAYGEVKEIRET-PH  312 (780)
Q Consensus       273 -----------------------------~~~~~~~L~V~NLp~~vt----------eedL~~~Fs~yG~I~~v~~~-g~  312 (780)
                                                   ......+|+|.||-...+          .+||++.|++||.|+.|.+. +.
T Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~  408 (457)
T TIGR01622       329 GIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKN  408 (457)
T ss_pred             ccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCC
Confidence                                         012235688888854443          36899999999999999875 77


Q ss_pred             cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       313 srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..|++||+|.++++|++|++.|||+.++|+.|.+.+....
T Consensus       409 ~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       409 SAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             CceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            7899999999999999999999999999999999988643

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.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.93  E-value=3.6e-25  Score=255.27  Aligned_cols=238  Identities=16%  Similarity=0.208  Sum_probs=174.6

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---------EEeccCccCcccceEEEeecCccccCcc---cccccCCCCccc
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---------ELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAGTV  181 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---------~V~~d~~esa~~g~~~v~~~~~~~a~~~---~~~~l~n~~~k~  181 (780)
                      ..+|||++||.++++.+|.++|..++..         .+..+......++++++.|.+...|..+   .+..+.+...++
T Consensus       175 ~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v  254 (509)
T TIGR01642       175 ARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKI  254 (509)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEe
Confidence            5689999999999999999999974110         0001111234467888888776555422   111111111111


Q ss_pred             CCC------------------------------CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCC
Q 004002          182 AGE------------------------------HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TAC  226 (780)
Q Consensus       182 ~g~------------------------------~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tg  226 (780)
                      ...                              ........++|||+|||..+|+++|+++|+.||.|..+.     .++
T Consensus       255 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g  334 (509)
T TIGR01642       255 RRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATG  334 (509)
T ss_pred             cCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCC
Confidence            000                              000123457999999999999999999999999998876     268


Q ss_pred             CcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCCCC------------------------CCCCccceee
Q 004002          227 KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD------------------------KDLNQGTLVV  282 (780)
Q Consensus       227 kskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~------------------------~~~~~~~L~V  282 (780)
                      +++|||||+|.+.++|+.|++.|+|..|.|++|.|.++........                        ......+|+|
T Consensus       335 ~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l  414 (509)
T TIGR01642       335 LSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQL  414 (509)
T ss_pred             CcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCceEEEe
Confidence            8999999999999999999999999999999999998754321110                        0123467899


Q ss_pred             cCCCCC--C--------ChhHHHHHhcccCCeeEEEeC--------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 004002          283 FNLDPS--V--------SNEDLRQIFGAYGEVKEIRET--------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (780)
Q Consensus       283 ~NLp~~--v--------teedL~~~Fs~yG~I~~v~~~--------g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L  344 (780)
                      .||...  +        ..++|+++|++||.|+.|++.        +..+|++||+|.++++|++||.+|||..|.|+.|
T Consensus       415 ~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v  494 (509)
T TIGR01642       415 TNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVV  494 (509)
T ss_pred             ccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            998532  1        136799999999999999863        1246899999999999999999999999999999


Q ss_pred             EEEecCC
Q 004002          345 KLEPSRP  351 (780)
Q Consensus       345 ~V~~a~~  351 (780)
                      .|.|...
T Consensus       495 ~~~~~~~  501 (509)
T TIGR01642       495 VAAFYGE  501 (509)
T ss_pred             EEEEeCH
Confidence            9998764

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.93  E-value=1.9e-25  Score=257.63  Aligned_cols=163  Identities=20%  Similarity=0.405  Sum_probs=143.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++++++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|.+..
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            458999999999999999999999999999987     368899999999999999999999999999999999998654


Q ss_pred             CCCCCC-------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 004002          266 PKDNPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       266 pk~~~s-------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                      ......       .......+|||+||+.++++++|+++|++||.|++|++     ++++||||||+|++.++|.+||..
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            321110       11123468999999999999999999999999999976     456899999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCCc
Q 004002          334 LNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       334 LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      |||.+++|+.|+|.++.++.
T Consensus       266 mNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             hCCCeeCCeEEEEEecCCCc
Confidence            99999999999999887654

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=9.1e-24  Score=231.57  Aligned_cols=243  Identities=19%  Similarity=0.294  Sum_probs=193.0

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC---------cccccccCCCCccc-
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---------GLLHYSVPNGAGTV-  181 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~---------~~~~~~l~n~~~k~-  181 (780)
                      ..++|++||.++...++-++|+.+|+|   +|..+...+..+||.+++|+-.+..+         .+.++.+...+.+. 
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            469999999999999999999999998   88888888899999999988543332         12222221110000 


Q ss_pred             -------CC-----CCCC---------CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEE
Q 004002          182 -------AG-----EHPY---------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISY  236 (780)
Q Consensus       182 -------~g-----~~~~---------~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F  236 (780)
                             .+     +.+.         ...+..+|+|+|||+.+.+.+|+.+|+.||.|..|.+    .++.+|||||+|
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                   00     0011         1233678999999999999999999999999999973    567789999999


Q ss_pred             ecHHHHHHHHHHccCccccccccccccCCCCCCCCC-----------------------------------------C--
Q 004002          237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD-----------------------------------------K--  273 (780)
Q Consensus       237 ~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~-----------------------------------------~--  273 (780)
                      .+..+|.+||+.+|+..|.||+|.|.||.+++....                                         +  
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            999999999999999999999999999866532100                                         0  


Q ss_pred             CC-------------------------------------------CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-
Q 004002          274 DL-------------------------------------------NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-  309 (780)
Q Consensus       274 ~~-------------------------------------------~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-  309 (780)
                      +.                                           ...+|||.|||+++|+++|.+.|++||+|..+.+ 
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            00                                           0048999999999999999999999999998753 


Q ss_pred             ----CCCcccEEEEEEcCHHHHHHHHHHh-----CC-CccCCceEEEEecCCCchhhh
Q 004002          310 ----TPHKRHHKFIEFYDVRAAEAALKSL-----NR-SDIAGKRIKLEPSRPGGARRN  357 (780)
Q Consensus       310 ----~g~srG~aFV~F~~~e~A~~Ai~~L-----nG-~~i~Gr~L~V~~a~~k~~r~~  357 (780)
                          +++++|.|||.|.+..+|.+||.+.     .| ..+.||.|+|..+-.+.+...
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~d  383 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEAAD  383 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHHHH
Confidence                8899999999999999999999987     23 578999999999988766543

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=1.4e-24  Score=232.63  Aligned_cols=241  Identities=19%  Similarity=0.329  Sum_probs=194.7

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----ccc-ccccCCC--CcccCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLL-HYSVPNG--AGTVAG  183 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~-~~~l~n~--~~k~~g  183 (780)
                      +.++||+.+|+.++|.+++.+|+.+|.|   .|..|+.+.+.+|++|+.+.....+.    .+. ...+++.  ...+..
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            4689999999999999999999999997   67788999999999999998765443    221 2222322  112211


Q ss_pred             CCCCCC--CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcc-ccc
Q 004002          184 EHPYGE--HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKP-LRR  256 (780)
Q Consensus       184 ~~~~~e--~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~-l~g  256 (780)
                      ....++  ...++|||+-|++.+||+|++++|++||.|++|+    ..+.+||||||.|.+.+.|..||++|||.. +.|
T Consensus       114 Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeG  193 (510)
T KOG0144|consen  114 ADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEG  193 (510)
T ss_pred             cchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeecc
Confidence            111112  3468999999999999999999999999999998    357899999999999999999999999964 544


Q ss_pred             --cccccccCCCCCCCCCCC------------------------------------------------------------
Q 004002          257 --RKLDIHFSIPKDNPSDKD------------------------------------------------------------  274 (780)
Q Consensus       257 --r~I~V~~a~pk~~~s~~~------------------------------------------------------------  274 (780)
                        .+|.|+|+++++++..+.                                                            
T Consensus       194 cs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~  273 (510)
T KOG0144|consen  194 CSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQ  273 (510)
T ss_pred             CCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhH
Confidence              589999987765431000                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q 004002          275 --------------------------------------------------------------------------------  274 (780)
Q Consensus       275 --------------------------------------------------------------------------------  274 (780)
                                                                                                      
T Consensus       274 ~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~  353 (510)
T KOG0144|consen  274 LQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAG  353 (510)
T ss_pred             HHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhccccccccc
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------CCccceeecCCC
Q 004002          275 --------------------------------------------------------------------LNQGTLVVFNLD  286 (780)
Q Consensus       275 --------------------------------------------------------------------~~~~~L~V~NLp  286 (780)
                                                                                          ....+|||.+||
T Consensus       354 a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlP  433 (510)
T KOG0144|consen  354 AGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLP  433 (510)
T ss_pred             ccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCc
Confidence                                                                                000379999999


Q ss_pred             CCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          287 PSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       287 ~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      .+.-+.+|-..|.+||.|++.++     ++.++.|+||.|++..+|.+||..|||..|++++++|...+.+..
T Consensus       434 qefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  434 QEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             hhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence            99999999999999999998763     778899999999999999999999999999999999988876543

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=4.9e-24  Score=228.56  Aligned_cols=163  Identities=23%  Similarity=0.442  Sum_probs=143.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcc-ccc--cccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKP-LRR--RKLDIH  262 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~-l~g--r~I~V~  262 (780)
                      +.-+|||+-||+.++|+|||.+|++||.|.+|.     .++.++|||||.|.+.++|.+|+.+|++.. |.|  .+|.|+
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            447999999999999999999999999998876     578899999999999999999999998865 544  588889


Q ss_pred             cCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCC-
Q 004002          263 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRS-  337 (780)
Q Consensus       263 ~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~-  337 (780)
                      |+....+..   ..+.+|||+-|++.+||.|++++|++||.|++|++    .+.+||||||+|.+.+.|..||++|||. 
T Consensus       113 ~Ad~E~er~---~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  113 YADGERERI---VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQ  189 (510)
T ss_pred             ccchhhhcc---ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccce
Confidence            887544322   34678999999999999999999999999999975    5789999999999999999999999996 


Q ss_pred             ccCC--ceEEEEecCCCchhh
Q 004002          338 DIAG--KRIKLEPSRPGGARR  356 (780)
Q Consensus       338 ~i~G--r~L~V~~a~~k~~r~  356 (780)
                      ++.|  .+|.|+||++++.+.
T Consensus       190 tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  190 TMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             eeccCCCceEEEecccCCCch
Confidence            7777  589999999887653

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.90  E-value=1.7e-23  Score=238.44  Aligned_cols=162  Identities=26%  Similarity=0.458  Sum_probs=142.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      +...++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++||. |+|..|.|++|.|.+
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            456789999999999999999999999999999873     57899999999999999999997 899999999999988


Q ss_pred             CCCCCCCCC--------CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHH
Q 004002          264 SIPKDNPSD--------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAA  330 (780)
Q Consensus       264 a~pk~~~s~--------~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~A  330 (780)
                      +........        ......+|||+|||..+++++|+++|++||.|+.|++     ++.++|||||+|.+.++|.+|
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            654322211        1122478999999999999999999999999999875     357789999999999999999


Q ss_pred             HHHhCCCccCCceEEEEecCC
Q 004002          331 LKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       331 i~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ++.|||..|.|+.|+|.++..
T Consensus       245 ~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       245 LEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHhcCCcEECCEEEEEEEccC
Confidence            999999999999999999984

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.89  E-value=6.4e-22  Score=228.50  Aligned_cols=153  Identities=13%  Similarity=0.236  Sum_probs=125.3

Q ss_pred             CCceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCCCC
Q 004002          113 IMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH  185 (780)
Q Consensus       113 v~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~~  185 (780)
                      .+.++||++|+.+++|.+++++|+.+|.|   .+.+|..++..+|++|+.|.+...+.    .+++..+.+...++....
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            46899999999999999999999999997   67778888899999999999887664    233444444332222110


Q ss_pred             C------------CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHH
Q 004002          186 P------------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA  248 (780)
Q Consensus       186 ~------------~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~  248 (780)
                      .            ......++|||+|||+++++++|+++|++||+|.+|+     .++++||||||+|.+.++|.+|++.
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            0            1112347999999999999999999999999999987     2578999999999999999999999


Q ss_pred             ccCccccccccccccCC
Q 004002          249 LQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       249 Lng~~l~gr~I~V~~a~  265 (780)
                      ||+..|+|+.|+|.++.
T Consensus       266 mNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             hCCCeeCCeEEEEEecC
Confidence            99999999999997754

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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.89  E-value=1.5e-22  Score=233.36  Aligned_cols=178  Identities=22%  Similarity=0.319  Sum_probs=153.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcccc-ccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~-gr~I~V~~a~  265 (780)
                      ..++|||+|||++++|++|+++|++||.|.+|+    .++++||||||+|.+.++|++||+.|++..|. ++.|.|.++.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            458999999999999999999999999999987    36889999999999999999999999999985 7888887653


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCC-eeEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCC--
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNR--  336 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~-I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~LnG--  336 (780)
                                ..++|||+|||.++++++|++.|++++. |+++.+      .++++|||||+|+++++|++|++.|+.  
T Consensus       137 ----------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gk  206 (578)
T TIGR01648       137 ----------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGR  206 (578)
T ss_pred             ----------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccc
Confidence                      2468999999999999999999999863 333322      345789999999999999999999864  


Q ss_pred             CccCCceEEEEecCCCch---------hhhHhhhhchhccHHHHHHHHhhh
Q 004002          337 SDIAGKRIKLEPSRPGGA---------RRNLMLQLNQELEQDESRILQHQV  378 (780)
Q Consensus       337 ~~i~Gr~L~V~~a~~k~~---------r~~~l~ql~~~~~~~~~~~~~~~~  378 (780)
                      ..+.|+.|.|+++.++..         +..++.++...+++++++.+|.++
T Consensus       207 i~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f  257 (578)
T TIGR01648       207 IQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEF  257 (578)
T ss_pred             eEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhc
Confidence            367899999999987542         235678898999999999999988

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.

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.88  E-value=5.3e-23  Score=232.36  Aligned_cols=323  Identities=19%  Similarity=0.237  Sum_probs=218.1

Q ss_pred             CCCceeecCCCccccccCCCccccccCCcccccccccCcCCCCCCcccccccCcccccCCCCCCCCcccccccccCCCCC
Q 004002           24 GGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLP  103 (780)
Q Consensus        24 ~~~~~~~~~~a~~~~~~~~~~~fsssl~~~~~~kl~~~~s~~~~~~~d~~~~~~k~~~~eee~~e~~ee~e~~~i~nlLP  103 (780)
                      +-.+|++|..|+++...+|+..|+||+.++++.+-.-+..    ...+.....|++    +.+.........-..||.|.
T Consensus       249 a~v~~~~~~~avka~~~~D~k~fqgrmlhvlp~~~k~~~~----~~~~~~~~~~k~----~ke~~rk~~~~~~~~wn~l~  320 (725)
T KOG0110|consen  249 AFVTFMFPEHAVKAYSELDGKVFQGRMLHVLPSKEKSTAK----EDASELGSDYKK----EKELKRKAASASFHSWNTLF  320 (725)
T ss_pred             HHHhhhhhHHHHhhhhhccccccccceeeecCcchhhhhh----hhHhhcCCcHHH----HHHhccccchhcceeccccc
Confidence            3456899999999999999999999999999887653222    111111111322    22222222222222344444


Q ss_pred             CchHHhhhcC------------------------------------------------------CceeeeccCCCCCChH
Q 004002          104 DDEDELLAGI------------------------------------------------------MDDFDLRGLPSSLEDL  129 (780)
Q Consensus       104 ~deddl~s~v------------------------------------------------------~~el~V~~Lp~s~~E~  129 (780)
                      ..++.++..+                                                      -+-+.+++||....+.
T Consensus       321 ~~~~ava~~~a~k~~v~k~~i~d~~~~gsavr~al~etr~~~e~~~~~ee~gV~l~~F~~~~rs~~vil~kNlpa~t~~~  400 (725)
T KOG0110|consen  321 MGANAVAGILAQKLGVEKSRILDGSLSGSAVRLALGETRVVQEVRRFFEENGVKLDAFSQAERSDTVILVKNLPAGTLSE  400 (725)
T ss_pred             ccccHHHHHHHHHhCCeeeeeechhhcchHHHHHHHHhhhchhhhhhHHhhCcccccchhhhhhcceeeeccCccccccH
Confidence            3322211110                                                      0236689999999999


Q ss_pred             HHHHHhcCCCcE------------EEeccCccCcccceEEEeecCccccC--------cccc-----cccCCCCccc---
Q 004002          130 EDYDIFGSGGGM------------ELEGEPQESLSMSMSKISISDSASGN--------GLLH-----YSVPNGAGTV---  181 (780)
Q Consensus       130 el~dlFs~~G~i------------~V~~d~~esa~~g~~~v~~~~~~~a~--------~~~~-----~~l~n~~~k~---  181 (780)
                      ++.++|..+|.|            .|+|.....+-.++.++.+.....+.        .+..     -.+.+.....   
T Consensus       401 elt~~F~~fG~i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee  480 (725)
T KOG0110|consen  401 ELTEAFLRFGEIGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEE  480 (725)
T ss_pred             HHHHHhhcccccceeecCcccceeeeeecCccchHHHHHHhchhhhccCccccccChhhhccCCcccccccccccccccc
Confidence            999999999976            22333333333344333332111110        1111     0000000000   


Q ss_pred             ---------CC-----CC-----C-----CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC--------CCcc
Q 004002          182 ---------AG-----EH-----P-----YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--------CKHR  229 (780)
Q Consensus       182 ---------~g-----~~-----~-----~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t--------gksk  229 (780)
                               .+     ..     +     ......++|||+||++++|.++|..+|..+|.|.++.+.        ..+.
T Consensus       481 ~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSm  560 (725)
T KOG0110|consen  481 NPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSM  560 (725)
T ss_pred             CcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEecccccccccccc
Confidence                     00     00     0     001112349999999999999999999999999998521        2356


Q ss_pred             eEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCC-----CCCCCCccceeecCCCCCCChhHHHHHhcccCCe
Q 004002          230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP-----SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV  304 (780)
Q Consensus       230 G~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~-----s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I  304 (780)
                      |||||+|.+.++|++|++.|+|+.|.|..|.|+++..+...     .......++|+|+|||+..+..+++++|+.||.|
T Consensus       561 GfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGql  640 (725)
T KOG0110|consen  561 GFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQL  640 (725)
T ss_pred             ceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccce
Confidence            99999999999999999999999999999999998721110     0111224689999999999999999999999999


Q ss_pred             eEEEeCCC-----cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          305 KEIRETPH-----KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       305 ~~v~~~g~-----srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      ++|++..+     .+|||||+|-+..+|.+|+.+|.++.+.||+|.++|++....
T Consensus       641 ksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  641 KSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             eeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccchH
Confidence            99987432     489999999999999999999999999999999999998765

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.88  E-value=6.7e-22  Score=218.47  Aligned_cols=235  Identities=15%  Similarity=0.307  Sum_probs=191.6

Q ss_pred             eeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCCCCCCC
Q 004002          116 DFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYG  188 (780)
Q Consensus       116 el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~~~~~  188 (780)
                      .++|+   .+++|..++++|+..|.+   +|+.|. +  +.|++++.|.+...|.    .++...+.+....+.-.   .
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s---~   73 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWS---Q   73 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehh---c
Confidence            46777   899999999999999996   888888 5  8889999998876654    23222333333332211   1


Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                       +....|||+||++++|.++|.++|+.||+|.+|++   ...++|| ||+|.++++|++|++.+||..+.+++|.|....
T Consensus        74 -rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   74 -RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             -cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence             12233999999999999999999999999999983   2339999 999999999999999999999999999998776


Q ss_pred             CCCCCCCC----CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCC
Q 004002          266 PKDNPSDK----DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRS  337 (780)
Q Consensus       266 pk~~~s~~----~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~  337 (780)
                      ++..+...    .....+++|.|++.+++++.|..+|+.||.|..+.+    .+++++|+||.|++.++|..|++.|+|.
T Consensus       152 ~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~  231 (369)
T KOG0123|consen  152 RKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGK  231 (369)
T ss_pred             chhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCC
Confidence            65543322    223468999999999999999999999999999875    4567999999999999999999999999


Q ss_pred             ccCCceEEEEecCCCchhhhHhhh
Q 004002          338 DIAGKRIKLEPSRPGGARRNLMLQ  361 (780)
Q Consensus       338 ~i~Gr~L~V~~a~~k~~r~~~l~q  361 (780)
                      .+.++.+.|..++++.++...++.
T Consensus       232 ~~~~~~~~V~~aqkk~e~~~~l~~  255 (369)
T KOG0123|consen  232 IFGDKELYVGRAQKKSEREAELKR  255 (369)
T ss_pred             cCCccceeecccccchhhHHHHhh
Confidence            999999999999987766554443

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.88  E-value=3.8e-22  Score=230.17  Aligned_cols=163  Identities=17%  Similarity=0.290  Sum_probs=135.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcC------------CCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQY------------GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~y------------G~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                      .....++|||+|||+++|+++|+++|.++            +.|..+ ..++.+|||||+|.+.++|.+||+ |+|..|.
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~-~~~~~kg~afVeF~~~e~A~~Al~-l~g~~~~  248 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSV-NINKEKNFAFLEFRTVEEATFAMA-LDSIIYS  248 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEE-EECCCCCEEEEEeCCHHHHhhhhc-CCCeEee
Confidence            34566899999999999999999999975            234444 357789999999999999999995 9999999


Q ss_pred             ccccccccCCCCCCC-------C------------------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-
Q 004002          256 RRKLDIHFSIPKDNP-------S------------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-  309 (780)
Q Consensus       256 gr~I~V~~a~pk~~~-------s------------------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-  309 (780)
                      |+.|.|.........       .                  .......+|||+|||..+++++|+++|+.||.|+.+.+ 
T Consensus       249 g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~  328 (509)
T TIGR01642       249 NVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLI  328 (509)
T ss_pred             CceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEE
Confidence            999999753211100       0                  00112358999999999999999999999999998865 


Q ss_pred             ----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          310 ----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       310 ----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                          ++.++|||||+|.+.++|.+||..|||..|.|++|.|.++..+
T Consensus       329 ~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       329 KDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             ecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence                5678999999999999999999999999999999999998643

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=1.8e-21  Score=209.97  Aligned_cols=180  Identities=22%  Similarity=0.343  Sum_probs=157.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccc-ccccccccC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFS  264 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~-gr~I~V~~a  264 (780)
                      ..+.|||+.||.++.|+||.-+|++.|+|-+++     .+|.+||||||.|.+.++|++|++.||+.+|. |+.|.|+.+
T Consensus        82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen   82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             CCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEe
Confidence            458999999999999999999999999999988     47999999999999999999999999999995 899999876


Q ss_pred             CCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCC-eeEEEe------CCCcccEEEEEEcCHHHHHHHHHHhC-C
Q 004002          265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLN-R  336 (780)
Q Consensus       265 ~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~-I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~Ln-G  336 (780)
                      .          ..+.|||+|||+.+++|+|++.+++.++ |+.|.+      ..++||||||+|+++..|..|.++|- |
T Consensus       162 v----------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g  231 (506)
T KOG0117|consen  162 V----------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPG  231 (506)
T ss_pred             e----------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCC
Confidence            5          3468999999999999999999998854 444432      45789999999999999999999884 3


Q ss_pred             -CccCCceEEEEecCCCchh---------hhHhhhhchhccHHHHHHHHhhhCC
Q 004002          337 -SDIAGKRIKLEPSRPGGAR---------RNLMLQLNQELEQDESRILQHQVGS  380 (780)
Q Consensus       337 -~~i~Gr~L~V~~a~~k~~r---------~~~l~ql~~~~~~~~~~~~~~~~Gs  380 (780)
                       .++.|..+.|+||.|...-         ..+++++....+++.+...|.++|.
T Consensus       232 ~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~  285 (506)
T KOG0117|consen  232 KIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGK  285 (506)
T ss_pred             ceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccc
Confidence             3778999999999986542         3468899999999999999998863

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.86  E-value=1.4e-21  Score=189.87  Aligned_cols=161  Identities=25%  Similarity=0.345  Sum_probs=143.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...||||+||+..++++.|.++|-+.|+|..++     ++.+.+|||||+|.++|+|+-|++.|+...|.||+|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            458999999999999999999999999999987     467899999999999999999999999999999999998776


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEE----E--eCCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----R--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v----~--~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i  339 (780)
                      ..   ........+|||+||++.+++..|.++|+.||.|...    +  .++.++++|||.|++.+.+.+||.+|||..+
T Consensus        88 ~~---~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l  164 (203)
T KOG0131|consen   88 AH---QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYL  164 (203)
T ss_pred             cc---cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchh
Confidence            21   1222234799999999999999999999999998763    2  4678999999999999999999999999999


Q ss_pred             CCceEEEEecCCCch
Q 004002          340 AGKRIKLEPSRPGGA  354 (780)
Q Consensus       340 ~Gr~L~V~~a~~k~~  354 (780)
                      ..++|.|+++.++..
T Consensus       165 ~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  165 CNRPITVSYAFKKDT  179 (203)
T ss_pred             cCCceEEEEEEecCC
Confidence            999999999877653

>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=1.3e-21  Score=201.36  Aligned_cols=148  Identities=28%  Similarity=0.462  Sum_probs=137.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD  272 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~  272 (780)
                      -+|||+|||.++++.+|+.+|++||+|.+|.+   -|.||||..++...|+.||+.|++..|+|..|.|+-++.+.    
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDI---vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs----   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDI---VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS----   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeee---ecccceEEeecccccHHHHhhcccceecceEEEEEeccccC----
Confidence            47999999999999999999999999999985   46799999999999999999999999999999999876553    


Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                        ....+|+|+||.+.++.+||+..|++||.|++|++.   ++|+||.|+-.++|..||+.|+++++.|++++|..+..+
T Consensus        76 --k~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv---kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   76 --KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV---KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             --CCccccccCCCCccccCHHHhhhhcccCCceeeeee---cceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence              345689999999999999999999999999999986   789999999999999999999999999999999988664

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=3.1e-21  Score=213.21  Aligned_cols=240  Identities=24%  Similarity=0.395  Sum_probs=193.3

Q ss_pred             eeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCcc----cccccCCCCccc-------C
Q 004002          117 FDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL----LHYSVPNGAGTV-------A  182 (780)
Q Consensus       117 l~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~----~~~~l~n~~~k~-------~  182 (780)
                      ++|.+|+.+++..+++|+|+.+|.|   .|..+..-  .+|+ ++.|.+...|..+    ++..+.+..+.+       .
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g--~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG--SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC--ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            8999999999999999999999997   66666433  8888 9999987766522    222222221111       1


Q ss_pred             CCCCCCC--CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccc
Q 004002          183 GEHPYGE--HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRR  256 (780)
Q Consensus       183 g~~~~~e--~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g  256 (780)
                      ...+..+  ..-++++|+|++.++++++|..+|..||.|.++.    ..++++||+||.|.+.++|..|++.|++..+.+
T Consensus       156 r~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~  235 (369)
T KOG0123|consen  156 REAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGD  235 (369)
T ss_pred             hcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCc
Confidence            1111111  2346899999999999999999999999999987    457799999999999999999999999999999


Q ss_pred             cccccccCCCCCCCC--------------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEE
Q 004002          257 RKLDIHFSIPKDNPS--------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKF  318 (780)
Q Consensus       257 r~I~V~~a~pk~~~s--------------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aF  318 (780)
                      ..+.|..+..+....              .......+|||.|++..++++.|+.+|+.||+|..+++    .+.++|+||
T Consensus       236 ~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gf  315 (369)
T KOG0123|consen  236 KELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFGF  315 (369)
T ss_pred             cceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCccceEE
Confidence            999998776532211              11234579999999999999999999999999999875    577899999


Q ss_pred             EEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchhhhHh
Q 004002          319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM  359 (780)
Q Consensus       319 V~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r~~~l  359 (780)
                      |+|...++|.+|+..+|+..+.++.|.|.+++.+..++..+
T Consensus       316 V~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~~~~  356 (369)
T KOG0123|consen  316 VEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRRARL  356 (369)
T ss_pred             EEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccchhhh
Confidence            99999999999999999999999999999998666555433

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.83  E-value=6.2e-20  Score=201.72  Aligned_cols=161  Identities=22%  Similarity=0.375  Sum_probs=143.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      .||||++||+.++.++|.++|+.+|+|..|.+     ++.+||||||+|.-.+++++|++.+.+..+.|+.|.|.++.++
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            79999999999999999999999999999872     3568999999999999999999999999999999999998765


Q ss_pred             CCCCC----------C------------CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEE
Q 004002          268 DNPSD----------K------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEF  321 (780)
Q Consensus       268 ~~~s~----------~------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F  321 (780)
                      ....+          +            +.....|.|.|||+.+.+++|+.+|+.||.|.+|.+    .++-+|||||.|
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            43220          0            112458999999999999999999999999999987    344569999999


Q ss_pred             cCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       322 ~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      .+..+|.+||+.+||..|.||+|-|.||-++.
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            99999999999999999999999999998765

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.78  E-value=1.5e-19  Score=183.95  Aligned_cols=166  Identities=23%  Similarity=0.431  Sum_probs=141.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcc-ccc--ccccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKP-LRR--RKLDIHF  263 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~-l~g--r~I~V~~  263 (780)
                      .+++|||+-|.+.-.|||++.+|..||.|++|.    ..+.+||||||.|.+..+|..||..|+|.. +.|  ..|.|+|
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            569999999999999999999999999999987    367899999999999999999999999965 333  4566666


Q ss_pred             CCCCCCCCC-----------------------------------------------------------------------
Q 004002          264 SIPKDNPSD-----------------------------------------------------------------------  272 (780)
Q Consensus       264 a~pk~~~s~-----------------------------------------------------------------------  272 (780)
                      ++..+++.-                                                                       
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            443322100                                                                       


Q ss_pred             --------------------------------------------------------------------------------
Q 004002          273 --------------------------------------------------------------------------------  272 (780)
Q Consensus       273 --------------------------------------------------------------------------------  272 (780)
                                                                                                      
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             -----------------------CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCH
Q 004002          273 -----------------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDV  324 (780)
Q Consensus       273 -----------------------~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~  324 (780)
                                             +....++|||.+||.+..+.||.++|-+||.|++.++     +..+|.||||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                                   0001158999999999999999999999999999864     778999999999999


Q ss_pred             HHHHHHHHHhCCCccCCceEEEEecCCCchhh
Q 004002          325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  356 (780)
Q Consensus       325 e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r~  356 (780)
                      .+|++||.+|||..|+-|+|+|...+|+.+.+
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            99999999999999999999999999987654

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.77  E-value=9.1e-19  Score=184.37  Aligned_cols=157  Identities=22%  Similarity=0.468  Sum_probs=139.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      |++||+.|.+++.|+.||..|..||+|.++.     .++++||||||+|+-+|.|+.|++.|||..++||.|+|..  |.
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr--Ps  191 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR--PS  191 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC--CC
Confidence            7999999999999999999999999999998     5899999999999999999999999999999999999974  33


Q ss_pred             CCCCC---------CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 004002          268 DNPSD---------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       268 ~~~s~---------~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                      ..+..         +...-..|||..+.++++++||+..|+.||+|+.|.+     .+..||||||+|.+..+...||..
T Consensus       192 NmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             CCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            22211         1123358999999999999999999999999999976     345689999999999999999999


Q ss_pred             hCCCccCCceEEEEecCC
Q 004002          334 LNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       334 LnG~~i~Gr~L~V~~a~~  351 (780)
                      ||=..++|.-|+|..+-.
T Consensus       272 MNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  272 MNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             cchhhcccceEecccccC
Confidence            999999999999976643

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=5.7e-18  Score=186.26  Aligned_cols=154  Identities=20%  Similarity=0.308  Sum_probs=126.8

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  186 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~~~  186 (780)
                      .++|+|++|+.+++|.+|+++|+.+|.|   .|..|..+...+++++|.|.+...|.    .++...+.+..+++....+
T Consensus       107 ~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p  186 (346)
T TIGR01659       107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP  186 (346)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccc
Confidence            4789999999999999999999999997   66778888889999999999876664    3344445555444433322


Q ss_pred             C-CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccc--cc
Q 004002          187 Y-GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RK  258 (780)
Q Consensus       187 ~-~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~  258 (780)
                      . .....++|||+|||+++|+++|+++|++||+|..|+     .++++||||||+|.+.++|++||++|++..+.+  ++
T Consensus       187 ~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~  266 (346)
T TIGR01659       187 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQP  266 (346)
T ss_pred             cccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCcee
Confidence            2 223467899999999999999999999999998876     367889999999999999999999999998865  68


Q ss_pred             cccccCCCC
Q 004002          259 LDIHFSIPK  267 (780)
Q Consensus       259 I~V~~a~pk  267 (780)
                      |.|.++...
T Consensus       267 l~V~~a~~~  275 (346)
T TIGR01659       267 LTVRLAEEH  275 (346)
T ss_pred             EEEEECCcc
Confidence            888887654

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).

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.73  E-value=4.7e-17  Score=164.04  Aligned_cols=161  Identities=27%  Similarity=0.464  Sum_probs=141.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHH----HhhcCCCEEEEE--eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRA----LFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~----lF~~yG~I~sv~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      .+..||||+||+..+..++|+.    +|++||.|..|.  .+.+.||.|||.|.+.+.|..|+++|+|..+.|++++|+|
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            3556999999999999999988    999999999987  5789999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCC----------------------------------------------CCCccceeecCCCCCCChhHHHHH
Q 004002          264 SIPKDNPSDK----------------------------------------------DLNQGTLVVFNLDPSVSNEDLRQI  297 (780)
Q Consensus       264 a~pk~~~s~~----------------------------------------------~~~~~~L~V~NLp~~vteedL~~~  297 (780)
                      |..+.....+                                              ......|++.|||..++.+.|..+
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            8654321110                                              112357999999999999999999


Q ss_pred             hcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecC
Q 004002          298 FGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSR  350 (780)
Q Consensus       298 Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~  350 (780)
                      |.+|..-++|+.....++.|||+|.+...|..|.+.|.|..|. ...++|.+++
T Consensus       167 f~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  167 FEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999999999987777899999999999999999999998886 7888888775

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=1.7e-17  Score=169.75  Aligned_cols=135  Identities=25%  Similarity=0.426  Sum_probs=114.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      +..|||||+||+.+|||+-|..||.+.|.|.+|++-          |+                    .|+|.|+....+
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i----------~~--------------------e~~v~wa~~p~n   53 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVI----------FD--------------------ELKVNWATAPGN   53 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceee----------hh--------------------hhccccccCccc
Confidence            456999999999999999999999999999988732          22                    466777655444


Q ss_pred             CCCCCCC-ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce
Q 004002          270 PSDKDLN-QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  343 (780)
Q Consensus       270 ~s~~~~~-~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~  343 (780)
                      .+....+ .--+||+.|...++.|+||+.|.+||+|.++++     ++++||||||.|-+.++|+.||..|||.+|++|.
T Consensus        54 Qsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~  133 (321)
T KOG0148|consen   54 QSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRT  133 (321)
T ss_pred             CCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccce
Confidence            4333333 346999999999999999999999999999875     7899999999999999999999999999999999


Q ss_pred             EEEEecCCCch
Q 004002          344 IKLEPSRPGGA  354 (780)
Q Consensus       344 L~V~~a~~k~~  354 (780)
                      |+-.||..|..
T Consensus       134 IRTNWATRKp~  144 (321)
T KOG0148|consen  134 IRTNWATRKPS  144 (321)
T ss_pred             eeccccccCcc
Confidence            99999977653

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.71  E-value=7.4e-17  Score=178.94  Aligned_cols=236  Identities=20%  Similarity=0.252  Sum_probs=172.8

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC---cccccccCCCCccc-------
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTV-------  181 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~---~~~~~~l~n~~~k~-------  181 (780)
                      ..+++-.+.....+-+++++|+..|.|   .+..|..+.+.+|++++.|.+...-.   .+.+-.+.+-+..+       
T Consensus       180 Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaek  259 (549)
T KOG0147|consen  180 RTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEK  259 (549)
T ss_pred             HHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHHH
Confidence            345555666666788999999999986   67788888899999999988653211   11111111111000       


Q ss_pred             --------CCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHH
Q 004002          182 --------AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA  248 (780)
Q Consensus       182 --------~g~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~  248 (780)
                              .........+-+.|||+||..++++++|+.+|+.||.|+.|.     .+|+++|||||+|.+.++|++|+..
T Consensus       260 nr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~  339 (549)
T KOG0147|consen  260 NRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQ  339 (549)
T ss_pred             HHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHH
Confidence                    000001122334499999999999999999999999999886     3899999999999999999999999


Q ss_pred             ccCccccccccccccCCCCCCCCC--------------------------------------------------------
Q 004002          249 LQNKPLRRRKLDIHFSIPKDNPSD--------------------------------------------------------  272 (780)
Q Consensus       249 Lng~~l~gr~I~V~~a~pk~~~s~--------------------------------------------------------  272 (780)
                      |||..|.|+.|+|.....+-...+                                                        
T Consensus       340 lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~  419 (549)
T KOG0147|consen  340 LNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAA  419 (549)
T ss_pred             hccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHH
Confidence            999999999999865321100000                                                        


Q ss_pred             ------------CC-------CCccceeecCC--CCCCC--------hhHHHHHhcccCCeeEEEeCCCcccEEEEEEcC
Q 004002          273 ------------KD-------LNQGTLVVFNL--DPSVS--------NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYD  323 (780)
Q Consensus       273 ------------~~-------~~~~~L~V~NL--p~~vt--------eedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~  323 (780)
                                  ..       +...++.++|+  |.+.|        .||+.+.+++||.|.-|.+...+-|+.||+|.+
T Consensus       420 ~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s  499 (549)
T KOG0147|consen  420 QFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPS  499 (549)
T ss_pred             hhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCc
Confidence                        00       11124455555  22222        477888889999999999988888999999999


Q ss_pred             HHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          324 VRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       324 ~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      .++|..|+++|||.+|+|+.|...+-.
T Consensus       500 ~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  500 AEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             HHHHHHHHHHHhhhhhccceeEEEEee
Confidence            999999999999999999999998764

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.69  E-value=2.4e-16  Score=166.23  Aligned_cols=238  Identities=14%  Similarity=0.257  Sum_probs=180.8

Q ss_pred             cCCceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCCC
Q 004002          112 GIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGE  184 (780)
Q Consensus       112 ~v~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~  184 (780)
                      ++|+++||+.+...+.|+.++..|..||.|   ...-|+.+...++|+|+.+.-.+.+.    .|++.-+-+..+++...
T Consensus       111 aiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  111 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            368999999999999999999999999997   56678889999999999888665543    33333333333333221


Q ss_pred             CC------------CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHH
Q 004002          185 HP------------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMR  247 (780)
Q Consensus       185 ~~------------~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~  247 (780)
                      ..            ...+.-.+|||..+.++.+|+||+.+|+.||+|..|.     ..+.+|||+||+|.+..+-..|+.
T Consensus       191 sNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAia  270 (544)
T KOG0124|consen  191 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  270 (544)
T ss_pred             CCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhh
Confidence            11            0112347999999999999999999999999999998     356799999999999999999999


Q ss_pred             HccCccccccccccccCCCCCCCC--------------------------------------------------------
Q 004002          248 ALQNKPLRRRKLDIHFSIPKDNPS--------------------------------------------------------  271 (780)
Q Consensus       248 ~Lng~~l~gr~I~V~~a~pk~~~s--------------------------------------------------------  271 (780)
                      .||-..|+|..|+|..+....+.-                                                        
T Consensus       271 sMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~  350 (544)
T KOG0124|consen  271 SMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLG  350 (544)
T ss_pred             hcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCC
Confidence            999999999988886632111000                                                        


Q ss_pred             ----------------------------------------------------CC--------------------------
Q 004002          272 ----------------------------------------------------DK--------------------------  273 (780)
Q Consensus       272 ----------------------------------------------------~~--------------------------  273 (780)
                                                                          ++                          
T Consensus       351 ~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~  430 (544)
T KOG0124|consen  351 TLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGS  430 (544)
T ss_pred             CccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCc
Confidence                                                                00                          


Q ss_pred             ------------CCCccceeecCC--CCCCC---hhHHHHHhcccCCeeEEEeCCCccc---------EEEEEEcCHHHH
Q 004002          274 ------------DLNQGTLVVFNL--DPSVS---NEDLRQIFGAYGEVKEIRETPHKRH---------HKFIEFYDVRAA  327 (780)
Q Consensus       274 ------------~~~~~~L~V~NL--p~~vt---eedL~~~Fs~yG~I~~v~~~g~srG---------~aFV~F~~~e~A  327 (780)
                                  ....+.+.++|+  |.+++   +.+|++.+++||.|..|-+.....+         .-||+|....++
T Consensus       431 sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~  510 (544)
T KOG0124|consen  431 SARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASET  510 (544)
T ss_pred             cHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHH
Confidence                        000134667776  55565   5788999999999999866333222         269999999999


Q ss_pred             HHHHHHhCCCccCCceEEEEec
Q 004002          328 EAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       328 ~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .+|+++|+|+.|+|+++..+..
T Consensus       511 ~rak~ALdGRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  511 HRAKQALDGRFFGGRKVVAEVY  532 (544)
T ss_pred             HHHHHhhccceecCceeehhhh
Confidence            9999999999999999876543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.66  E-value=1.6e-16  Score=170.75  Aligned_cols=162  Identities=19%  Similarity=0.402  Sum_probs=141.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||++|++++++|.|++.|.+||+|.+|.     .+++++||+||+|.+.+...+++.. ....|.++.|.+..+.
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            578999999999999999999999999999987     4689999999999999999988884 5677899999999998


Q ss_pred             CCCCCCCCCC--CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          266 PKDNPSDKDL--NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       266 pk~~~s~~~~--~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      ++....+...  ...++||++||.++++++|++.|.+||.|..+.+     +.+.++|+||.|++.+++.+++. ..-+.
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            8765443322  3568999999999999999999999998877643     56789999999999999999987 57789


Q ss_pred             cCCceEEEEecCCCch
Q 004002          339 IAGKRIKLEPSRPGGA  354 (780)
Q Consensus       339 i~Gr~L~V~~a~~k~~  354 (780)
                      |.|+.+.|+.|.|+..
T Consensus       163 ~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEV  178 (311)
T ss_pred             ecCceeeEeeccchhh
Confidence            9999999999998763

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.61  E-value=3.9e-16  Score=173.23  Aligned_cols=163  Identities=23%  Similarity=0.373  Sum_probs=139.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      .+...+++|+--|+..++..+|.++|+.+|.|..|+     .+++++|.|||+|.+.+....||. |.|..+.|.+|.|+
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            345668999999999999999999999999999987     467899999999999999999996 99999999999998


Q ss_pred             cCCCCCCCCCC----------CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHH
Q 004002          263 FSIPKDNPSDK----------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAA  327 (780)
Q Consensus       263 ~a~pk~~~s~~----------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A  327 (780)
                      .....++....          ..+...|||+||...+++++|+.+|++||.|..|.+     +|.++|||||+|.+.++|
T Consensus       254 ~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~a  333 (549)
T KOG0147|consen  254 LSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDA  333 (549)
T ss_pred             ccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHH
Confidence            75433322110          111123999999999999999999999999999853     788999999999999999


Q ss_pred             HHHHHHhCCCccCCceEEEEecCC
Q 004002          328 EAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       328 ~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .+|+..|||.++.|+.|+|..-..
T Consensus       334 r~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  334 RKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             HHHHHHhccceecCceEEEEEeee
Confidence            999999999999999999976543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.60  E-value=4.4e-15  Score=159.29  Aligned_cols=240  Identities=23%  Similarity=0.317  Sum_probs=169.1

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE------------EEeccCccCcccceEEEeecCccccC--cccccc----cC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM------------ELEGEPQESLSMSMSKISISDSASGN--GLLHYS----VP  175 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i------------~V~~d~~esa~~g~~~v~~~~~~~a~--~~~~~~----l~  175 (780)
                      ..-+.+++||++++|.|+++++..||.+            +|++.+.+++..-...++-.......  ...+|.    +.
T Consensus        28 SkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~sn~~~lk  107 (492)
T KOG1190|consen   28 SKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYSNHSELK  107 (492)
T ss_pred             cceeEeccCCccccHHHHHHhcccccceeeeeeeccchhhhhhhcchhhhhheeecccccCccccCcceeehhhhHHHHh
Confidence            3568999999999999999999999987            55555555443311111100000000  000000    00


Q ss_pred             -----C----C------------CcccC--CCC---CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcc
Q 004002          176 -----N----G------------AGTVA--GEH---PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR  229 (780)
Q Consensus       176 -----n----~------------~~k~~--g~~---~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgksk  229 (780)
                           +    .            +....  ...   .....+--.++|.|+-..|+-+-|..+|++||.|..|.+..|.-
T Consensus       108 t~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn  187 (492)
T KOG1190|consen  108 TDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNN  187 (492)
T ss_pred             ccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEeccc
Confidence                 0    0            00000  010   11111224678999999999999999999999999999888888


Q ss_pred             eE-EEEEEecHHHHHHHHHHccCcccc--ccccccccCCC----------CCC-------CCC-----------------
Q 004002          230 GF-VMISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIP----------KDN-------PSD-----------------  272 (780)
Q Consensus       230 G~-aFV~F~~~e~A~~Al~~Lng~~l~--gr~I~V~~a~p----------k~~-------~s~-----------------  272 (780)
                      || |.|+|.+.+.|+.|..+|+|..|.  .+.|+|.|+.-          +..       +..                 
T Consensus       188 ~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~  267 (492)
T KOG1190|consen  188 GFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSV  267 (492)
T ss_pred             chhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhcccccc
Confidence            87 999999999999999999999884  34666665321          100       000                 


Q ss_pred             ---------------------C--CC--CccceeecCCCC-CCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHH
Q 004002          273 ---------------------K--DL--NQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRA  326 (780)
Q Consensus       273 ---------------------~--~~--~~~~L~V~NLp~-~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~  326 (780)
                                           .  ..  ....|.|.||.. .+|.+.|..+|+.||+|..|++.-+++..|.|+|.|...
T Consensus       268 ~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~q  347 (492)
T KOG1190|consen  268 PAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQ  347 (492)
T ss_pred             ccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhH
Confidence                                 0  00  024678888864 689999999999999999999876667889999999999


Q ss_pred             HHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          327 AEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       327 A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      |+-|+..|+|.++.||+|+|.+++...
T Consensus       348 AqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  348 AQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             HHHHHHHhhcceecCceEEEeeccCcc
Confidence            999999999999999999999998654

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=9.3e-15  Score=142.52  Aligned_cols=149  Identities=22%  Similarity=0.327  Sum_probs=126.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCC--CcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC--KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tg--kskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ..+++|||+|||.++-+.||.++|-+||.|..|....  ...+||||+|++..+|+.||..-+|..+.|..|+|+|+.--
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            3568999999999999999999999999999987433  34579999999999999999999999999999999997644


Q ss_pred             CCCCCC----------------------CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHH
Q 004002          268 DNPSDK----------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR  325 (780)
Q Consensus       268 ~~~s~~----------------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e  325 (780)
                      ...+..                      ...+-.|.|.+||.+-+++||+++..+-|.|....+..  .|++.|+|...|
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~r--Dg~GvV~~~r~e  161 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQR--DGVGVVEYLRKE  161 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeec--ccceeeeeeehh
Confidence            211110                      11234799999999999999999999999998888753  468999999999


Q ss_pred             HHHHHHHHhCCCccC
Q 004002          326 AAEAALKSLNRSDIA  340 (780)
Q Consensus       326 ~A~~Ai~~LnG~~i~  340 (780)
                      +.+-|++.|....+.
T Consensus       162 DMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  162 DMKYAVRKLDDQKFR  176 (241)
T ss_pred             hHHHHHHhhcccccc
Confidence            999999999877654

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.57  E-value=2e-14  Score=163.41  Aligned_cols=191  Identities=25%  Similarity=0.373  Sum_probs=153.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcce-EEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG-~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      +...+.++|+|||..+..++|..+|..||+|..+-..  .-| -+.|.|.+..+|.+|++.|.+..+...++++.|+...
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~d  459 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPED  459 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecC--cccceeeeeecCccchHHHHHHhchhhhccCccccccChhh
Confidence            3455889999999999999999999999999988432  334 4999999999999999999999999999888875211


Q ss_pred             C-------C-------------CCC------------CC-------------CCc-cceeecCCCCCCChhHHHHHhccc
Q 004002          268 D-------N-------------PSD------------KD-------------LNQ-GTLVVFNLDPSVSNEDLRQIFGAY  301 (780)
Q Consensus       268 ~-------~-------------~s~------------~~-------------~~~-~~L~V~NLp~~vteedL~~~Fs~y  301 (780)
                      .       .             +.+            ++             ... .+|||.||+++.|.++|...|.++
T Consensus       460 vf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~  539 (725)
T KOG0110|consen  460 VFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQ  539 (725)
T ss_pred             hccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhc
Confidence            0       0             000            00             011 249999999999999999999999


Q ss_pred             CCeeEEEeCC--------CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC--------CCch-----hhhHhh
Q 004002          302 GEVKEIRETP--------HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR--------PGGA-----RRNLML  360 (780)
Q Consensus       302 G~I~~v~~~g--------~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~--------~k~~-----r~~~l~  360 (780)
                      |.|.++.+..        .+.|||||+|++.++|++|++.|+|+.++|+.|.|+++.        ++..     .+.+++
T Consensus       540 G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVR  619 (725)
T KOG0110|consen  540 GTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVR  619 (725)
T ss_pred             CeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeee
Confidence            9999997632        234999999999999999999999999999999999887        1111     133567


Q ss_pred             hhchhccHHHHHHHHhhhCCC
Q 004002          361 QLNQELEQDESRILQHQVGSP  381 (780)
Q Consensus       361 ql~~~~~~~~~~~~~~~~Gsp  381 (780)
                      ++.-+.+..+++.+|..+|.-
T Consensus       620 NipFeAt~rEVr~LF~aFGql  640 (725)
T KOG0110|consen  620 NIPFEATKREVRKLFTAFGQL  640 (725)
T ss_pred             ccchHHHHHHHHHHHhcccce
Confidence            777788888999999888744

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.56  E-value=2.4e-12  Score=139.09  Aligned_cols=158  Identities=23%  Similarity=0.383  Sum_probs=130.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhh-cCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFE-QYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~-~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .|.+||.|||+++...+|+++|. +.|+|+.|.    ..+|.||||.|+|+++|.+++|++.||...+.||+|.|+--..
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            46799999999999999999996 789999886    5799999999999999999999999999999999998864211


Q ss_pred             CCC------------------------------------------CCCCC------------------------------
Q 004002          267 KDN------------------------------------------PSDKD------------------------------  274 (780)
Q Consensus       267 k~~------------------------------------------~s~~~------------------------------  274 (780)
                      ...                                          +.+++                              
T Consensus       124 ~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~F  203 (608)
T KOG4212|consen  124 EQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASF  203 (608)
T ss_pred             hhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhh
Confidence            000                                          00000                              


Q ss_pred             ---------CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 004002          275 ---------LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (780)
Q Consensus       275 ---------~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G  341 (780)
                               .....+||.||+..+..+.|++.|.--|.|+.|.+    .+.++|++.|+|+.+-+|..||..|++.-+..
T Consensus       204 lr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~  283 (608)
T KOG4212|consen  204 LRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFD  283 (608)
T ss_pred             hhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCcc
Confidence                     01136899999999999999999999999998853    56789999999999999999999999876666


Q ss_pred             ceEEEEec
Q 004002          342 KRIKLEPS  349 (780)
Q Consensus       342 r~L~V~~a  349 (780)
                      ++..+...
T Consensus       284 ~~~~~Rl~  291 (608)
T KOG4212|consen  284 RRMTVRLD  291 (608)
T ss_pred             ccceeecc
Confidence            77666553

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.51  E-value=2.4e-14  Score=148.22  Aligned_cols=145  Identities=21%  Similarity=0.339  Sum_probs=119.0

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE-EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCCCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYG  188 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i-~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~~~~~  188 (780)
                      +.++||++||...++.+++.+|..+|.| ++.      ..+.+.||++.+...+.    .+.+|.+-+..++++..+. +
T Consensus         2 ~~KLFIGNLp~~~~~~elr~lFe~ygkVlECD------IvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSks-K   74 (346)
T KOG0109|consen    2 PVKLFIGNLPREATEQELRSLFEQYGKVLECD------IVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKS-K   74 (346)
T ss_pred             ccchhccCCCcccchHHHHHHHHhhCceEeee------eecccceEEeecccccHHHHhhcccceecceEEEEEeccc-c
Confidence            4679999999999999999999999987 222      22346666666665554    3556777766666654432 3


Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ...+++|+|+||.+.++.+||+..|++||.|.+|++   -++|+||.|.-.++|..|++.|++.++.|+++.|+.+..+-
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdi---vkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDI---VKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeee---ecceeEEEEeeccchHHHHhcccccccccceeeeeeecccc
Confidence            567899999999999999999999999999999975   46899999999999999999999999999999999886543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.49  E-value=9.7e-13  Score=141.50  Aligned_cols=161  Identities=26%  Similarity=0.342  Sum_probs=136.0

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCC
Q 004002          192 SRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP  270 (780)
Q Consensus       192 s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~  270 (780)
                      +..|.|.||.. .||.+-|..+|.-||+|.+|++....+--|.|+|.+...|+-|+..|+|..|.|++|+|.+++-..-.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            47888999875 58999999999999999999976666688999999999999999999999999999999987543211


Q ss_pred             C------CC-------------------------CCCccceeecCCCCCCChhHHHHHhcccCCe-eEEEeCCCcccEEE
Q 004002          271 S------DK-------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-KEIRETPHKRHHKF  318 (780)
Q Consensus       271 s------~~-------------------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I-~~v~~~g~srG~aF  318 (780)
                      .      +.                         -....+|++.|+|.+++||+|+.+|..-|.. +..+..++.+.+++
T Consensus       377 lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal  456 (492)
T KOG1190|consen  377 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMAL  456 (492)
T ss_pred             CCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceee
Confidence            0      00                         0123589999999999999999999988765 55567777888999


Q ss_pred             EEEcCHHHHHHHHHHhCCCccCC-ceEEEEecCCC
Q 004002          319 IEFYDVRAAEAALKSLNRSDIAG-KRIKLEPSRPG  352 (780)
Q Consensus       319 V~F~~~e~A~~Ai~~LnG~~i~G-r~L~V~~a~~k  352 (780)
                      +.+.++|+|..|+..++.+.+++ ..|+|+|++..
T Consensus       457 ~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks~  491 (492)
T KOG1190|consen  457 PQLESVEEAIQALIDLHNHYLGENHHLRVSFSKST  491 (492)
T ss_pred             cccCChhHhhhhccccccccCCCCceEEEEeeccc
Confidence            99999999999999999998875 59999998753

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=3e-14  Score=145.12  Aligned_cols=149  Identities=26%  Similarity=0.433  Sum_probs=128.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC----
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD----  268 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~----  268 (780)
                      ..+||++||+.+.+++|..+|..||.|..+...   .||+||.|.+..+|..|+..|+++.|.+..+.|.|+....    
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk---~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g   78 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK---NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRG   78 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee---cccceeccCchhhhhcccchhcCceecceeeeeecccccccccC
Confidence            468999999999999999999999999988753   4899999999999999999999999999889999987421    


Q ss_pred             --CCC----------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC
Q 004002          269 --NPS----------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR  336 (780)
Q Consensus       269 --~~s----------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG  336 (780)
                        ...          ........|.|.++...+.+.+|.+.|+++|.+.....   ..+++||+|...++|.+|+..|+|
T Consensus        79 ~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~  155 (216)
T KOG0106|consen   79 RPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDG  155 (216)
T ss_pred             CCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccc
Confidence              100          01223357889999999999999999999999955554   578999999999999999999999


Q ss_pred             CccCCceEEEE
Q 004002          337 SDIAGKRIKLE  347 (780)
Q Consensus       337 ~~i~Gr~L~V~  347 (780)
                      ..+.+++|.+.
T Consensus       156 ~~~~~~~l~~~  166 (216)
T KOG0106|consen  156 KKLNGRRISVE  166 (216)
T ss_pred             hhhcCceeeec
Confidence            99999999993

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.46  E-value=2.1e-13  Score=132.58  Aligned_cols=80  Identities=24%  Similarity=0.441  Sum_probs=73.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|++..|.|++|+|.++
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            4568999999999999999999999999999987     26789999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 004002          265 IPKDN  269 (780)
Q Consensus       265 ~pk~~  269 (780)
                      .++..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76543

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.44  E-value=3.4e-13  Score=131.04  Aligned_cols=78  Identities=24%  Similarity=0.453  Sum_probs=72.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++     +++++|||||+|++.++|++||+.||+..|.|++|+|+++.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            3468999999999999999999999999999875     56789999999999999999999999999999999999997


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      ++.
T Consensus       113 ~~~  115 (144)
T PLN03134        113 DRP  115 (144)
T ss_pred             cCC
Confidence            653

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.43  E-value=7.1e-13  Score=132.86  Aligned_cols=150  Identities=21%  Similarity=0.345  Sum_probs=115.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE--EeCCC----cceEEEEEEecHHHHHHHHHHccCcccc---cccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL--YTACK----HRGFVMISYYDIRAARTAMRALQNKPLR---RRKLDI  261 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv--~~tgk----skG~aFV~F~~~e~A~~Al~~Lng~~l~---gr~I~V  261 (780)
                      .-|||||.+||.++.-.||+.+|.+|-.-+.+  +.+.+    .+-+|||.|.+.++|..|+.+|||.++.   +..|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            35999999999999999999999988665554  33433    3479999999999999999999999985   667777


Q ss_pred             ccCCCCCCCCC----------------------C-----------------------------C----------------
Q 004002          262 HFSIPKDNPSD----------------------K-----------------------------D----------------  274 (780)
Q Consensus       262 ~~a~pk~~~s~----------------------~-----------------------------~----------------  274 (780)
                      ++++......+                      .                             +                
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            77542211000                      0                             0                


Q ss_pred             ---------------CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCC-cccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          275 ---------------LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH-KRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       275 ---------------~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~-srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                                     ....+|||.||...++|++|+++|+.|-.....++..+ ....|||+|++.+.|..|+..|.|..
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~  272 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNL  272 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcce
Confidence                           00038999999999999999999999976666555322 23579999999999999999999876


Q ss_pred             cC
Q 004002          339 IA  340 (780)
Q Consensus       339 i~  340 (780)
                      |.
T Consensus       273 ~s  274 (284)
T KOG1457|consen  273 LS  274 (284)
T ss_pred             ec
Confidence            63

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.41  E-value=2.9e-12  Score=135.69  Aligned_cols=164  Identities=15%  Similarity=0.251  Sum_probs=132.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE--------EE----eCCCcceEEEEEEecHHHHHHHHHHccCccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRR  256 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s--------v~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g  256 (780)
                      ...++.|||.|||.++|.+++.++|+++|-|..        |+    ..|+.||=|.|.|...++.+.|++.|++..|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            344577999999999999999999999998754        22    358899999999999999999999999999999


Q ss_pred             cccccccCCCCCC-------------C---------------------CCCCCCccceeecCCCC----CCC-------h
Q 004002          257 RKLDIHFSIPKDN-------------P---------------------SDKDLNQGTLVVFNLDP----SVS-------N  291 (780)
Q Consensus       257 r~I~V~~a~pk~~-------------~---------------------s~~~~~~~~L~V~NLp~----~vt-------e  291 (780)
                      ++|+|+.|.-...             .                     ..+....++|.++|+=.    ..+       +
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            9999987632100             0                     00112236889998821    122       5


Q ss_pred             hHHHHHhcccCCeeEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          292 EDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       292 edL~~~Fs~yG~I~~v~~-~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ++|++-.++||.|..|.+ ..++.|.+-|.|.+.++|..||+.|+|+.++||+|..+...-+
T Consensus       291 edl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            677888999999999876 4677899999999999999999999999999999998766544

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.41  E-value=8e-12  Score=133.05  Aligned_cols=233  Identities=19%  Similarity=0.267  Sum_probs=169.7

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE------------EEeccCccCcccceEEEeecCccccC-----cccccccCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM------------ELEGEPQESLSMSMSKISISDSASGN-----GLLHYSVPN  176 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i------------~V~~d~~esa~~g~~~v~~~~~~~a~-----~~~~~~l~n  176 (780)
                      .--+.|++|...+.|.++.+..+.+|.+            .|+|+..+++..+   ++|+....-.     .+.+|....
T Consensus        31 spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~---Vnfaa~n~i~i~gq~Al~NyStsq  107 (494)
T KOG1456|consen   31 SPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNC---VNFAADNQIYIAGQQALFNYSTSQ  107 (494)
T ss_pred             CceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhh---eehhccCcccccCchhhcccchhh
Confidence            3458999999999999999999999997            3444443333222   2222111100     111111111


Q ss_pred             CCcccCCCCCCCCCCCcEEEEe--CCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccc
Q 004002          177 GAGTVAGEHPYGEHPSRTLFVR--NINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (780)
Q Consensus       177 ~~~k~~g~~~~~e~~s~tLfVg--NLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l  254 (780)
                         ++.........++..|.+.  |--+.+|-+-|..+....|+|.+|.+..|.--.|+|+|++.+.|++|..+|||..|
T Consensus       108 ---~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADI  184 (494)
T KOG1456|consen  108 ---CIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADI  184 (494)
T ss_pred             ---hhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccc
Confidence               1111112222344555555  44467999999999999999999988777666899999999999999999999988


Q ss_pred             c--ccccccccCCCCCCCCCC-----------------------------------------------------------
Q 004002          255 R--RRKLDIHFSIPKDNPSDK-----------------------------------------------------------  273 (780)
Q Consensus       255 ~--gr~I~V~~a~pk~~~s~~-----------------------------------------------------------  273 (780)
                      .  ..+|+|+|++|.+....+                                                           
T Consensus       185 YsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~  264 (494)
T KOG1456|consen  185 YSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPP  264 (494)
T ss_pred             cccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCC
Confidence            4  568999998775321000                                                           


Q ss_pred             ---------C----------CCccceeecCCCCC-CChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHH
Q 004002          274 ---------D----------LNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       274 ---------~----------~~~~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                               +          .....+.|.+|+.. +.-+.|..+|..||.|..|++...+.|.|.|++.|..+.++|+..
T Consensus       265 P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~h  344 (494)
T KOG1456|consen  265 PSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTH  344 (494)
T ss_pred             CCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHH
Confidence                     0          00136888999864 678999999999999999998777789999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCC
Q 004002          334 LNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       334 LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ||+..+-|.+|.|.+++..
T Consensus       345 Lnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  345 LNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             hccCccccceEEEeecccc
Confidence            9999999999999998754

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.34  E-value=3.7e-11  Score=130.06  Aligned_cols=70  Identities=23%  Similarity=0.291  Sum_probs=64.6

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ++|+|+|||.++|++.|++-|..||.|..+.+  .++++|  .|+|.++++|++|+..|+|..+.|+.|+|.+.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            47999999999999999999999999999887  666665  99999999999999999999999999999863

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.32  E-value=1.2e-11  Score=136.30  Aligned_cols=158  Identities=18%  Similarity=0.274  Sum_probs=125.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      .-.|.+++|||++|++||.++|+.++ |+.+.   .+|+..|-|||+|.+.+++++|+++ +...+..|-|.|--+.+++
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~~e   87 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGGAE   87 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCCcc
Confidence            35688899999999999999999885 55443   5699999999999999999999994 8888888988887665443


Q ss_pred             CCC-------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeE-EEe----CCCcccEEEEEEcCHHHHHHHHHHhCC
Q 004002          269 NPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  336 (780)
Q Consensus       269 ~~s-------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~-v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG  336 (780)
                      ...       ........|-+.+||+.+|++||.++|+..-.|.. |.+    .+++.|-|||+|++.+.|++|+.. |.
T Consensus        88 ~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hr  166 (510)
T KOG4211|consen   88 ADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HR  166 (510)
T ss_pred             ccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HH
Confidence            211       01134568999999999999999999998754444 221    345778999999999999999985 77


Q ss_pred             CccCCceEEEEecCCC
Q 004002          337 SDIAGKRIKLEPSRPG  352 (780)
Q Consensus       337 ~~i~Gr~L~V~~a~~k  352 (780)
                      ..|.-+-|.|-.+...
T Consensus       167 e~iGhRYIEvF~Ss~~  182 (510)
T KOG4211|consen  167 ENIGHRYIEVFRSSRA  182 (510)
T ss_pred             HhhccceEEeehhHHH
Confidence            7888888888776543

>PF00076 RRM_1: RNA recognition motif

Probab=99.32  E-value=4.4e-12  Score=105.99  Aligned_cols=66  Identities=36%  Similarity=0.645  Sum_probs=61.5

Q ss_pred             eeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       280 L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      |||+|||.++|+++|+++|++||.|..+++    .+..+++|||+|.+.++|++|++.|+|..+.|+.|+
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            799999999999999999999999988875    345789999999999999999999999999999885

(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=99.31  E-value=4.5e-12  Score=105.93  Aligned_cols=66  Identities=29%  Similarity=0.610  Sum_probs=61.5

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccc
Q 004002          195 LFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (780)
Q Consensus       195 LfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~  260 (780)
                      |||+|||+++|+++|+++|++||.|..+.    ..++.+|+|||+|.+.++|++|++.|+|..+.|++|+
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            79999999999999999999999998877    2467899999999999999999999999999998874

(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 ....

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.30  E-value=4e-12  Score=124.39  Aligned_cols=157  Identities=15%  Similarity=0.240  Sum_probs=126.6

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCCCC--
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH--  185 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~~--  185 (780)
                      ..+||++|+..++|..++++|-+.|.|   .+-.|.......|++|+.|...+.+.    .++..++-++.+++....  
T Consensus        10 ~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~   89 (203)
T KOG0131|consen   10 ATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAH   89 (203)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccc
Confidence            579999999999999999999999986   55566677778899999988776654    333444555544443322  


Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE----E--eCCCcceEEEEEEecHHHHHHHHHHccCcccccccc
Q 004002          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----Y--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (780)
Q Consensus       186 ~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv----~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I  259 (780)
                      ...-....+|||+||.++++|..|.+.|+.||.|...    +  .++..+|||||.|.+.+.+.+|+..++|..+..+++
T Consensus        90 ~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~i  169 (203)
T KOG0131|consen   90 QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPI  169 (203)
T ss_pred             cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCce
Confidence            2233455899999999999999999999999988652    1  468899999999999999999999999999999999


Q ss_pred             ccccCCCCCCCC
Q 004002          260 DIHFSIPKDNPS  271 (780)
Q Consensus       260 ~V~~a~pk~~~s  271 (780)
                      .|.++..++...
T Consensus       170 tv~ya~k~~~kg  181 (203)
T KOG0131|consen  170 TVSYAFKKDTKG  181 (203)
T ss_pred             EEEEEEecCCCc
Confidence            999997665443

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.26  E-value=3.2e-11  Score=124.26  Aligned_cols=118  Identities=27%  Similarity=0.450  Sum_probs=101.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .++|||+|||.++|+++|+++|.+||.|..++     .+++++|||||.|.+.++|..|++.+++..|.|++|.|.++.+
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            69999999999999999999999999997776     3689999999999999999999999999999999999999542


Q ss_pred             ----CCCCC----------------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe
Q 004002          267 ----KDNPS----------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  309 (780)
Q Consensus       267 ----k~~~s----------------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~  309 (780)
                          +....                ........+++.+++..++..++...|..+|.+..+.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  257 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASL  257 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeec
Confidence                22111                01123358999999999999999999999999977765

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=1e-11  Score=120.84  Aligned_cols=76  Identities=30%  Similarity=0.488  Sum_probs=72.1

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      .++|||+||+..+++.||+.+|..||.|..|.+...+.|||||+|+++.+|+.|+..|+|+.|.|.+|+|+++.-.
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            5689999999999999999999999999999998888999999999999999999999999999999999988654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=7.9e-11  Score=132.98  Aligned_cols=163  Identities=17%  Similarity=0.351  Sum_probs=126.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ....++||++||..+++.+++++...||++....     .++-++||||.+|.+.-....|+..|+|+.+.+++|.|+.+
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            3457899999999999999999999999987654     45789999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCC--------------------CCccceeecCC--CCCC-C-------hhHHHHHhcccCCeeEEEeCC---
Q 004002          265 IPKDNPSDKD--------------------LNQGTLVVFNL--DPSV-S-------NEDLRQIFGAYGEVKEIRETP---  311 (780)
Q Consensus       265 ~pk~~~s~~~--------------------~~~~~L~V~NL--p~~v-t-------eedL~~~Fs~yG~I~~v~~~g---  311 (780)
                      .+........                    +....|.+.|+  +.++ +       -|+++.-+++||.|..|.+..   
T Consensus       367 ~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~  446 (500)
T KOG0120|consen  367 IVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYP  446 (500)
T ss_pred             hccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCC
Confidence            6533211110                    11123333333  1111 1       255667788999999997521   


Q ss_pred             -----CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          312 -----HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       312 -----~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                           -..|..||+|.+.+++++|..+|+|.+++|+.|...+-...
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence                 23567899999999999999999999999999999887643

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.24  E-value=3.2e-11  Score=130.17  Aligned_cols=191  Identities=15%  Similarity=0.219  Sum_probs=136.5

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCcc-ccCccc--ccccCCCCcccCCCCC-
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSA-SGNGLL--HYSVPNGAGTVAGEHP-  186 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~-~a~~~~--~~~l~n~~~k~~g~~~-  186 (780)
                      ..+++|++|.|+.+++.+++.|+++|.+   .|+.|+.....+++.+++|.+.. ....+.  .+.+.+..+....+.+ 
T Consensus         6 ~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r   85 (311)
T KOG4205|consen    6 SGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSR   85 (311)
T ss_pred             CcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCc
Confidence            3789999999999999999999999997   78888889999999999999543 322222  2223333222111111 


Q ss_pred             ------CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          187 ------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       187 ------~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                            .......++||+.||.+++++++++.|++||.|..+.     .+.+.+||+||.|.+++++++++. ...+.|.
T Consensus        86 ~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~  164 (311)
T KOG4205|consen   86 EDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFN  164 (311)
T ss_pred             ccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeec
Confidence                  1112345999999999999999999999999887765     468899999999999999999988 5888999


Q ss_pred             ccccccccCCCCCCCCCCCCCc-cceeecCCCCCCChhHHHHHhcccCCee
Q 004002          256 RRKLDIHFSIPKDNPSDKDLNQ-GTLVVFNLDPSVSNEDLRQIFGAYGEVK  305 (780)
Q Consensus       256 gr~I~V~~a~pk~~~s~~~~~~-~~L~V~NLp~~vteedL~~~Fs~yG~I~  305 (780)
                      ++++.|+.|.|++......... ...+..++....+.-.|...|.-|+.+.
T Consensus       165 gk~vevkrA~pk~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~~  215 (311)
T KOG4205|consen  165 GKKVEVKRAIPKEVMQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPVG  215 (311)
T ss_pred             CceeeEeeccchhhccccccccccccccccccccccccccchhccccCccc
Confidence            9999999999887543221111 1112223444444444555555555543

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.23  E-value=2.2e-11  Score=128.32  Aligned_cols=99  Identities=18%  Similarity=0.295  Sum_probs=80.3

Q ss_pred             cCccccccccccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHH
Q 004002          250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRA  326 (780)
Q Consensus       250 ng~~l~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~  326 (780)
                      ++-...|..+.+..+..    ++.....+.|+|+|||+...|.||+.+|.+||.|.+|.|   ...+||||||+|++.++
T Consensus        73 ~~~~t~g~~~~~~~st~----s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~d  148 (376)
T KOG0125|consen   73 NGAPTDGQPIQTQPSTN----SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPAD  148 (376)
T ss_pred             CCCCCCCCccccCCCCc----CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhh
Confidence            44455566665553322    122223468999999999999999999999999999875   45679999999999999


Q ss_pred             HHHHHHHhCCCccCCceEEEEecCCC
Q 004002          327 AEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       327 A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      |++|-.+|||..|.||+|+|..+..+
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchh
Confidence            99999999999999999999988653

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.21  E-value=3.2e-10  Score=125.31  Aligned_cols=232  Identities=14%  Similarity=0.171  Sum_probs=156.3

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcEEEeccCccCcccceEEEeecCccccCcc---cccccCCC----------Cccc
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNG----------AGTV  181 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i~V~~d~~esa~~g~~~v~~~~~~~a~~~---~~~~l~n~----------~~k~  181 (780)
                      -.+-+++|||+++++|+.++|++++--.|.+-..+++..|-++|.+...+..+..   ..-.+.+.          ....
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~   90 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEADW   90 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCccccc
Confidence            4577899999999999999999998656666666688888888887765433311   11111111          0011


Q ss_pred             CCCC--CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE-----EEeCCCcceEEEEEEecHHHHHHHHHHccCccc
Q 004002          182 AGEH--PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-----LYTACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (780)
Q Consensus       182 ~g~~--~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s-----v~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l  254 (780)
                      ...+  +........|.+++||+.||++||.++|+..-.|..     ....++..|-|||+|.+.+.|++|+.. +...|
T Consensus        91 ~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~i  169 (510)
T KOG4211|consen   91 VMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENI  169 (510)
T ss_pred             cccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhh
Confidence            1111  111235578999999999999999999996533332     113577889999999999999999985 66666


Q ss_pred             cccccccccCC-----------------C------CCCCC----------------------------------------
Q 004002          255 RRRKLDIHFSI-----------------P------KDNPS----------------------------------------  271 (780)
Q Consensus       255 ~gr~I~V~~a~-----------------p------k~~~s----------------------------------------  271 (780)
                      ..|-|.|-.+.                 |      ...+.                                        
T Consensus       170 GhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~g  249 (510)
T KOG4211|consen  170 GHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFG  249 (510)
T ss_pred             ccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccc
Confidence            66555543210                 0      00000                                        


Q ss_pred             ----CCCC---------------------Cc-cceeecCCCCCCChhHHHHHhcccCCe---eEEEeCCCcccEEEEEEc
Q 004002          272 ----DKDL---------------------NQ-GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFY  322 (780)
Q Consensus       272 ----~~~~---------------------~~-~~L~V~NLp~~vteedL~~~Fs~yG~I---~~v~~~g~srG~aFV~F~  322 (780)
                          .++.                     .. ..++..+||.+.++.++..+|+..-.+   .+|..+++..|-|+|+|.
T Consensus       250 s~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~  329 (510)
T KOG4211|consen  250 SYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFA  329 (510)
T ss_pred             ccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecc
Confidence                0000                     00 257788999999999999999976443   223347788899999999


Q ss_pred             CHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          323 DVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       323 ~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      +.++|..|+.+ ++.-+..+-|.+-.
T Consensus       330 t~edav~Amsk-d~anm~hrYVElFl  354 (510)
T KOG4211|consen  330 TGEDAVGAMGK-DGANMGHRYVELFL  354 (510)
T ss_pred             cchhhHhhhcc-CCcccCcceeeecc
Confidence            99999999874 66666666666643

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.17  E-value=7.6e-11  Score=120.16  Aligned_cols=78  Identities=22%  Similarity=0.434  Sum_probs=73.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +..++|.|.||+.+++|++|+++|.+||.|..++     .+|.+||||||.|.+.++|++||+.|+|.-+..--|.|+|+
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            3568999999999999999999999999999987     58999999999999999999999999999999999999999


Q ss_pred             CCC
Q 004002          265 IPK  267 (780)
Q Consensus       265 ~pk  267 (780)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            885

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.16  E-value=3.5e-11  Score=117.23  Aligned_cols=77  Identities=26%  Similarity=0.512  Sum_probs=72.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      -.++|||+||+..+++.||..+|..||.|.+|-+.....|||||+|++..+|+.|+..|+|+.|.|..|.|+.+.-.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            35899999999999999999999999999999988889999999999999999999999999999999999987643

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.15  E-value=9.6e-11  Score=105.02  Aligned_cols=79  Identities=29%  Similarity=0.499  Sum_probs=72.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ...+.|||+|||.++|.|+..++|.+||.|+.|++  +...+|-|||.|+++.+|++|++.|.|..+.++.+.|.|-.+.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            45689999999999999999999999999999994  5568999999999999999999999999999999999987664


Q ss_pred             C
Q 004002          268 D  268 (780)
Q Consensus       268 ~  268 (780)
                      +
T Consensus        96 ~   96 (124)
T KOG0114|consen   96 D   96 (124)
T ss_pred             H
Confidence            3

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.15  E-value=9e-11  Score=119.64  Aligned_cols=77  Identities=25%  Similarity=0.428  Sum_probs=72.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|-|.||+.++++++|+++|.+||.|..|.     .+|.+||||||.|.++++|++||..|||.-++.-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            446899999999999999999999999999985     489999999999999999999999999999999999999999


Q ss_pred             CC
Q 004002          351 PG  352 (780)
Q Consensus       351 ~k  352 (780)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            86

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.14  E-value=6.9e-11  Score=120.12  Aligned_cols=76  Identities=22%  Similarity=0.421  Sum_probs=66.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      +..-++|||++|+|++..|+|++.|++||+|++..     .++++||||||+|.|.++|.+|++. .+-.|.||+..|..
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccch
Confidence            34458999999999999999999999999998865     4799999999999999999999995 45668899888876


Q ss_pred             CC
Q 004002          264 SI  265 (780)
Q Consensus       264 a~  265 (780)
                      +.
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            53

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.14  E-value=1.3e-10  Score=121.54  Aligned_cols=74  Identities=20%  Similarity=0.407  Sum_probs=67.9

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeC--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~--g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+||++.+|+++|+++|+.||.|+.|++.  +..+|||||+|.+.++|+.||. |||..|.|+.|+|.++..
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 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            4689999999999999999999999999999873  3357999999999999999996 999999999999999864

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=4.8e-10  Score=100.62  Aligned_cols=81  Identities=23%  Similarity=0.404  Sum_probs=73.9

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      ..-|||.|||+++|.|+..++|++||.|..||+  +...+|.|||.|++..+|.+|++.|+|..+.++-|.|-+-++..+
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~~   97 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPEDA   97 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHHH
Confidence            467999999999999999999999999999997  556689999999999999999999999999999999999888765


Q ss_pred             hhh
Q 004002          355 RRN  357 (780)
Q Consensus       355 r~~  357 (780)
                      .+.
T Consensus        98 ~~~  100 (124)
T KOG0114|consen   98 FKL  100 (124)
T ss_pred             HHH
Confidence            443

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.13  E-value=7.2e-11  Score=109.54  Aligned_cols=75  Identities=27%  Similarity=0.487  Sum_probs=69.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..++||||+||+..++||+|.++|+++|+|..|.     -+....|||||+|.+.++|+.|++-++|..|..++|.|.|-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            4679999999999999999999999999999986     24557899999999999999999999999999999999874

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.12  E-value=1.8e-10  Score=120.63  Aligned_cols=76  Identities=18%  Similarity=0.293  Sum_probs=68.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      .++|||+|||+.+|+++|+++|+.||+|.+|++  .+..+|||||+|.+.++|+.||. |+|..|.|+.|.|.++..-.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCC
Confidence            479999999999999999999999999999984  33468999999999999999996 99999999999999876433

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.11  E-value=2.1e-10  Score=96.74  Aligned_cols=66  Identities=35%  Similarity=0.639  Sum_probs=58.8

Q ss_pred             eeecCCCCCCChhHHHHHhcccCCeeEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       280 L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~----g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      |||+|||.++++++|+++|+.||.|..+++.    +..+++|||+|.+.++|.+|++.++|..+.|++|+
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            7999999999999999999999999998763    33579999999999999999999999999999885

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=99.11  E-value=1.7e-10  Score=97.35  Aligned_cols=66  Identities=23%  Similarity=0.548  Sum_probs=58.4

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccc
Q 004002          195 LFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (780)
Q Consensus       195 LfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~  260 (780)
                      |||+|||+++++++|+++|+.||.|..++.    .++.+|+|||+|.+.++|++|++.+++..++|++|+
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            799999999999999999999999988872    256799999999999999999999998999998864

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 ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.10  E-value=1.6e-10  Score=121.95  Aligned_cols=79  Identities=23%  Similarity=0.418  Sum_probs=72.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ....++|+|.|||...-|-||+.+|++||+|.+|.+   ...+||||||+|++.++|++|-++|+|..+.||+|.|..+.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            344589999999999999999999999999998872   45599999999999999999999999999999999999887


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      ++
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            65

>smart00362 RRM_2 RNA recognition motif

Probab=99.09  E-value=3.6e-10  Score=93.15  Aligned_cols=69  Identities=32%  Similarity=0.644  Sum_probs=63.0

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEeCC---CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g---~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      +|+|+|||..+++++|+++|++||.|..+++..   ..+++|||+|.+.++|++|++.++|..+.|++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            589999999999999999999999999987643   347999999999999999999999999999999874

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.09  E-value=4.2e-10  Score=120.45  Aligned_cols=164  Identities=12%  Similarity=0.200  Sum_probs=119.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhc---C--C--CEEEEE-eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQ---Y--G--DIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~---y--G--~I~sv~-~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      .-.|.+++||.++++.++.++|..   .  |  .|.=|+ ..|+..|-|||.|..+++|+.|+.+ +...|+-|.|.+-.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            346778899999999999999962   2  2  122233 3688999999999999999999996 55555555554433


Q ss_pred             CCCCC---------------------------CCCCCCCCccceeecCCCCCCChhHHHHHhcccCC-eeE--EE----e
Q 004002          264 SIPKD---------------------------NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKE--IR----E  309 (780)
Q Consensus       264 a~pk~---------------------------~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~-I~~--v~----~  309 (780)
                      +...+                           ..........+|.+++||+..+.|+|..+|..|-. |..  |.    -
T Consensus       240 STaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~  319 (508)
T KOG1365|consen  240 STAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG  319 (508)
T ss_pred             HhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC
Confidence            21100                           00011223568999999999999999999998743 222  32    2


Q ss_pred             CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchhh
Q 004002          310 TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  356 (780)
Q Consensus       310 ~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r~  356 (780)
                      .|+..|.|||+|.+.++|.+|..+-+.+...++-|+|-.+.-..-..
T Consensus       320 qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eeln~  366 (508)
T KOG1365|consen  320 QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEELNE  366 (508)
T ss_pred             CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHHHH
Confidence            56778999999999999999999988888889999998876544333

>PLN03213 repressor of silencing 3; Provisional

Probab=99.08  E-value=2.7e-10  Score=124.93  Aligned_cols=86  Identities=26%  Similarity=0.359  Sum_probs=74.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCH--HHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDV--RAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~--e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .....|||+||.+++++++|+.+|+.||.|..|.+   ++  ||||||+|.+.  .++.+||..|||.++.|+.|+|..|
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            34468999999999999999999999999999865   44  89999999987  7899999999999999999999999


Q ss_pred             CCCchhhhHhhhhchhcc
Q 004002          350 RPGGARRNLMLQLNQELE  367 (780)
Q Consensus       350 ~~k~~r~~~l~ql~~~~~  367 (780)
                      ++.     ++.+|.++.+
T Consensus        86 KP~-----YLeRLkrERe   98 (759)
T PLN03213         86 KEH-----YLARLKREWE   98 (759)
T ss_pred             cHH-----HHHHHHHHHH
Confidence            875     4555544443

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.05  E-value=2.4e-10  Score=106.16  Aligned_cols=76  Identities=21%  Similarity=0.345  Sum_probs=69.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+||...++||+|.++|+++|+|+.|-     .+....||+||+|...++|+.|++-++|+.++.+.|.+.|..
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            457999999999999999999999999999984     356678999999999999999999999999999999999875


Q ss_pred             C
Q 004002          351 P  351 (780)
Q Consensus       351 ~  351 (780)
                      -
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            4

>PF13893 RRM_5: RNA recognition motif

Probab=99.04  E-value=7.2e-10  Score=89.90  Aligned_cols=56  Identities=34%  Similarity=0.594  Sum_probs=51.4

Q ss_pred             HHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          294 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       294 L~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      |+++|++||+|+.+.+....+++|||+|.+.++|++|++.|||..+.|++|+|.+|
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999986665799999999999999999999999999999999986

(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 ....

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.03  E-value=2.8e-10  Score=127.46  Aligned_cols=162  Identities=27%  Similarity=0.404  Sum_probs=129.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ..+.++|+|-|||.+|++++|+.+|+.||+|+.++.+.-.+|.+||+|.|..+|++|+++|++..+.|+.|+........
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~~  151 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARRA  151 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccccc
Confidence            45679999999999999999999999999999999888899999999999999999999999999999988833221111


Q ss_pred             CC------------------CCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHH
Q 004002          269 NP------------------SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAA  330 (780)
Q Consensus       269 ~~------------------s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~A  330 (780)
                      .-                  ....-....++.- |++..+..-++.+|+.+|.+.. +.++..+..-|++|.+..++..+
T Consensus       152 ~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~~  229 (549)
T KOG4660|consen  152 MGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAFS  229 (549)
T ss_pred             chhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhhc
Confidence            00                  0000112334433 9999988889999999999998 88877777889999999999777


Q ss_pred             HHHhCCCccCCceEEEEecCCCc
Q 004002          331 LKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       331 i~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ...+ |..+.++.....++.+..
T Consensus       230 ~~~~-G~~~s~~~~v~t~S~~~g  251 (549)
T KOG4660|consen  230 EPRG-GFLISNSSGVITFSGPGG  251 (549)
T ss_pred             ccCC-ceecCCCCceEEecCCCc
Confidence            7744 777788887778887744

>smart00362 RRM_2 RNA recognition motif

Probab=99.00  E-value=1.1e-09  Score=90.15  Aligned_cols=69  Identities=30%  Similarity=0.580  Sum_probs=62.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC---CCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t---gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      +|+|+|||..+++++|+++|++||+|..++..   +.++|+|||+|.+.++|++|++.+++..+.|+++.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999888732   4568999999999999999999999999999888763

>smart00360 RRM RNA recognition motif

Probab=98.98  E-value=1.6e-09  Score=88.87  Aligned_cols=66  Identities=35%  Similarity=0.662  Sum_probs=59.9

Q ss_pred             ecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          282 VFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       282 V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      |+|||..+++++|+++|++||.|..+++     ++.++++|||+|.+.++|.+|++.|++..+.|++|+|+
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            6799999999999999999999999875     24457899999999999999999999999999999874

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.98  E-value=6.3e-10  Score=109.12  Aligned_cols=78  Identities=29%  Similarity=0.456  Sum_probs=70.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCC--CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP--HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g--~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..+.|||+|||.++.+.||+++|.+||.|.+|.+..  ....||||+|++..+|+.||..-+|..++|++|+|++++...
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr   84 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGR   84 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCC
Confidence            457899999999999999999999999999997643  335799999999999999999999999999999999998654

>PLN03213 repressor of silencing 3; Provisional

Probab=98.98  E-value=9.3e-10  Score=120.77  Aligned_cols=75  Identities=15%  Similarity=0.239  Sum_probs=68.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecH--HHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDI--RAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~--e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...+||||||++++|+++|+.+|..||.|.+|.   .+|  ||||||+|.+.  .++.+||..|+|..+.|+.|+|..|+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            457999999999999999999999999999887   355  99999999987  78999999999999999999999886


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      |.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            63

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.97  E-value=1.1e-09  Score=114.39  Aligned_cols=78  Identities=27%  Similarity=0.491  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ..++-+||||.-|+.+++|.+|+..|+.||+|..|+     ++++++|||||+|+++.+...|.+..+|.+|.|+.|.|.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            346889999999999999999999999999999886     689999999999999999999999999999999999998


Q ss_pred             cCC
Q 004002          263 FSI  265 (780)
Q Consensus       263 ~a~  265 (780)
                      +..
T Consensus       177 vER  179 (335)
T KOG0113|consen  177 VER  179 (335)
T ss_pred             ecc
Confidence            754

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.97  E-value=8e-10  Score=110.16  Aligned_cols=75  Identities=28%  Similarity=0.523  Sum_probs=70.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .-..|.|-||..-++.++|+.+|++||.|-+|+     .+..++|||||.|.+..+|+.|+++|+|.+|.|+.|.|++|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            447899999999999999999999999999998     478899999999999999999999999999999999998875

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.96  E-value=7e-10  Score=112.88  Aligned_cols=79  Identities=28%  Similarity=0.361  Sum_probs=69.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      +..-++|||+||+..++.|+|++.|++||+|+++.+     ++++||||||+|.|.++|.+|.+. -.-.|+||+..|.+
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccch
Confidence            334578999999999999999999999999999754     789999999999999999999985 34689999999988


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      |.-+.
T Consensus        88 A~lg~   92 (247)
T KOG0149|consen   88 ASLGG   92 (247)
T ss_pred             hhhcC
Confidence            86543

>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=98.94  E-value=3.7e-09  Score=87.50  Aligned_cols=70  Identities=39%  Similarity=0.672  Sum_probs=63.8

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEeCCC----cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH----KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~----srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      +|+|+|||..+++++|+++|+.||.|..+.+...    .+++|||+|.+.++|..|++.+++..+.|++|.|.+
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            4899999999999999999999999999876433    378999999999999999999999999999999864

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).

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.94  E-value=2.5e-09  Score=110.48  Aligned_cols=74  Identities=22%  Similarity=0.327  Sum_probs=66.9

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ..+|||+||++.+|+++|+++|+.||+|..|++  .+..+++|||+|.+.++|+.|+. |+|..|.+++|.|.....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            358999999999999999999999999999986  34556899999999999999995 999999999999987653

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.93  E-value=3.1e-09  Score=111.15  Aligned_cols=91  Identities=31%  Similarity=0.418  Sum_probs=79.8

Q ss_pred             cCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCC
Q 004002          263 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRS  337 (780)
Q Consensus       263 ~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~  337 (780)
                      ...|..++......-+||||+-|+.+++|.+|+..|+.||.|+.|+     ++++++|||||+|++..+..+|.+...|.
T Consensus        87 ~wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~  166 (335)
T KOG0113|consen   87 LWDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGI  166 (335)
T ss_pred             hcCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCc
Confidence            3455555555556678999999999999999999999999999986     58999999999999999999999999999


Q ss_pred             ccCCceEEEEecCCCc
Q 004002          338 DIAGKRIKLEPSRPGG  353 (780)
Q Consensus       338 ~i~Gr~L~V~~a~~k~  353 (780)
                      .|+|+.|.|.+-+-..
T Consensus       167 ~Idgrri~VDvERgRT  182 (335)
T KOG0113|consen  167 KIDGRRILVDVERGRT  182 (335)
T ss_pred             eecCcEEEEEeccccc
Confidence            9999999998876543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.93  E-value=1.5e-08  Score=108.39  Aligned_cols=168  Identities=20%  Similarity=0.318  Sum_probs=130.8

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHc--cCccccccccccc
Q 004002          185 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLDIH  262 (780)
Q Consensus       185 ~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~L--ng~~l~gr~I~V~  262 (780)
                      .+....++-.+.|++|-..++|.+|.+..+.||.|..+. ....+..|.|+|++++.|++++.--  +...+.|+..-+.
T Consensus        24 dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt-~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~N  102 (494)
T KOG1456|consen   24 DPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVT-CMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFN  102 (494)
T ss_pred             CCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEE-eccccceeeeeeccccchhhheehhccCcccccCchhhcc
Confidence            344455678999999999999999999999999998775 3556778999999999999988632  3344667777777


Q ss_pred             cCCCCCCCC---CCCCCcccee--ecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC
Q 004002          263 FSIPKDNPS---DKDLNQGTLV--VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS  337 (780)
Q Consensus       263 ~a~pk~~~s---~~~~~~~~L~--V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~  337 (780)
                      |+..+.-..   +.....+.|.  |-|--+.+|-+-|.++.-+.|.|..|.+..+.--.|.|||++.+.|++|..+|||.
T Consensus       103 yStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGA  182 (494)
T KOG1456|consen  103 YSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGA  182 (494)
T ss_pred             cchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccc
Confidence            764332111   1111223343  44555688999999999999999999887665446999999999999999999999


Q ss_pred             ccC-C-ceEEEEecCCCc
Q 004002          338 DIA-G-KRIKLEPSRPGG  353 (780)
Q Consensus       338 ~i~-G-r~L~V~~a~~k~  353 (780)
                      .|. | +.|+|++|+|..
T Consensus       183 DIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  183 DIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             cccccceeEEEEecCcce
Confidence            885 4 789999999875

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.92  E-value=6.2e-10  Score=111.64  Aligned_cols=79  Identities=27%  Similarity=0.519  Sum_probs=74.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||++|..+|+|.-|...|-+||+|..|.     .+.++||||||+|...|+|..||..|++..|.||.|+|.++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            468999999999999999999999999999987     478999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      |.+.
T Consensus        89 P~ki   92 (298)
T KOG0111|consen   89 PEKI   92 (298)
T ss_pred             Cccc
Confidence            8654

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.92  E-value=9.9e-10  Score=109.50  Aligned_cols=76  Identities=33%  Similarity=0.543  Sum_probs=70.7

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ...|-|-||-+.++.++|+.+|++||.|-+|.|     +..++|||||.|.+..+|+.|+++|+|..++|+.|.|.+|+=
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            458999999999999999999999999999965     778999999999999999999999999999999999988864


Q ss_pred             C
Q 004002          352 G  352 (780)
Q Consensus       352 k  352 (780)
                      +
T Consensus        93 g   93 (256)
T KOG4207|consen   93 G   93 (256)
T ss_pred             C
Confidence            4

>smart00360 RRM RNA recognition motif

Probab=98.92  E-value=2.3e-09  Score=87.84  Aligned_cols=66  Identities=32%  Similarity=0.584  Sum_probs=59.6

Q ss_pred             EeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          197 VRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       197 VgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      |+|||..+++++|+.+|++||.|..+..     +++++|+|||+|.+.++|.+|++.+++..+.|+++.|+
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            5799999999999999999999988862     35678999999999999999999999999999888763

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.91  E-value=3.1e-09  Score=109.81  Aligned_cols=72  Identities=17%  Similarity=0.214  Sum_probs=66.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+|||+||++.+|+++|+++|+.||+|.+|+  ..++.+|+|||+|+++++|+.|+. |+|..|.+++|.|...
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~   78 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRW   78 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeC
Confidence            47999999999999999999999999999988  356678999999999999999996 9999999999998654

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.88  E-value=3.9e-09  Score=108.61  Aligned_cols=97  Identities=20%  Similarity=0.354  Sum_probs=82.5

Q ss_pred             ccccccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHH
Q 004002          256 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAAL  331 (780)
Q Consensus       256 gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai  331 (780)
                      +|+|.|+.+.....    ...+++|||+-|.+.-.|||++.+|.+||+|.+|.+    ++.+||++||.|.+..+|..||
T Consensus         2 nrpiqvkpadsesr----g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI   77 (371)
T KOG0146|consen    2 NRPIQVKPADSESR----GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAI   77 (371)
T ss_pred             CCCccccccccccC----CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHH
Confidence            47788876654332    235679999999999999999999999999999976    6778999999999999999999


Q ss_pred             HHhCCC-ccCC--ceEEEEecCCCchhh
Q 004002          332 KSLNRS-DIAG--KRIKLEPSRPGGARR  356 (780)
Q Consensus       332 ~~LnG~-~i~G--r~L~V~~a~~k~~r~  356 (780)
                      ..|+|. .+.|  ..|.|++++..++|.
T Consensus        78 ~aLHgSqTmpGASSSLVVK~ADTdkER~  105 (371)
T KOG0146|consen   78 NALHGSQTMPGASSSLVVKFADTDKERT  105 (371)
T ss_pred             HHhcccccCCCCccceEEEeccchHHHH
Confidence            999996 5666  789999999887764

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.88  E-value=1.2e-09  Score=109.56  Aligned_cols=80  Identities=28%  Similarity=0.509  Sum_probs=74.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||++|-.+++|.-|...|-+||.|+.|.+     ..+.||||||+|+..|+|.+||..||+.++-||.|+|.+|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            4579999999999999999999999999999974     67789999999999999999999999999999999999999


Q ss_pred             CCchh
Q 004002          351 PGGAR  355 (780)
Q Consensus       351 ~k~~r  355 (780)
                      |...+
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            86543

>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=98.86  E-value=6.9e-09  Score=85.88  Aligned_cols=70  Identities=34%  Similarity=0.660  Sum_probs=62.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC----CCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTA----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t----gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      +|+|+|||..+++++|+++|+.||+|..+...    .+.+|+|||+|.+.++|..|++.+++..+.++++.|.+
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            48999999999999999999999999888732    24589999999999999999999999999999988764

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).

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.85  E-value=7.3e-09  Score=106.70  Aligned_cols=75  Identities=36%  Similarity=0.625  Sum_probs=70.2

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ..+|||+|||.++++++|+++|.+||.|..+++     ++.++|+|||+|.+.++|..|++.++|..+.|++|.|.++.+
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            589999999999999999999999999988754     578899999999999999999999999999999999999764

>PF13893 RRM_5: RNA recognition motif

Probab=98.83  E-value=4.4e-09  Score=85.23  Aligned_cols=56  Identities=23%  Similarity=0.591  Sum_probs=50.2

Q ss_pred             HHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          209 LRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       209 Lr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      |+++|++||+|..+....+.+++|||+|.+.++|++|++.|+|..+.|++|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999864444799999999999999999999999999999999885

(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 ....

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.83  E-value=4.5e-09  Score=98.46  Aligned_cols=81  Identities=22%  Similarity=0.422  Sum_probs=73.2

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      +......|||.++....|+++|.+.|..||+|+.+.+     ++-.+|||+|+|++.++|++||.+|||..+-|..|.|.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VD  147 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVD  147 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEE
Confidence            3445678999999999999999999999999999965     67789999999999999999999999999999999999


Q ss_pred             ecCCCc
Q 004002          348 PSRPGG  353 (780)
Q Consensus       348 ~a~~k~  353 (780)
                      |+--++
T Consensus       148 w~Fv~g  153 (170)
T KOG0130|consen  148 WCFVKG  153 (170)
T ss_pred             EEEecC
Confidence            886443

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.83  E-value=2.2e-08  Score=111.78  Aligned_cols=144  Identities=18%  Similarity=0.302  Sum_probs=104.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-------eCCCcce---EEEEEEecHHHHHHHHHHccC----ccc-
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRG---FVMISYYDIRAARTAMRALQN----KPL-  254 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-------~tgkskG---~aFV~F~~~e~A~~Al~~Lng----~~l-  254 (780)
                      .-+++|||++||++++|++|...|.+||.+..=-       .....+|   |+|+.|+++...+.-+.++.-    ..| 
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~  336 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFK  336 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEE
Confidence            4568999999999999999999999999875311       1123566   999999999998887776432    111 


Q ss_pred             ------cccccccccCCCCC-----CCCCCCCCccceeecCCCCCCChhHHHHHhc-ccCCeeEEEeC-----CCcccEE
Q 004002          255 ------RRRKLDIHFSIPKD-----NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG-AYGEVKEIRET-----PHKRHHK  317 (780)
Q Consensus       255 ------~gr~I~V~~a~pk~-----~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs-~yG~I~~v~~~-----g~srG~a  317 (780)
                            +.+.+.|..-...+     ..+..-...+||||++||..++.++|-.||. -||.|..+-|+     +-.+|-|
T Consensus       337 vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaG  416 (520)
T KOG0129|consen  337 VSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAG  416 (520)
T ss_pred             EecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcc
Confidence                  11222221111000     0111223457999999999999999999999 79999988653     3468999


Q ss_pred             EEEEcCHHHHHHHHHH
Q 004002          318 FIEFYDVRAAEAALKS  333 (780)
Q Consensus       318 FV~F~~~e~A~~Ai~~  333 (780)
                      -|.|.+..+-.+||.+
T Consensus       417 RVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  417 RVTFSNQQAYIKAISA  432 (520)
T ss_pred             eeeecccHHHHHHHhh
Confidence            9999999999999984

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.80  E-value=5.5e-09  Score=117.54  Aligned_cols=77  Identities=25%  Similarity=0.449  Sum_probs=72.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      +.+||||||++++|++|..+|+..|.|.+++     .+|+.+||||++|.+.++|++|++.|+|..+.|++|+|.|+...
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            8999999999999999999999999999987     68999999999999999999999999999999999999998654


Q ss_pred             CC
Q 004002          268 DN  269 (780)
Q Consensus       268 ~~  269 (780)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.78  E-value=1.2e-08  Score=114.74  Aligned_cols=79  Identities=27%  Similarity=0.389  Sum_probs=73.9

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..+||+|+|+++++++|..+|+..|.|.++++     +|+.+||||++|.+.++|++|++.|||.++.|++|+|.++...
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            68999999999999999999999999999874     8899999999999999999999999999999999999999876


Q ss_pred             chhh
Q 004002          353 GARR  356 (780)
Q Consensus       353 ~~r~  356 (780)
                      ..+.
T Consensus        99 ~~~~  102 (435)
T KOG0108|consen   99 KNAE  102 (435)
T ss_pred             chhH
Confidence            6543

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.77  E-value=8.5e-10  Score=108.06  Aligned_cols=75  Identities=20%  Similarity=0.435  Sum_probs=70.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .+.-|||+|||.+.||.+|..+|++||+|..|.     .||+++||||+.|++..+...|+..|||..|.||.|+|....
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            567899999999999999999999999999876     589999999999999999999999999999999999997654

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.76  E-value=8.9e-09  Score=96.54  Aligned_cols=81  Identities=17%  Similarity=0.444  Sum_probs=73.2

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       187 ~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      .+....-.|||.++....||++|.+.|..||+|..+.     .+|-.||||+|+|.+.++|++|+.++||..|-+++|.|
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            3344457899999999999999999999999999886     57889999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 004002          262 HFSIPK  267 (780)
Q Consensus       262 ~~a~pk  267 (780)
                      .|+.-+
T Consensus       147 Dw~Fv~  152 (170)
T KOG0130|consen  147 DWCFVK  152 (170)
T ss_pred             EEEEec
Confidence            997544

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.76  E-value=1.3e-09  Score=106.74  Aligned_cols=75  Identities=23%  Similarity=0.396  Sum_probs=69.8

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....-|||+|||+++||.||.-.|++||+|+.|.+     ||+++||||.+|+|..+..-|+..|||..|.||.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            35568999999999999999999999999999864     8999999999999999999999999999999999999744

>smart00361 RRM_1 RNA recognition motif

Probab=98.75  E-value=2.2e-08  Score=85.28  Aligned_cols=57  Identities=33%  Similarity=0.513  Sum_probs=50.9

Q ss_pred             hhHHHHHhc----ccCCeeEEE---e---C--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          291 NEDLRQIFG----AYGEVKEIR---E---T--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       291 eedL~~~Fs----~yG~I~~v~---~---~--g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      +++|+++|+    +||.|..|.   +   +  +.++|+|||+|.+.++|.+|++.|||+.+.|+.|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            678999998    999999884   2   2  6789999999999999999999999999999999863

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.67  E-value=1.2e-08  Score=119.28  Aligned_cols=157  Identities=21%  Similarity=0.372  Sum_probs=136.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..+++||++||+.++++.+|+..|..+|.|.+|.+    .+.-.-||||.|.+...+-.|+.++.+..|..-.+++.+..
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            34689999999999999999999999999999873    23445699999999999999999999999987777777765


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ce
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KR  343 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G--r~  343 (780)
                      ++      ....+.++|++|...+....|.+.|..||.|..|.+. +..-|++|.|++...|++|.+.|.|..++|  ++
T Consensus       450 ~k------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~-hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r  522 (975)
T KOG0112|consen  450 PK------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR-HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRR  522 (975)
T ss_pred             cc------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc-cCCcceeeecccCccchhhHHHHhcCcCCCCCcc
Confidence            52      2345679999999999999999999999999999874 345699999999999999999999999987  78


Q ss_pred             EEEEecCCCc
Q 004002          344 IKLEPSRPGG  353 (780)
Q Consensus       344 L~V~~a~~k~  353 (780)
                      |.|.++.+..
T Consensus       523 ~rvdla~~~~  532 (975)
T KOG0112|consen  523 LRVDLASPPG  532 (975)
T ss_pred             cccccccCCC
Confidence            9999998765

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.65  E-value=3.8e-08  Score=113.64  Aligned_cols=77  Identities=30%  Similarity=0.528  Sum_probs=71.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      ++||||+.|+..++|.||+.+|+.||+|.+|.. ...+|||||.+...++|.+|+.+|.+..+.++.|+|.|+.-+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~l-i~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~  497 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIIL-IPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGP  497 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEee-ccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCc
Confidence            589999999999999999999999999999975 45899999999999999999999999999999999999976543

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.63  E-value=5.7e-08  Score=112.25  Aligned_cols=80  Identities=29%  Similarity=0.397  Sum_probs=74.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchh
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r  355 (780)
                      ..+||||++|+..+++.||..+|+.||+|.+|.+. .+++||||.+..+.+|++|+.+|+...+.++.|+|.|+..++.+
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPK  498 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcc
Confidence            34799999999999999999999999999999986 46899999999999999999999999999999999999988876


Q ss_pred             h
Q 004002          356 R  356 (780)
Q Consensus       356 ~  356 (780)
                      .
T Consensus       499 s  499 (894)
T KOG0132|consen  499 S  499 (894)
T ss_pred             h
Confidence            5

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.62  E-value=6.2e-08  Score=109.85  Aligned_cols=165  Identities=19%  Similarity=0.347  Sum_probs=131.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcC-----------C-CEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQY-----------G-DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~y-----------G-~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr  257 (780)
                      ...+.++|+++|..+++++.-.+|..-           | .+..+. .+..+.|||++|.+.++|..|+. +++..+.|.
T Consensus       173 ~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~-~n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g~  250 (500)
T KOG0120|consen  173 RQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQ-LNLEKNFAFIEFRSISEATEAMA-LDGIIFEGR  250 (500)
T ss_pred             hhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeee-ecccccceeEEecCCCchhhhhc-ccchhhCCC
Confidence            345799999999999999999988743           3 255554 46788999999999999999998 788888887


Q ss_pred             ccccccCCCCCC-------------------CCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCc
Q 004002          258 KLDIHFSIPKDN-------------------PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHK  313 (780)
Q Consensus       258 ~I~V~~a~pk~~-------------------~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~s  313 (780)
                      ++.+..-.....                   ..........++|++||..+++++++++.+.||.++..++     ++.+
T Consensus       251 ~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~s  330 (500)
T KOG0120|consen  251 PLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNS  330 (500)
T ss_pred             CceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccc
Confidence            776643111000                   0011122358999999999999999999999999877642     5788


Q ss_pred             ccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchhh
Q 004002          314 RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  356 (780)
Q Consensus       314 rG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r~  356 (780)
                      +||||.+|.+......|+..|||..+.+++|.|..|..+....
T Consensus       331 kg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~  373 (500)
T KOG0120|consen  331 KGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNA  373 (500)
T ss_pred             cceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhc
Confidence            9999999999999999999999999999999999998776443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.60  E-value=7.3e-08  Score=98.09  Aligned_cols=77  Identities=29%  Similarity=0.588  Sum_probs=71.8

Q ss_pred             cceeecCCCCCCChhHHHH----HhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~----~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .||||.||+..+..++|+.    +|++||+|.+|..  +++.||-|||.|++.+.|..|+++|+|..+-|+.+++.+|+.
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s   89 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKS   89 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccC
Confidence            3999999999999999998    9999999999875  677899999999999999999999999999999999999988


Q ss_pred             Cch
Q 004002          352 GGA  354 (780)
Q Consensus       352 k~~  354 (780)
                      +..
T Consensus        90 ~sd   92 (221)
T KOG4206|consen   90 DSD   92 (221)
T ss_pred             ccc
Confidence            754

>smart00361 RRM_1 RNA recognition motif

Probab=98.56  E-value=1.1e-07  Score=80.97  Aligned_cols=56  Identities=20%  Similarity=0.377  Sum_probs=50.0

Q ss_pred             HHHHHHHhh----cCCCEEEEE------eC--CCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          206 DSELRALFE----QYGDIRTLY------TA--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       206 eeeLr~lF~----~yG~I~sv~------~t--gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      +++|+++|+    +||.|.++.      .+  ++++|||||+|.+.++|.+|++.|+|..+.|+.|.+
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            678899998    999998873      12  778999999999999999999999999999999875

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.48  E-value=2.3e-07  Score=99.14  Aligned_cols=83  Identities=24%  Similarity=0.458  Sum_probs=71.3

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHc-cCccccccccccc
Q 004002          184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIH  262 (780)
Q Consensus       184 ~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~L-ng~~l~gr~I~V~  262 (780)
                      ..+..+...++|||++|-..++|.+|++.|.+||+|++++.. ..+++|||+|.+.++|+.|..++ +...|.|++|.|.
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~-~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRIL-PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEee-cccccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            445566677999999999999999999999999999999853 35679999999999999998875 4456799999999


Q ss_pred             cCCCC
Q 004002          263 FSIPK  267 (780)
Q Consensus       263 ~a~pk  267 (780)
                      |..++
T Consensus       299 Wg~~~  303 (377)
T KOG0153|consen  299 WGRPK  303 (377)
T ss_pred             eCCCc
Confidence            99883

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.43  E-value=2.6e-07  Score=99.59  Aligned_cols=163  Identities=20%  Similarity=0.288  Sum_probs=129.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..+++|++++...+.+.++..++..+|.+..+.     ....++|++.|.|...+.+..|+.......+.++.+......
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            468999999999999999999999999766554     457799999999999999999999655456655554443332


Q ss_pred             CCCCCC-----C-CCCCcccee-ecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 004002          266 PKDNPS-----D-KDLNQGTLV-VFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       266 pk~~~s-----~-~~~~~~~L~-V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                      ......     . ......+++ |++|+..+++++|+..|..+|.|..+++     ++..+++|+|+|.+...+..|+..
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence            222110     0 111223455 9999999999999999999999999975     567789999999999999999987


Q ss_pred             hCCCccCCceEEEEecCCCch
Q 004002          334 LNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       334 LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                       ....+.++.+.+....+...
T Consensus       247 -~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  247 -QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             -ccCcccCcccccccCCCCcc
Confidence             88999999999999887653

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.42  E-value=1.8e-07  Score=96.38  Aligned_cols=159  Identities=18%  Similarity=0.225  Sum_probs=115.0

Q ss_pred             EEEEeCCCCCCCHHH-H--HHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          194 TLFVRNINSNVEDSE-L--RALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       194 tLfVgNLp~~vteee-L--r~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .+++.++-.++..+- |  ...|+.|-.+...+    ..++-++++|+.|....+-.++-..-+++.++-+.+++.-...
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            344555555554443 2  45566554433222    3567889999999988888888777677777766666654433


Q ss_pred             CCCCC--CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEE-----EeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 004002          267 KDNPS--DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (780)
Q Consensus       267 k~~~s--~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v-----~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i  339 (780)
                      -.+++  +-+...-.||.+.|..+++++-|-..|.+|-.-...     +-+++++||+||.|.+..++..|++.|+|+.+
T Consensus       178 wedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyV  257 (290)
T KOG0226|consen  178 WEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYV  257 (290)
T ss_pred             cCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccccc
Confidence            33332  233455689999999999999999999998544332     23789999999999999999999999999999


Q ss_pred             CCceEEEEecCCC
Q 004002          340 AGKRIKLEPSRPG  352 (780)
Q Consensus       340 ~Gr~L~V~~a~~k  352 (780)
                      +.+.|++..+.-+
T Consensus       258 gsrpiklRkS~wk  270 (290)
T KOG0226|consen  258 GSRPIKLRKSEWK  270 (290)
T ss_pred             ccchhHhhhhhHH
Confidence            9999998655443

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.42  E-value=4.3e-07  Score=97.15  Aligned_cols=77  Identities=35%  Similarity=0.510  Sum_probs=68.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHh-CCCccCCceEEEEecCC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~L-nG~~i~Gr~L~V~~a~~  351 (780)
                      +..-++|||++|...+++.+|+++|.+||+|++|++... +++|||+|.++++|+.|..++ |...|+|++|+|.|+++
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            344579999999999999999999999999999998654 569999999999999988765 55588999999999998

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.41  E-value=9.6e-08  Score=96.32  Aligned_cols=131  Identities=22%  Similarity=0.305  Sum_probs=108.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      ..+||||.|+-..|+|+-|.++|-+-|+|..+.+    .++.| ||||.|.++-...-|++-+||..+.++.++|++   
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~---   83 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL---   83 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccc---
Confidence            4689999999999999999999999999999872    45556 999999999999999999999999999988864   


Q ss_pred             CCCCCCCCCCccceeecC----CCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          267 KDNPSDKDLNQGTLVVFN----LDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       267 k~~~s~~~~~~~~L~V~N----Lp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                                    +.++    |+..++++.+.+.|+.-|.|..+++    +++.+.++|+.+....+.-.|++.-.+..
T Consensus        84 --------------r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen   84 --------------RCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLE  149 (267)
T ss_pred             --------------ccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccC
Confidence                          2333    6677899999999999999988875    45577888988877776666766544443


Q ss_pred             c
Q 004002          339 I  339 (780)
Q Consensus       339 i  339 (780)
                      .
T Consensus       150 ~  150 (267)
T KOG4454|consen  150 L  150 (267)
T ss_pred             c
Confidence            3

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.30  E-value=8.9e-08  Score=111.96  Aligned_cols=138  Identities=14%  Similarity=0.232  Sum_probs=118.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      .++||.||+..+.+.+|...|..+|.+..+.     ..++.||+|||.|...++|.+|+....+..++            
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g------------  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG------------  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh------------
Confidence            5899999999999999999999999877654     36889999999999999999999954433333            


Q ss_pred             CCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce
Q 004002          268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  343 (780)
Q Consensus       268 ~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~  343 (780)
                               ...|+|.|+|+..|.++|+.+++.+|.+++.++    .++.+|.++|.|.+..+|.+++..+.+..+.-+.
T Consensus       736 ---------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~  806 (881)
T KOG0128|consen  736 ---------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENN  806 (881)
T ss_pred             ---------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcC
Confidence                     236899999999999999999999999999864    5678999999999999999999888888777777


Q ss_pred             EEEEecCC
Q 004002          344 IKLEPSRP  351 (780)
Q Consensus       344 L~V~~a~~  351 (780)
                      +.|..+.|
T Consensus       807 ~~v~vsnp  814 (881)
T KOG0128|consen  807 GEVQVSNP  814 (881)
T ss_pred             ccccccCC
Confidence            77777665

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.26  E-value=8e-07  Score=94.95  Aligned_cols=79  Identities=20%  Similarity=0.404  Sum_probs=72.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .|...|||..|.+-+|+++|.-+|++||.|.+|.     .+|.+..||||+|.+.+++++|.-+|++..|..+.|.|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            3668999999999999999999999999999986     57889999999999999999999999999999999999998


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      ..-.
T Consensus       317 QSVs  320 (479)
T KOG0415|consen  317 QSVS  320 (479)
T ss_pred             hhhh
Confidence            6543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.24  E-value=1.1e-06  Score=93.80  Aligned_cols=78  Identities=27%  Similarity=0.422  Sum_probs=71.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      +...|||--|.+-+|++||+-||+.||.|+.|.+     ++.+-.||||+|++.+++++|.-+|....|+.++|.|.|++
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            4568999999999999999999999999999865     66677899999999999999999999999999999999998


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      .-.
T Consensus       318 SVs  320 (479)
T KOG0415|consen  318 SVS  320 (479)
T ss_pred             hhh
Confidence            644

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.24  E-value=2.6e-06  Score=85.73  Aligned_cols=79  Identities=18%  Similarity=0.265  Sum_probs=72.2

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhccc-CCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAY-GEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~y-G~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ....+.+||..+|.-+-+.++...|.++ |.|..+++     ||.++|||||+|++.+.|+-|-+.||++.+.++.|.|.
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            3455789999999999999999999998 77777765     89999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 004002          348 PSRPG  352 (780)
Q Consensus       348 ~a~~k  352 (780)
                      +-.|.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            98887

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.23  E-value=1.5e-06  Score=89.22  Aligned_cols=148  Identities=18%  Similarity=0.269  Sum_probs=97.3

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE----------EEeccCccCcccceEEEeecCccccCcccccccCC--CCccc
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM----------ELEGEPQESLSMSMSKISISDSASGNGLLHYSVPN--GAGTV  181 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i----------~V~~d~~esa~~g~~~v~~~~~~~a~~~~~~~l~n--~~~k~  181 (780)
                      |.+++|++|++...+.++..+|..+|.+          +|+|+....+.-++....-.+.........+....  ..+..
T Consensus         1 m~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~   80 (216)
T KOG0106|consen    1 MPRVYIGRLPYRARERDVERFFKGYGKIPDADMKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRP   80 (216)
T ss_pred             CCceeecccCCccchhHHHHHHhhccccccceeecccceeccCchhhhhcccchhcCceecceeeeeecccccccccCCC
Confidence            4578999999999999999999999987          34444333322222211111000000000000000  00000


Q ss_pred             C-CC----CC---CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcc
Q 004002          182 A-GE----HP---YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP  253 (780)
Q Consensus       182 ~-g~----~~---~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~  253 (780)
                      . +.    ..   ......+.|+|.+++..+.+.+|...|..+|.+.....   .++++||+|...++|.+|+..|++..
T Consensus        81 ~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~~~  157 (216)
T KOG0106|consen   81 RGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDGKK  157 (216)
T ss_pred             CCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccchh
Confidence            0 10    00   11334578999999999999999999999999954332   78999999999999999999999999


Q ss_pred             ccccccccccC
Q 004002          254 LRRRKLDIHFS  264 (780)
Q Consensus       254 l~gr~I~V~~a  264 (780)
                      +.++.|.+...
T Consensus       158 ~~~~~l~~~~~  168 (216)
T KOG0106|consen  158 LNGRRISVEKN  168 (216)
T ss_pred             hcCceeeeccc
Confidence            99999999543

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.22  E-value=1.6e-06  Score=97.11  Aligned_cols=74  Identities=24%  Similarity=0.466  Sum_probs=67.7

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ++|||.+|...+...+|+.||++||.|+-.++     ++.-+.||||++.+.++|.+||..|+.+++.|+.|.|+.++.
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            58999999999999999999999999988775     344578999999999999999999999999999999998865

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.20  E-value=3.1e-06  Score=85.23  Aligned_cols=80  Identities=18%  Similarity=0.369  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcC-CCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQY-GDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~y-G~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      .......++|..+|.-+-+.++..+|.++ |.|..++     .||.+||||||+|++.+.|+-|-+.||+..|.++-|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            33456789999999999999999999998 6666665     58999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 004002          262 HFSIPK  267 (780)
Q Consensus       262 ~~a~pk  267 (780)
                      ++-.|.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            987654

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.16  E-value=4e-06  Score=93.98  Aligned_cols=78  Identities=18%  Similarity=0.328  Sum_probs=69.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ....++|||.+|...+-..+|+.+|++||+|.-.+     .+...++|+||++.+.++|.+||..|+...|+|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34568999999999999999999999999998766     2345789999999999999999999999999999999987


Q ss_pred             CCC
Q 004002          264 SIP  266 (780)
Q Consensus       264 a~p  266 (780)
                      +..
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            643

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.11  E-value=2.4e-07  Score=100.63  Aligned_cols=152  Identities=19%  Similarity=0.338  Sum_probs=122.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCc-cccccccccccCCCCCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK-PLRRRKLDIHFSIPKDNPS  271 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~-~l~gr~I~V~~a~pk~~~s  271 (780)
                      .+||++||.+.++-.+|+.+|..- .+-.....--..||+||.+.+...|.+|++.++|+ .+.|+++.|.++.++..++
T Consensus         2 nklyignL~p~~~psdl~svfg~a-k~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrs   80 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDA-KIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRS   80 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccc-cCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHh
Confidence            468999999999999999999743 11100011124689999999999999999999996 5899999999988876543


Q ss_pred             CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCc--ccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       272 ~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~s--rG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                            +.+-|.|+|....++-|..+...||.|+.|..+...  .-..-|.|...+.+..||.+|+|..+....+++.+-
T Consensus        81 ------rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   81 ------RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             ------hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence                  358999999999999999999999999998643221  223457788999999999999999999999999876


Q ss_pred             CC
Q 004002          350 RP  351 (780)
Q Consensus       350 ~~  351 (780)
                      -.
T Consensus       155 Pd  156 (584)
T KOG2193|consen  155 PD  156 (584)
T ss_pred             ch
Confidence            43

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.07  E-value=1.3e-05  Score=81.40  Aligned_cols=79  Identities=20%  Similarity=0.283  Sum_probs=66.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEE--EeCCCc----ccEEEEEEcCHHHHHHHHHHhCCCccC---CceEEE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHK----RHHKFIEFYDVRAAEAALKSLNRSDIA---GKRIKL  346 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v--~~~g~s----rG~aFV~F~~~e~A~~Ai~~LnG~~i~---Gr~L~V  346 (780)
                      ..+||||.+||.++..-||..+|.+|-.-+.+  +.+.+.    +-+|||.|.+..+|++|+.+|||..|+   +..|++
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            35799999999999999999999998554444  444433    368999999999999999999999886   688999


Q ss_pred             EecCCCch
Q 004002          347 EPSRPGGA  354 (780)
Q Consensus       347 ~~a~~k~~  354 (780)
                      ++++....
T Consensus       113 ElAKSNtK  120 (284)
T KOG1457|consen  113 ELAKSNTK  120 (284)
T ss_pred             eehhcCcc
Confidence            99987654

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.02  E-value=9.4e-06  Score=93.46  Aligned_cols=84  Identities=18%  Similarity=0.375  Sum_probs=72.6

Q ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe--------CCCcceEEEEEEecHHHHHHHHHHccCccc
Q 004002          183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--------ACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (780)
Q Consensus       183 g~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~--------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l  254 (780)
                      |....++...++|||+||++.++++.|...|.+||+|.++++        ..+-+-||||.|.+..+|++|++.|+|..+
T Consensus       165 gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv  244 (877)
T KOG0151|consen  165 GSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV  244 (877)
T ss_pred             CcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee
Confidence            333334456689999999999999999999999999999882        345677999999999999999999999999


Q ss_pred             cccccccccCCC
Q 004002          255 RRRKLDIHFSIP  266 (780)
Q Consensus       255 ~gr~I~V~~a~p  266 (780)
                      .+..+++.|+++
T Consensus       245 ~~~e~K~gWgk~  256 (877)
T KOG0151|consen  245 MEYEMKLGWGKA  256 (877)
T ss_pred             eeeeeeeccccc
Confidence            999999999854

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.01  E-value=4.7e-05  Score=82.48  Aligned_cols=142  Identities=15%  Similarity=0.202  Sum_probs=106.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcC-----CCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~y-----G~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ....+..++|||.-++.+|..+|.-.     |.+......++..|.|.|.|.+.|.-+-|++. +...+.++.|.|-.+.
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~  137 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKAT  137 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccC
Confidence            34567788999999999999999732     33333335678889999999999999999995 7777888888887654


Q ss_pred             CCCCC------------CCCCCCccceeecCCCCCCChhHHHHHhccc----CCeeEE---E-eCCCcccEEEEEEcCHH
Q 004002          266 PKDNP------------SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY----GEVKEI---R-ETPHKRHHKFIEFYDVR  325 (780)
Q Consensus       266 pk~~~------------s~~~~~~~~L~V~NLp~~vteedL~~~Fs~y----G~I~~v---~-~~g~srG~aFV~F~~~e  325 (780)
                      ..+--            --...++-.|.+++||++.++.|+.++|.+-    |.++.|   + -+++..|-|||.|...+
T Consensus       138 ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee  217 (508)
T KOG1365|consen  138 GEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEE  217 (508)
T ss_pred             chhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHH
Confidence            43210            0011234467789999999999999999732    222333   2 26778899999999999


Q ss_pred             HHHHHHHH
Q 004002          326 AAEAALKS  333 (780)
Q Consensus       326 ~A~~Ai~~  333 (780)
                      +|+.||.+
T Consensus       218 ~aq~aL~k  225 (508)
T KOG1365|consen  218 DAQFALRK  225 (508)
T ss_pred             HHHHHHHH
Confidence            99999985

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.95  E-value=1.7e-05  Score=83.25  Aligned_cols=76  Identities=22%  Similarity=0.369  Sum_probs=68.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      ...+|+|.|||..|++++|+++|+.||.+..+-    ..|++.|.|-|.|...++|.+|++.+++..+.|++|++....+
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            347899999999999999999999999877664    5788999999999999999999999999999999998876544

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.93  E-value=1.1e-05  Score=92.89  Aligned_cols=78  Identities=29%  Similarity=0.417  Sum_probs=70.6

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe--------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--------~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      +...++|||+||++.++++.|...|+.||.|..+++        ....+.+|||-|-++.+|++|++.|+|..+.+..++
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            456689999999999999999999999999999975        233467999999999999999999999999999999


Q ss_pred             EEecCC
Q 004002          346 LEPSRP  351 (780)
Q Consensus       346 V~~a~~  351 (780)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999965

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.86  E-value=3.7e-05  Score=80.65  Aligned_cols=78  Identities=24%  Similarity=0.350  Sum_probs=69.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ....|+|.|||..|+++||+++|..||.++.+-+    .+.+.|.|-|.|...++|++|++.+||..++|+.+++....+
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            3467999999999999999999999998888754    677789999999999999999999999999999999987766


Q ss_pred             Cc
Q 004002          352 GG  353 (780)
Q Consensus       352 k~  353 (780)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            54

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.86  E-value=0.00012  Score=82.52  Aligned_cols=148  Identities=18%  Similarity=0.225  Sum_probs=102.1

Q ss_pred             CCCCCchHHhhhcCCceeeeccCCCCCChHHHHHHhcCCCcEEEeccC-----ccCcccc---eEEEeecCccccCcc--
Q 004002          100 NSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEP-----QESLSMS---MSKISISDSASGNGL--  169 (780)
Q Consensus       100 nlLP~deddl~s~v~~el~V~~Lp~s~~E~el~dlFs~~G~i~V~~d~-----~esa~~g---~~~v~~~~~~~a~~~--  169 (780)
                      +.++.. +.-...+..+++|++||++++|.++...|..||.+.|+-..     .....+|   ++++-|.+...-..+  
T Consensus       246 ~~~~~~-~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~  324 (520)
T KOG0129|consen  246 GSLPPR-GYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLS  324 (520)
T ss_pred             cccCCC-CCCccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHH
Confidence            344433 33344457899999999999999999999999999776541     1122345   888777754322100  


Q ss_pred             ------ccc-------ccCCCCcc----------cCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhh-cCCCEEEEE--
Q 004002          170 ------LHY-------SVPNGAGT----------VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFE-QYGDIRTLY--  223 (780)
Q Consensus       170 ------~~~-------~l~n~~~k----------~~g~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~-~yG~I~sv~--  223 (780)
                            ..+       .+..+...          ...+....-++.+|||||+||.-++.+||..+|+ -||.|..+-  
T Consensus       325 aC~~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGID  404 (520)
T KOG0129|consen  325 ACSEGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGID  404 (520)
T ss_pred             HHhhcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEec
Confidence                  000       11111000          0112223456789999999999999999999999 899998764  


Q ss_pred             ---eCCCcceEEEEEEecHHHHHHHHHH
Q 004002          224 ---TACKHRGFVMISYYDIRAARTAMRA  248 (780)
Q Consensus       224 ---~tgkskG~aFV~F~~~e~A~~Al~~  248 (780)
                         ..+-.+|-|-|+|.+..+-.+||.+
T Consensus       405 tD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  405 TDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCCCCCcceeeecccHHHHHHHhh
Confidence               2345789999999999999999985

>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=97.83  E-value=1.2e-05  Score=80.95  Aligned_cols=78  Identities=19%  Similarity=0.349  Sum_probs=51.0

Q ss_pred             CCcceeEEEecCCCCCCHHHHHHHHhhcCCCcceeEEee--ccccC--CcceeeEEeccCCccchHHHHHHhcCceeEEE
Q 004002          691 EDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP--IDFKN--KCNVGYAFINMLSPLHIIPFYEVLFSCAIGIL  766 (780)
Q Consensus       691 ~d~rtt~mirniPn~~~~~~l~~~i~~~~~~~ydf~ylp--~d~~~--~~n~gyafin~~~~~~~~~f~~~f~~~~~~~~  766 (780)
                      +..++.|.||+||+.+|.+.+++.|+......++|-|++  .+...  .+-..-|||||.+.+++..|.+.|+|+.    
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~----   79 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHV----   79 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEE----
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcE----
Confidence            346789999999999999999998887666676666665  33332  2334569999999999999999999997    


Q ss_pred             EeeCCCc
Q 004002          767 FFNNNNN  773 (780)
Q Consensus       767 ~~~~~~~  773 (780)
                       |-|+..
T Consensus        80 -F~D~kg   85 (176)
T PF03467_consen   80 -FVDSKG   85 (176)
T ss_dssp             -EE-TTS
T ss_pred             -EECCCC
Confidence             555543

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.

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.79  E-value=2.9e-05  Score=87.41  Aligned_cols=75  Identities=27%  Similarity=0.493  Sum_probs=65.0

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~-----g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..|||+|||.++++++|+++|..||.|+..++.     ++...||||+|++.++++.||++ +-..+++++|.|+..++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            459999999999999999999999999987541     33338999999999999999996 577889999999988775


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            4

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.79  E-value=2.3e-05  Score=88.18  Aligned_cols=71  Identities=24%  Similarity=0.406  Sum_probs=61.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE---e--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY---T--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~---~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+|||+|||.++++++|+++|..||+|+...   .  .++..+||||+|.+.++++.||.+ +-..|+++++.|+--
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            5699999999999999999999999998765   1  255559999999999999999997 577788999988743

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.76  E-value=3.8e-05  Score=79.54  Aligned_cols=77  Identities=19%  Similarity=0.336  Sum_probs=66.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE-----EEeCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-----LYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s-----v~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ...+-+||.+.|..+++++.|-..|.+|-....     -+.+++++||+||.|.++.++..|+++|+|+.++.++|+++.
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            344579999999999999999999999864332     226899999999999999999999999999999999999875


Q ss_pred             CC
Q 004002          264 SI  265 (780)
Q Consensus       264 a~  265 (780)
                      +.
T Consensus       267 S~  268 (290)
T KOG0226|consen  267 SE  268 (290)
T ss_pred             hh
Confidence            53

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.73  E-value=5.7e-05  Score=81.18  Aligned_cols=74  Identities=14%  Similarity=0.314  Sum_probs=66.4

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEE--------Ee----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--------RE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v--------~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L  344 (780)
                      .+.|||.|||.++|.+++.++|++||.|..=        ++    .|+-+|-|.|.|-..++..-|++.|++..+.|+.|
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~  213 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKL  213 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEE
Confidence            4579999999999999999999999988652        22    56778999999999999999999999999999999


Q ss_pred             EEEecC
Q 004002          345 KLEPSR  350 (780)
Q Consensus       345 ~V~~a~  350 (780)
                      +|+.|+
T Consensus       214 rVerAk  219 (382)
T KOG1548|consen  214 RVERAK  219 (382)
T ss_pred             EEehhh
Confidence            998775

>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=97.70  E-value=0.00013  Score=63.91  Aligned_cols=70  Identities=26%  Similarity=0.325  Sum_probs=48.4

Q ss_pred             cceeecCCCCCCChh----HHHHHhccc-CCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          278 GTLVVFNLDPSVSNE----DLRQIFGAY-GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       278 ~~L~V~NLp~~vtee----dL~~~Fs~y-G~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..|+|.|||.+.+..    .|++++.-+ |.|..|  .   .+.|+|+|.+.+.|++|.+.|+|..+-|.+|.|.+....
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~---~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S---GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e---CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            469999999988754    467788888 567766  2   367999999999999999999999999999999998543

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=97.69  E-value=4.9e-05  Score=79.69  Aligned_cols=80  Identities=24%  Similarity=0.371  Sum_probs=70.2

Q ss_pred             CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEE
Q 004002          272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  346 (780)
Q Consensus       272 ~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V  346 (780)
                      .+.+....+||+|++..+|.+++..+|+.||.|..+.     ..++.+||+||+|.+.+.+++|++ |+|..|.|+.|+|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            3455667899999999999999999999999996443     466789999999999999999999 9999999999999


Q ss_pred             EecCCC
Q 004002          347 EPSRPG  352 (780)
Q Consensus       347 ~~a~~k  352 (780)
                      .+.+-.
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            887644

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.66  E-value=0.00011  Score=84.65  Aligned_cols=161  Identities=14%  Similarity=0.036  Sum_probs=116.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhc-CCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQ-YGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~-yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .++.+-++..+.+.++.+++++|.. +-.-..+.   +.+...|-++|.|....++++|++. +......|.+.|..+..
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCc
Confidence            4466667789999999999999963 32222222   3444578999999999999999984 55556666666543211


Q ss_pred             CCC-------------CC-------------CC---------CCCccceeecCCCCCCChhHHHHHhcccCCeeE-EEe-
Q 004002          267 KDN-------------PS-------------DK---------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE-  309 (780)
Q Consensus       267 k~~-------------~s-------------~~---------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~-v~~-  309 (780)
                      ...             ..             +.         .....+|||..||..+++.++-++|...-.|++ |.+ 
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt  468 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELT  468 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEec
Confidence            100             00             00         011258999999999999999999998777766 665 


Q ss_pred             ---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          310 ---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       310 ---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                         +++-++.|||.|...+++.+|+..-+...++.+.|+|.....+
T Consensus       469 ~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~  514 (944)
T KOG4307|consen  469 RLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADY  514 (944)
T ss_pred             cCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhH
Confidence               3455688999999999999999877777788899999765443

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.49  E-value=4.1e-05  Score=83.22  Aligned_cols=157  Identities=17%  Similarity=0.154  Sum_probs=115.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC--------CCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t--------gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..|-|.||.+.+|.++++.||.-.|+|..++..        ....-.|||.|.+...+..|-. |.++++-++.|.|...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            489999999999999999999999999987732        2345689999999999887776 7777777766555331


Q ss_pred             CCCCCC-----------------------------C--CCC-------------------C--CccceeecCCCCCCChh
Q 004002          265 IPKDNP-----------------------------S--DKD-------------------L--NQGTLVVFNLDPSVSNE  292 (780)
Q Consensus       265 ~pk~~~-----------------------------s--~~~-------------------~--~~~~L~V~NLp~~vtee  292 (780)
                      ...-.+                             .  +..                   +  -..+++|.+|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            100000                             0  000                   0  01479999999999999


Q ss_pred             HHHHHhcccCCeeEEEeC-CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          293 DLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       293 dL~~~Fs~yG~I~~v~~~-g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ++-+.|..+|+|...++. +....+|-|+|........|++ ++|.++.-....+...+|
T Consensus       167 e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~kP  225 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIKP  225 (479)
T ss_pred             hhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcCc
Confidence            999999999999998763 3344678899999999999998 577777644444433333

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.47  E-value=0.00023  Score=84.42  Aligned_cols=152  Identities=20%  Similarity=0.255  Sum_probs=109.8

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE-EEeccCc-cCcccceEEEeecCccccC----cccccccCCCCcccCCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQ-ESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPY  187 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i-~V~~d~~-esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g~~~~  187 (780)
                      .+.+++++|...+++.+++..|..+|.+ .|.++.. -.+..+++++.+.....+-    ...+..+.++..+. +-...
T Consensus       372 trTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~-glG~~  450 (975)
T KOG0112|consen  372 TRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI-GLGQP  450 (975)
T ss_pred             hhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccc-ccccc
Confidence            4789999999999999999999999988 6766654 3344455555544332221    11111121111111 11111


Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccc--cccccccCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSI  265 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~I~V~~a~  265 (780)
                      ...+.+.+||++|...+....|...|..||.|..|.. -+..-||+|.|.+...|+.|++.|-|..|++  +.+.|.|+.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy-~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY-RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeec-ccCCcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            3456789999999999999999999999999998863 3345699999999999999999999999974  678888876


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      +.
T Consensus       530 ~~  531 (975)
T KOG0112|consen  530 PP  531 (975)
T ss_pred             CC
Confidence            54

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.46  E-value=0.0004  Score=63.15  Aligned_cols=73  Identities=18%  Similarity=0.352  Sum_probs=57.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcC--CCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccc----cccccc
Q 004002          193 RTLFVRNINSNVEDSELRALFEQY--GDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR----RRKLDI  261 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~y--G~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~----gr~I~V  261 (780)
                      +||-|+|||...|.++|.+++...  |...=++     .+..+.|||||.|.+++.|.+-.+.++|+.+.    .+...|
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            689999999999999999988753  3322222     35668999999999999999999999998875    334455


Q ss_pred             ccCC
Q 004002          262 HFSI  265 (780)
Q Consensus       262 ~~a~  265 (780)
                      .||+
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            5554

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.35  E-value=0.00011  Score=74.54  Aligned_cols=75  Identities=20%  Similarity=0.197  Sum_probs=66.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ..++|||.|+-..++||-|.++|-+-|.|..|.+    .++.| ||||.|.+.-...-|++-|||..+.+..|++++-.-
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            3579999999999999999999999999999976    33344 999999999999999999999999999999887543

>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=97.34  E-value=0.0005  Score=60.35  Aligned_cols=68  Identities=22%  Similarity=0.406  Sum_probs=48.5

Q ss_pred             cEEEEeCCCCCCCHHH----HHHHhhcCC-CEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          193 RTLFVRNINSNVEDSE----LRALFEQYG-DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       193 ~tLfVgNLp~~vteee----Lr~lF~~yG-~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..|+|.|||.+.+-..    |+.++.-+| .|..|     +.+.|.|.|.+.+.|++|.+.|+|..+.|++|.|.|..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            4799999999998765    556776775 67765     24789999999999999999999999999999999974

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=97.31  E-value=0.00024  Score=74.48  Aligned_cols=77  Identities=16%  Similarity=0.304  Sum_probs=67.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      .+...+.+||+|+...+|.+++...|+.||.|..+.     ..+..|||+||+|.+.+.+++|++ |++..|.++.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            345668999999999999999999999999996433     356789999999999999999999 99999999999997


Q ss_pred             cCC
Q 004002          263 FSI  265 (780)
Q Consensus       263 ~a~  265 (780)
                      +.+
T Consensus       176 ~~r  178 (231)
T KOG4209|consen  176 LKR  178 (231)
T ss_pred             eee
Confidence            754

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.30  E-value=0.00049  Score=74.49  Aligned_cols=156  Identities=16%  Similarity=0.231  Sum_probs=106.1

Q ss_pred             cCCceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCc---cccc-cc---------C
Q 004002          112 GIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG---LLHY-SV---------P  175 (780)
Q Consensus       112 ~v~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~---~~~~-~l---------~  175 (780)
                      +.....+++.+-+.+++.++..++...|..   .+.+.......+++..+.|........   +... .+         .
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            346788999999999988787888888864   222223344555666666554432221   1110 00         0


Q ss_pred             CCCcc-cCCCC-CCCCCCCcEEE-EeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHH
Q 004002          176 NGAGT-VAGEH-PYGEHPSRTLF-VRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMR  247 (780)
Q Consensus       176 n~~~k-~~g~~-~~~e~~s~tLf-VgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~  247 (780)
                      ..... ..... .....+..++| |++|+.++++++|+..|..+|.|..++     .++..+|||+|.|.+...+..|+.
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            00000 00000 11112334555 999999999999999999999999987     468899999999999999999999


Q ss_pred             HccCccccccccccccCCCCC
Q 004002          248 ALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       248 ~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      . +...+.++++.+.+..+..
T Consensus       246 ~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  246 D-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             c-ccCcccCcccccccCCCCc
Confidence            7 8889999999999877654

>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=97.28  E-value=0.00047  Score=63.69  Aligned_cols=82  Identities=24%  Similarity=0.387  Sum_probs=49.1

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC-----ccCCceEEEEecCCCc
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-----DIAGKRIKLEPSRPGG  353 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~-----~i~Gr~L~V~~a~~k~  353 (780)
                      .|.|.+++..++.++|++.|++||.|..|.+.. ....|+|+|.+.++|++|+.++.-.     .+.+..+.++.-.-. 
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~-G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLeGe-   80 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR-GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLEGE-   80 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--T-T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---HH-
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecC-CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECCCH-
Confidence            578899999999999999999999999999853 2347999999999999999988543     566666666554322 


Q ss_pred             hhhhHhhhh
Q 004002          354 ARRNLMLQL  362 (780)
Q Consensus       354 ~r~~~l~ql  362 (780)
                      +-..+++..
T Consensus        81 eE~~Yw~ki   89 (105)
T PF08777_consen   81 EEEEYWKKI   89 (105)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            223355444

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.17  E-value=0.00015  Score=85.68  Aligned_cols=148  Identities=18%  Similarity=0.198  Sum_probs=115.0

Q ss_pred             CcEEEEeCCCCCCCHH-HHHHHhhcCCCEEEEEeCC----Ccce-EEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          192 SRTLFVRNINSNVEDS-ELRALFEQYGDIRTLYTAC----KHRG-FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       192 s~tLfVgNLp~~vtee-eLr~lF~~yG~I~sv~~tg----kskG-~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .+...+.++.+...+. ..+..|..+|.|+.++...    .+.. ++++.+....+++.|.. ..+.-+.++.+.|..+.
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad  649 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLAD  649 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCCC
Confidence            3567788888887776 5678999999999987321    2223 78899999999999988 57888888988888877


Q ss_pred             CCCCCCCCC------CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHh
Q 004002          266 PKDNPSDKD------LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL  334 (780)
Q Consensus       266 pk~~~s~~~------~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~L  334 (780)
                      ++.......      ....++||+||+..+.+++|...|.++|.+..+++     .++-+|+|+|.|...++|.+||...
T Consensus       650 ~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~  729 (881)
T KOG0128|consen  650 AEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFR  729 (881)
T ss_pred             chhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhh
Confidence            654222111      12258999999999999999999999998877753     4667899999999999999999865


Q ss_pred             CCCccC
Q 004002          335 NRSDIA  340 (780)
Q Consensus       335 nG~~i~  340 (780)
                      .++.++
T Consensus       730 d~~~~g  735 (881)
T KOG0128|consen  730 DSCFFG  735 (881)
T ss_pred             hhhhhh
Confidence            555444

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.72  E-value=0.0042  Score=66.71  Aligned_cols=76  Identities=22%  Similarity=0.451  Sum_probs=62.3

Q ss_pred             ccceeecCCCCCCChhH----H--HHHhcccCCeeEEEeCCCc------ccE--EEEEEcCHHHHHHHHHHhCCCccCCc
Q 004002          277 QGTLVVFNLDPSVSNED----L--RQIFGAYGEVKEIRETPHK------RHH--KFIEFYDVRAAEAALKSLNRSDIAGK  342 (780)
Q Consensus       277 ~~~L~V~NLp~~vteed----L--~~~Fs~yG~I~~v~~~g~s------rG~--aFV~F~~~e~A~~Ai~~LnG~~i~Gr  342 (780)
                      ..-+||-+|++.+-.|+    |  .++|++||.|+.|.+..+-      .++  .||.|.+.++|.+||.+.+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            34689999999987766    3  3889999999999763321      122  39999999999999999999999999


Q ss_pred             eEEEEecCCC
Q 004002          343 RIKLEPSRPG  352 (780)
Q Consensus       343 ~L~V~~a~~k  352 (780)
                      .|+..+...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999987654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.57  E-value=0.0026  Score=66.35  Aligned_cols=89  Identities=24%  Similarity=0.347  Sum_probs=75.4

Q ss_pred             HHHHHHHHHccCccccccccccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEE----EeCCCccc
Q 004002          240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRH  315 (780)
Q Consensus       240 e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v----~~~g~srG  315 (780)
                      .-|+.|.++|++....++.++|.|+..           +.|||.||..-++.|.|++-|+.||.|...    +..++..+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~-----------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~   73 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH-----------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTR   73 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc-----------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccc
Confidence            357888899999999999999999863           469999999999999999999999998653    33556667


Q ss_pred             EEEEEEcCHHHHHHHHHHhCCCcc
Q 004002          316 HKFIEFYDVRAAEAALKSLNRSDI  339 (780)
Q Consensus       316 ~aFV~F~~~e~A~~Ai~~LnG~~i  339 (780)
                      -++|+|...-.|.+|+...+-.-+
T Consensus        74 eg~v~~~~k~~a~~a~rr~~~~g~   97 (275)
T KOG0115|consen   74 EGIVEFAKKPNARKAARRCREGGF   97 (275)
T ss_pred             cchhhhhcchhHHHHHHHhccCcc
Confidence            899999999999999998754433

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.53  E-value=0.002  Score=70.06  Aligned_cols=78  Identities=24%  Similarity=0.329  Sum_probs=69.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEE-------------EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v-------------~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr  342 (780)
                      ...++||.+||..+++++|.++|.++|.|+.=             +.|...|+-|.|.|+|...|+.||.-++++.+.|.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            34689999999999999999999999988653             24677899999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 004002          343 RIKLEPSRPGG  353 (780)
Q Consensus       343 ~L~V~~a~~k~  353 (780)
                      .|+|.++..+.
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99999887654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.42  E-value=0.0036  Score=69.35  Aligned_cols=67  Identities=33%  Similarity=0.469  Sum_probs=55.9

Q ss_pred             CCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCC------------------cccEEEEEEcCHHHHHHHHH
Q 004002          271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH------------------KRHHKFIEFYDVRAAEAALK  332 (780)
Q Consensus       271 s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~------------------srG~aFV~F~~~e~A~~Ai~  332 (780)
                      .++....++|.+.|||.+-.-|-|.+||+.+|.|+.|++-.-                  .+-+|+|+|+..+.|.+|.+
T Consensus       225 ~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  225 DEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            344567789999999999999999999999999999986211                  14579999999999999999


Q ss_pred             HhCCC
Q 004002          333 SLNRS  337 (780)
Q Consensus       333 ~LnG~  337 (780)
                      .|+-.
T Consensus       305 ~~~~e  309 (484)
T KOG1855|consen  305 LLNPE  309 (484)
T ss_pred             hhchh
Confidence            87644

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.40  E-value=0.0052  Score=49.72  Aligned_cols=52  Identities=21%  Similarity=0.429  Sum_probs=42.8

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHH
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAAL  331 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai  331 (780)
                      +.|-|.|.+.+..+. +...|..||+|..+.++ ......+|+|.++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            357888888777644 55588899999999986 44678999999999999995

>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=96.38  E-value=0.0069  Score=55.48  Aligned_cols=72  Identities=21%  Similarity=0.365  Sum_probs=52.2

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEE------------eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce-
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR------------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-  343 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~------------~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~-  343 (780)
                      ..-|.|.|.|... -..+.+.|++||+|.+..            -......+--|+|+++.+|.+||+ -||..+.|.. 
T Consensus         6 ~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            4568999999884 466778899999998885            123446789999999999999998 5999999864 


Q ss_pred             EEEEecC
Q 004002          344 IKLEPSR  350 (780)
Q Consensus       344 L~V~~a~  350 (780)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4466664

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.

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]

Probab=96.36  E-value=0.0025  Score=70.13  Aligned_cols=70  Identities=17%  Similarity=0.335  Sum_probs=58.8

Q ss_pred             CcceeEEEecCCCCCCHHHHHHHHhhcCCCcceeEEee-ccccCC-cceeeEEeccCCccchHHHHHHhcCce
Q 004002          692 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP-IDFKNK-CNVGYAFINMLSPLHIIPFYEVLFSCA  762 (780)
Q Consensus       692 d~rtt~mirniPn~~~~~~l~~~i~~~~~~~ydf~ylp-~d~~~~-~n~gyafin~~~~~~~~~f~~~f~~~~  762 (780)
                      +....|.||++|+++|.+.|++.||- +...+.|-|+- -|+... |-.+.|||||..+.++..|.+.|+|+.
T Consensus         5 ~~~~Kvv~rrlpp~l~~~~~~eqi~p-~~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~i   76 (376)
T KOG1295|consen    5 EAKVKVVVRRLPPKLTEEQLLEQINP-FPEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYI   76 (376)
T ss_pred             ccceeeeeecCCCcccHHHHhhhcCC-CccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceE
Confidence            34568999999999999999999999 77888888866 555433 335669999999999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.27  E-value=0.0059  Score=65.64  Aligned_cols=75  Identities=25%  Similarity=0.408  Sum_probs=61.2

Q ss_pred             CcEEEEeCCCCCCCHHH----H--HHHhhcCCCEEEEEeCCC------cceE--EEEEEecHHHHHHHHHHccCcccccc
Q 004002          192 SRTLFVRNINSNVEDSE----L--RALFEQYGDIRTLYTACK------HRGF--VMISYYDIRAARTAMRALQNKPLRRR  257 (780)
Q Consensus       192 s~tLfVgNLp~~vteee----L--r~lF~~yG~I~sv~~tgk------skG~--aFV~F~~~e~A~~Al~~Lng~~l~gr  257 (780)
                      ..-+||-+||+.+..|+    |  .++|.+||.|..|.+..+      ..+.  .||+|.+.++|.+||.+.+|..+.||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            35789999999998887    3  269999999998873222      1222  49999999999999999999999999


Q ss_pred             ccccccCCC
Q 004002          258 KLDIHFSIP  266 (780)
Q Consensus       258 ~I~V~~a~p  266 (780)
                      -|+..|...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999988653

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.22  E-value=0.0055  Score=67.59  Aligned_cols=100  Identities=26%  Similarity=0.351  Sum_probs=77.0

Q ss_pred             ceeecCCCCCCChhHHHHHhccc--CCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC-ccCCceEEEEecCCCchh
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-DIAGKRIKLEPSRPGGAR  355 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~y--G~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~-~i~Gr~L~V~~a~~k~~r  355 (780)
                      .||++||.+.++..||+.+|...  +.-...-   ...||+||.+.+..-|.+|++.++|+ ++.|+++.+..+-++..+
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl---~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqr   79 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL---VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQR   79 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCccee---eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHH
Confidence            68999999999999999999864  1111111   23589999999999999999999997 889999999999887765


Q ss_pred             h--hHhhhhchhccHHHHHHHHhhhCCC
Q 004002          356 R--NLMLQLNQELEQDESRILQHQVGSP  381 (780)
Q Consensus       356 ~--~~l~ql~~~~~~~~~~~~~~~~Gsp  381 (780)
                      .  ..+++.++++..+-+.....+||.+
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~v  107 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTV  107 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCH
Confidence            3  3455556666666666666666654

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=96.15  E-value=0.011  Score=54.62  Aligned_cols=59  Identities=14%  Similarity=0.247  Sum_probs=38.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCc
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK  252 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~  252 (780)
                      +.|.|.+++..++.++|++.|++||+|.-|.. .+...-|+|.|.+.++|++|+.++.-.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~-~~G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDF-SRGDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEe-cCCCCEEEEEECCcchHHHHHHHHHhc
Confidence            46889999999999999999999999998873 233457999999999999999987544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.05  E-value=0.014  Score=47.21  Aligned_cols=52  Identities=17%  Similarity=0.420  Sum_probs=42.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHH
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM  246 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al  246 (780)
                      +.|-|.+.+++..+.-| ..|..||+|..+... ...-+.+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~vl-~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVL-EHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHH-HHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            56788888887775555 588899999998754 45678999999999999985

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.04  E-value=0.0032  Score=65.72  Aligned_cols=68  Identities=29%  Similarity=0.523  Sum_probs=58.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCC-------------ccc----EEEEEEcCHHHHHHHHHHhCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH-------------KRH----HKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~-------------srG----~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      +.+.||+++||+.+....|++||+.||+|-.|.+.+.             ++.    -|.|+|.+-..|.++...||+..
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            5689999999999999999999999999999865321             111    28999999999999999999999


Q ss_pred             cCCce
Q 004002          339 IAGKR  343 (780)
Q Consensus       339 i~Gr~  343 (780)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99964

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.02  E-value=0.015  Score=67.81  Aligned_cols=71  Identities=21%  Similarity=0.252  Sum_probs=61.7

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCee-EE--E--eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVK-EI--R--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~-~v--~--~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      +.|-+.|+|++++-+||.++|..|-.+- +|  +  ..+...|.+.|.|++.++|.+|...|+++.|..++|+|..
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4788999999999999999999995442 22  2  3677889999999999999999999999999999998864

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=95.98  E-value=0.0071  Score=65.95  Aligned_cols=77  Identities=21%  Similarity=0.289  Sum_probs=68.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-------------eCCCcceEEEEEEecHHHHHHHHHHccCcccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-------------~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr  257 (780)
                      ...+|||-+||..+++++|.++|.++|.|..-+             .|++.||-|.|+|.+..+|+.|+.-++++.+.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            447999999999999999999999999886422             4788999999999999999999999999999999


Q ss_pred             ccccccCCCC
Q 004002          258 KLDIHFSIPK  267 (780)
Q Consensus       258 ~I~V~~a~pk  267 (780)
                      +|+|..+..+
T Consensus       145 ~ikvs~a~~r  154 (351)
T KOG1995|consen  145 TIKVSLAERR  154 (351)
T ss_pred             Cchhhhhhhc
Confidence            9999877543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.57  E-value=0.0058  Score=63.92  Aligned_cols=61  Identities=31%  Similarity=0.402  Sum_probs=49.3

Q ss_pred             hHHHHHhc-ccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          292 EDLRQIFG-AYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       292 edL~~~Fs-~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      |||...|+ +||+|+++++    -..-.|-++|.|...++|++|+..||+.++.|++|.+++..-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            44455555 8999999854    2233677999999999999999999999999999999887543

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.53  E-value=0.025  Score=64.75  Aligned_cols=73  Identities=19%  Similarity=0.231  Sum_probs=57.4

Q ss_pred             CCccceeecCCCCCC--C----hhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC-Cce
Q 004002          275 LNQGTLVVFNLDPSV--S----NEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKR  343 (780)
Q Consensus       275 ~~~~~L~V~NLp~~v--t----eedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~-Gr~  343 (780)
                      .-...|+|.|+|.--  .    ..-|..+|+++|+|.....    .+..+||.|++|.+..+|+.|++.|||+.++ .++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            344688999998522  1    2346688999999988753    5668999999999999999999999999886 466


Q ss_pred             EEEE
Q 004002          344 IKLE  347 (780)
Q Consensus       344 L~V~  347 (780)
                      ..|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            6664

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.18  E-value=0.019  Score=63.82  Aligned_cols=74  Identities=24%  Similarity=0.383  Sum_probs=59.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC----------CC--------cceEEEEEEecHHHHHHHHHHcc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA----------CK--------HRGFVMISYYDIRAARTAMRALQ  250 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t----------gk--------skG~aFV~F~~~e~A~~Al~~Ln  250 (780)
                      +-++++|.+-|||.+-.-+-|.++|+.+|.|..|++-          +.        .+-+|+|+|...+.|.+|.+.|+
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            4588999999999999999999999999999998731          11        26689999999999999999876


Q ss_pred             Cccccccccccc
Q 004002          251 NKPLRRRKLDIH  262 (780)
Q Consensus       251 g~~l~gr~I~V~  262 (780)
                      ...-+..-++|.
T Consensus       308 ~e~~wr~glkvk  319 (484)
T KOG1855|consen  308 PEQNWRMGLKVK  319 (484)
T ss_pred             hhhhhhhcchhh
Confidence            555444444443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.91  E-value=0.058  Score=52.54  Aligned_cols=73  Identities=32%  Similarity=0.454  Sum_probs=53.0

Q ss_pred             CccceeecCCCC------CCC---hhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEE
Q 004002          276 NQGTLVVFNLDP------SVS---NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  346 (780)
Q Consensus       276 ~~~~L~V~NLp~------~vt---eedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V  346 (780)
                      ..+|+.|.=+..      ...   -.+|.+.|..||+|.-||+.+   +.-.|.|.+-+.|.+|+. |+|.++.|+.|+|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l~i  101 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTLKI  101 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEEEE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEEEE
Confidence            446776664441      122   236788899999999999865   458999999999999997 8999999999999


Q ss_pred             EecCCC
Q 004002          347 EPSRPG  352 (780)
Q Consensus       347 ~~a~~k  352 (780)
                      +...|.
T Consensus       102 ~LKtpd  107 (146)
T PF08952_consen  102 RLKTPD  107 (146)
T ss_dssp             EE----
T ss_pred             EeCCcc
Confidence            988765

; PDB: 1UFW_A 2DNR_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=94.89  E-value=0.043  Score=50.36  Aligned_cols=73  Identities=11%  Similarity=0.172  Sum_probs=51.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE------------eCCCcceEEEEEEecHHHHHHHHHHccCcccccc-
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY------------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-  257 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~------------~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr-  257 (780)
                      ..+-|.|=+.|+. ....+.+.|++||+|.+..            ..........|+|.++.+|++||++ ||..|.|. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            3466888888888 5567788999999998875            1123456899999999999999995 99999875 


Q ss_pred             ccccccCC
Q 004002          258 KLDIHFSI  265 (780)
Q Consensus       258 ~I~V~~a~  265 (780)
                      .+-|.+..
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            44466653

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.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.86  E-value=0.05  Score=62.35  Aligned_cols=70  Identities=20%  Similarity=0.401  Sum_probs=54.7

Q ss_pred             CcEEEEeCCCCCCC------HHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcccc-ccccc
Q 004002          192 SRTLFVRNINSNVE------DSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLD  260 (780)
Q Consensus       192 s~tLfVgNLp~~vt------eeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~-gr~I~  260 (780)
                      ...|+|.|+|.-=.      ..-|..+|+++|+|...+    ..|+.+||.|++|.+..+|+.|++.|+|+.|. ..+..
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            35677888775322      234668999999998877    45779999999999999999999999999884 44444


Q ss_pred             c
Q 004002          261 I  261 (780)
Q Consensus       261 V  261 (780)
                      |
T Consensus       138 v  138 (698)
T KOG2314|consen  138 V  138 (698)
T ss_pred             e
Confidence            4

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=94.58  E-value=0.03  Score=60.66  Aligned_cols=70  Identities=16%  Similarity=0.284  Sum_probs=58.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCC--CEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYG--DIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG--~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      .-.+||+||-|.+|+++|.+.....|  .+.+++     ..|.+||||+|...+..+.++.|+.|..+.|+|+.-.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            35799999999999999998887666  233333     57999999999999999999999999999999876544

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=94.51  E-value=0.029  Score=58.80  Aligned_cols=68  Identities=21%  Similarity=0.414  Sum_probs=57.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC-------------CCcce----EEEEEEecHHHHHHHHHHccCcc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-------------CKHRG----FVMISYYDIRAARTAMRALQNKP  253 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t-------------gkskG----~aFV~F~~~e~A~~Al~~Lng~~  253 (780)
                      ....||+.+||+.+.-.-||++|+.||.|-.|+..             +.+++    -|.|+|.+...|.+....||+..
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            44689999999999999999999999999988721             22232    26799999999999999999999


Q ss_pred             ccccc
Q 004002          254 LRRRK  258 (780)
Q Consensus       254 l~gr~  258 (780)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99876

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.35  E-value=0.073  Score=56.69  Aligned_cols=61  Identities=20%  Similarity=0.256  Sum_probs=49.2

Q ss_pred             hhHHHHHhcccCCeeEEEe--C-CCc---ccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          291 NEDLRQIFGAYGEVKEIRE--T-PHK---RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       291 eedL~~~Fs~yG~I~~v~~--~-g~s---rG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ++++++.+++||.|..|-+  . +..   .---||+|...++|.+|+-.|||+.|+|+.+...|..-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            5678889999999988754  1 111   11379999999999999999999999999999887653

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.74  E-value=0.22  Score=48.14  Aligned_cols=76  Identities=20%  Similarity=0.311  Sum_probs=58.5

Q ss_pred             CCCCccceeecCCCCCCC-hhHHH---HHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          273 KDLNQGTLVVFNLDPSVS-NEDLR---QIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vt-eedL~---~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ++..-.+|.|.=|...+. .+||+   +..+.||.|.+|...|+  .-|.|.|.|..+|.+|+.++.. ...|..+.+.|
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr--qsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR--QSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC--ceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            344557888876666652 34444   55678999999998764  5699999999999999999876 66788888888


Q ss_pred             cCC
Q 004002          349 SRP  351 (780)
Q Consensus       349 a~~  351 (780)
                      .++
T Consensus       159 qqr  161 (166)
T PF15023_consen  159 QQR  161 (166)
T ss_pred             ccc
Confidence            754

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=93.56  E-value=0.031  Score=58.64  Aligned_cols=59  Identities=22%  Similarity=0.330  Sum_probs=47.8

Q ss_pred             HHHHHHhh-cCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          207 SELRALFE-QYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       207 eeLr~lF~-~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      +++...|+ +||+|+.+++    .-.-+|-++|.|...++|++|+..||+..+.|++|...++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34444555 8999998752    22357889999999999999999999999999999988753

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=93.54  E-value=0.23  Score=43.89  Aligned_cols=54  Identities=13%  Similarity=0.278  Sum_probs=42.4

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~Ln  335 (780)
                      ...+|. .|..+...||.++|++||.|.---+..   .-|||...+++.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~d---TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIND---TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEECT---TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcC---CcEEEEeecHHHHHHHHHHhc
Confidence            345565 999999999999999999998777753   359999999999999999886

; 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.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=90.70  E-value=0.25  Score=53.76  Aligned_cols=75  Identities=15%  Similarity=0.117  Sum_probs=60.9

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCC--eeEE-----EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGE--VKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~--I~~v-----~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      -++||+||-.-+|++||.+.....|.  +.++     +..+.+||||+|-..+..+.++-++-|-.++|.|..-.|....
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            47999999999999999988876653  3333     3478899999999999999999999999999999776665554


Q ss_pred             CC
Q 004002          351 PG  352 (780)
Q Consensus       351 ~k  352 (780)
                      +.
T Consensus       161 K~  162 (498)
T KOG4849|consen  161 KT  162 (498)
T ss_pred             hh
Confidence            33

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=90.60  E-value=0.18  Score=58.33  Aligned_cols=78  Identities=21%  Similarity=0.322  Sum_probs=61.8

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhc-CCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccc---ccccccc
Q 004002          187 YGEHPSRTLFVRNINSNVEDSELRALFEQ-YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR---RRKLDIH  262 (780)
Q Consensus       187 ~~e~~s~tLfVgNLp~~vteeeLr~lF~~-yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~---gr~I~V~  262 (780)
                      .....+..|+|.||-.-.|.-+|+.++.+ .|.|...- .-+-|-.|||.|.+.++|.+.+.+|+|..+.   .+.|.+.
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~W-mDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFW-MDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHH-HHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            45567889999999999999999999995 45555442 2345678999999999999999999998763   5666666


Q ss_pred             cCC
Q 004002          263 FSI  265 (780)
Q Consensus       263 ~a~  265 (780)
                      |..
T Consensus       518 f~~  520 (718)
T KOG2416|consen  518 FVR  520 (718)
T ss_pred             ecc
Confidence            653

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=90.51  E-value=0.37  Score=54.57  Aligned_cols=67  Identities=21%  Similarity=0.245  Sum_probs=55.2

Q ss_pred             CCCCC-ChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          285 LDPSV-SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       285 Lp~~v-teedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      .+..+ +.++|...|.+||+|..|.+.-. --.|.|+|.+..+|-+|-. .++..|+++-|+|.|-.+..
T Consensus       380 ~~~glnt~a~ln~hfA~fG~i~n~qv~~~-~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  380 SPFGLNTIADLNPHFAQFGEIENIQVDYS-SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             cCCCCchHhhhhhhhhhcCccccccccCc-hhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            34443 57899999999999999987433 4569999999999977765 68999999999999998855

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.33  E-value=1  Score=48.50  Aligned_cols=74  Identities=22%  Similarity=0.298  Sum_probs=57.6

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc-eEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr-~L~V~~a~~k~  353 (780)
                      +.=|.|.++|..-. .-|..+|++||+|++.... ....+-.|+|.++.+|.+||.. ||+.|+|. -|-|+.+..+.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtDks  271 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTDKS  271 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCCHH
Confidence            44577888887644 4577889999999887653 5567999999999999999985 99999985 45577765543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=90.08  E-value=1  Score=37.72  Aligned_cols=54  Identities=22%  Similarity=0.290  Sum_probs=41.5

Q ss_pred             cceeecCCCCCCChhHHHHHhccc---CCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHh
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAY---GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL  334 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~y---G~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~L  334 (780)
                      ..|+|.|++ +++.++|+.+|..|   .....|.+....  -+=|.|.+.+.|.+||.+|
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            479999996 48889999999998   123455543322  3789999999999999875

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=90.03  E-value=0.25  Score=57.27  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=62.5

Q ss_pred             ccceeecCCCCCCChhHHHHHhc-ccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc---CCceEEEEecCCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFG-AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI---AGKRIKLEPSRPG  352 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs-~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i---~Gr~L~V~~a~~k  352 (780)
                      ...|||.||-..+|.-+|+.++. ..|.|++..+ .+-|.+|||.|.+.++|.+.+.+|||...   +++.|.+.|....
T Consensus       444 SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~d  522 (718)
T KOG2416|consen  444 SNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRAD  522 (718)
T ss_pred             cceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecchh
Confidence            46899999999999999999999 5667777644 34567899999999999999999999744   3588999988654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=89.23  E-value=0.35  Score=53.52  Aligned_cols=72  Identities=22%  Similarity=0.517  Sum_probs=59.2

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCC--------cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH--------KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~--------srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      +.|.|.||.+.+|.++++.+|.-.|+|.++++.+.        ..-.|||.|.|...+..|.. |..+.+=++.|.|-+.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            47999999999999999999999999999987442        23479999999999888875 7777777777777655


Q ss_pred             C
Q 004002          350 R  350 (780)
Q Consensus       350 ~  350 (780)
                      -
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            4

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=88.96  E-value=1.3  Score=42.98  Aligned_cols=74  Identities=20%  Similarity=0.347  Sum_probs=56.6

Q ss_pred             CCCCcEEEEeCCCCCCCH-HHHH---HHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVED-SELR---ALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vte-eeLr---~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +.+-.||.|+=|..++.- +||+   ..++.||+|.+|...|+  --|.|.|.|..+|-+|+.+++. ...|..+.+.|.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr--qsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR--QSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC--ceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            446689999887777643 4444   55678999999876554  5699999999999999999876 556777787775


Q ss_pred             C
Q 004002          265 I  265 (780)
Q Consensus       265 ~  265 (780)
                      .
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            4

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=88.91  E-value=0.81  Score=52.78  Aligned_cols=73  Identities=15%  Similarity=0.206  Sum_probs=54.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhh--cCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccC--ccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFE--QYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~--~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng--~~l~gr~I~V~  262 (780)
                      ..+..|.|+++-||.++-.|+++.||.  .+-++.+|.- ... ---||+|++..+|++|.+.|..  +.|.|++|..+
T Consensus       171 p~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscef-a~N-~nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  171 PNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEF-AHN-DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             cCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeee-eec-CceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            334568899999999999999999997  3667777752 111 2368999999999999998754  44667665443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=88.88  E-value=0.67  Score=45.30  Aligned_cols=72  Identities=25%  Similarity=0.368  Sum_probs=51.7

Q ss_pred             CCcEEEEeCCCC-----CCCH----HHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          191 PSRTLFVRNINS-----NVED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       191 ~s~tLfVgNLp~-----~vte----eeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      +..||.|.=+.+     ..-+    .+|.+.|..||++.-+|..+   +.-.|+|.+-+.|-+|+. ++|..+.|+.|.|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l~i  101 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTLKI  101 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEEEE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEEEE
Confidence            567877775551     1223    36778899999998777333   467899999999999999 8999999999999


Q ss_pred             ccCCC
Q 004002          262 HFSIP  266 (780)
Q Consensus       262 ~~a~p  266 (780)
                      +...|
T Consensus       102 ~LKtp  106 (146)
T PF08952_consen  102 RLKTP  106 (146)
T ss_dssp             EE---
T ss_pred             EeCCc
Confidence            86554

; PDB: 1UFW_A 2DNR_A.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=88.54  E-value=0.25  Score=53.97  Aligned_cols=79  Identities=15%  Similarity=0.313  Sum_probs=61.9

Q ss_pred             ccceeecCCCCCCChhHH-H--HHhcccCCeeEEEeCCCc--------ccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          277 QGTLVVFNLDPSVSNEDL-R--QIFGAYGEVKEIRETPHK--------RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL-~--~~Fs~yG~I~~v~~~g~s--------rG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      ..-+||-+|+..+.++.+ +  +.|++||.|..|......        ..-++|.|...++|..||...+|...+|+.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            346788889887755544 3  579999999998763321        11389999999999999999999999999998


Q ss_pred             EEecCCCchh
Q 004002          346 LEPSRPGGAR  355 (780)
Q Consensus       346 V~~a~~k~~r  355 (780)
                      ..++..+...
T Consensus       157 a~~gttkycs  166 (327)
T KOG2068|consen  157 ASLGTTKYCS  166 (327)
T ss_pred             HhhCCCcchh
Confidence            8888776543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=87.26  E-value=1.2  Score=50.53  Aligned_cols=66  Identities=24%  Similarity=0.159  Sum_probs=57.1

Q ss_pred             ceeEEEecCCCCCCHHHHHHHHhhcCCCcceeEEeeccccCCcceeeEEeccCCccchHHHHHHhcCce
Q 004002          694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCA  762 (780)
Q Consensus       694 rtt~mirniPn~~~~~~l~~~i~~~~~~~ydf~ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~~~~  762 (780)
                      -|+|-|=-+|+.+|..+|+..+....+-=-|+--++ |  .--|.=-+-|-|.+..++..||+.|||+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivR-d--~~pnrymvLIkFr~q~da~~Fy~efNGk~  139 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVR-D--GMPNRYMVLIKFRDQADADTFYEEFNGKQ  139 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEee-c--CCCceEEEEEEeccchhHHHHHHHcCCCc
Confidence            589999999999999999999998887777888888 2  33344338999999999999999999998

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=87.15  E-value=0.95  Score=48.52  Aligned_cols=60  Identities=15%  Similarity=0.261  Sum_probs=47.8

Q ss_pred             HHHHHHHhhcCCCEEEEEeC---C--Cc-ceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          206 DSELRALFEQYGDIRTLYTA---C--KH-RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       206 eeeLr~lF~~yG~I~sv~~t---g--ks-kG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ++++++..++||.|..|.+.   +  .. .--.||+|...++|.+|+-.|||..|+||.+...|-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            35788899999999887621   1  11 1237999999999999999999999999998877643

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=86.61  E-value=2.6  Score=37.43  Aligned_cols=55  Identities=15%  Similarity=0.316  Sum_probs=41.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN  251 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng  251 (780)
                      ...+|. .|..+...||.++|+.||.|.---+.   -.-|||...+.+.|..|+..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~---dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN---DTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEEC---TTEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc---CCcEEEEeecHHHHHHHHHHhcc
Confidence            456676 99999999999999999998754332   24599999999999999998753

; 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.

>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=86.17  E-value=2.2  Score=39.88  Aligned_cols=68  Identities=18%  Similarity=0.133  Sum_probs=54.2

Q ss_pred             cceeEEEecCCCCCCHHHHHHHHhhcCCCcceeEEeeccccCCcceeeEEeccCCccchHHHHHHhcCce
Q 004002          693 TRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCA  762 (780)
Q Consensus       693 ~rtt~mirniPn~~~~~~l~~~i~~~~~~~ydf~ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~~~~  762 (780)
                      .+|+|-+=-+|+.++..+++..+-+.......-+.+.-|..  -|.==+-|-|.+...|..||+.|||++
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~   78 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKP   78 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCc
Confidence            34666666889999988877777787777777777776654  344338999999999999999999998

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=86.13  E-value=0.83  Score=46.20  Aligned_cols=76  Identities=8%  Similarity=0.055  Sum_probs=49.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhc-CCCE---EEEE--e-----CCCcceEEEEEEecHHHHHHHHHHccCcccccc--
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQ-YGDI---RTLY--T-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR--  257 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~-yG~I---~sv~--~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr--  257 (780)
                      ...+|.||+||+.+|++++.+.+.. +++-   ..+.  .     ....-.-|||.|.+.+++..-+..++|..+.+.  
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4569999999999999999987776 6665   2332  1     011234599999999999999999999887543  


Q ss_pred             ---ccccccCCC
Q 004002          258 ---KLDIHFSIP  266 (780)
Q Consensus       258 ---~I~V~~a~p  266 (780)
                         ...|.+|.-
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence               334555543

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.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=86.03  E-value=0.45  Score=51.99  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=59.8

Q ss_pred             cEEEEeCCCCCCCHHHHH---HHhhcCCCEEEEEeCCCc--------ceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          193 RTLFVRNINSNVEDSELR---ALFEQYGDIRTLYTACKH--------RGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr---~lF~~yG~I~sv~~tgks--------kG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      .-+||-+|+..+.++.+.   +.|.+||.|.++......        ..-++|+|...++|..||...+|..+.|+.++.
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            567888999887766554   489999999988732211        123899999999999999999999999999888


Q ss_pred             ccCCCC
Q 004002          262 HFSIPK  267 (780)
Q Consensus       262 ~~a~pk  267 (780)
                      .+..++
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            876654

>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=85.64  E-value=1.3  Score=45.06  Aligned_cols=63  Identities=17%  Similarity=0.275  Sum_probs=45.4

Q ss_pred             ChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhC--CCccCCceEEEEecCCCc
Q 004002          290 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN--RSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       290 teedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~Ln--G~~i~Gr~L~V~~a~~k~  353 (780)
                      ..+.|+++|..|+.+......+.- +-..|.|.+.++|.+|...|+  +..+.|..++|.+++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF-rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF-RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT-TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC-CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            357899999999998887654322 348999999999999999999  999999999999996544

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=84.77  E-value=2.1  Score=49.53  Aligned_cols=93  Identities=15%  Similarity=0.185  Sum_probs=66.6

Q ss_pred             HHHHHHHccCccccccccccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcc--cCCeeEEEeCCCcccEEEE
Q 004002          242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA--YGEVKEIRETPHKRHHKFI  319 (780)
Q Consensus       242 A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~--yG~I~~v~~~g~srG~aFV  319 (780)
                      -..+++...+..+..+-.+|+-.          .+.+.+.++-||..+-.|+++.||+.  +-.+++|.+.- .. -=||
T Consensus       150 I~Evlresp~VqvDekgekVrp~----------~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~-N~-nWyI  217 (684)
T KOG2591|consen  150 IVEVLRESPNVQVDEKGEKVRPN----------HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAH-ND-NWYI  217 (684)
T ss_pred             HHHHHhcCCCceeccCccccccC----------cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeee-cC-ceEE
Confidence            34455655555565555555422          23457888999999999999999984  77888887632 22 2599


Q ss_pred             EEcCHHHHHHHHHHhCC--CccCCceEEE
Q 004002          320 EFYDVRAAEAALKSLNR--SDIAGKRIKL  346 (780)
Q Consensus       320 ~F~~~e~A~~Ai~~LnG--~~i~Gr~L~V  346 (780)
                      +|++..||+.|.+.|..  ++|.||.|..
T Consensus       218 Tfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  218 TFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             EeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            99999999999998864  4777776554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=84.25  E-value=1  Score=47.59  Aligned_cols=70  Identities=19%  Similarity=0.275  Sum_probs=57.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccc----cccccccc
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPL----RRRKLDIH  262 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l----~gr~I~V~  262 (780)
                      ..|+|.||..-+..+.|..-|+.||+|+...    ..++..+-++|.|...-.|.+|++.+.-.-+    .+++.-|.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVE  109 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCC
Confidence            7899999999999999999999999987633    4677888999999999999999998743332    34555554

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=80.41  E-value=2.6  Score=40.65  Aligned_cols=105  Identities=16%  Similarity=0.194  Sum_probs=72.7

Q ss_pred             CCCHHHHHH----HhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCCCCCCCCc-
Q 004002          203 NVEDSELRA----LFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ-  277 (780)
Q Consensus       203 ~vteeeLr~----lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~~~~~~-  277 (780)
                      ..+-..|..    ++...|.+.-..   -..++..+.|.+.+++.++++. ....+.+..+.++.-.|...+.+..... 
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~---l~~~~fl~~F~~~~d~~~vl~~-~p~~~~~~~~~l~~W~~~~~~~~~~~~~~  103 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRD---LGDNLFLFQFESEEDRQRVLKG-GPWNFNGHFLILQRWSPDFNPSEVKFEHI  103 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEE---eCCCeEEEEEEeccceeEEEec-ccccccccchhhhhhcccccccccceecc
Confidence            345555544    444455544322   2468999999999999999983 5566778888887666555444333222 


Q ss_pred             -cceeecCCCCC-CChhHHHHHhcccCCeeEEEeCC
Q 004002          278 -GTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETP  311 (780)
Q Consensus       278 -~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~g  311 (780)
                       -=|.|.|||.. ++++-|+++-+.+|++.+++...
T Consensus       104 ~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t  139 (153)
T PF14111_consen  104 PVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENT  139 (153)
T ss_pred             chhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCC
Confidence             23667899987 58889999999999999998643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	780
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-06
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		8e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		9e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-05
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		4e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		7e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		7e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-05
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		1e-04
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		2e-04
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		2e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-04
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		5e-04
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-04
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		6e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		9e-04

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 53.9 bits (128), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L N PL
Sbjct: 25  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           R ++L + F+           +  +L V NL   VSNE L + F  +G+V+
Sbjct: 84  RGKQLRVRFAC----------HSASLTVRNLPQYVSNELLEEAFSVFGQVE 124

>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 = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/169 (21%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+  +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           ++K   +   P    HK   FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 38/124 (30%), Positives = 57/124 (45%), Gaps = 13/124 (10%)
Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           GE  Y +     LFV N+ +++ + + + LFE+YG+   ++   + RGF  I       A
Sbjct: 15  GEKTYTQRCR--LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLA 71
Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG 302
             A   L    L+ R L I F+           +   L V NL P VSNE L Q F  +G
Sbjct: 72  EIAKAELDGTILKSRPLRIRFAT----------HGAALTVKNLSPVVSNELLEQAFSQFG 121
Query: 303 EVKE 306
            V++
Sbjct: 122 PVEK 125

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 37/169 (21%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+  +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           ++K   +   P    HK   FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 70/151 (46%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           L V  +  ++ D EL ALF   G I T      Y      G+  + +     ++ A++ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 306
               +R ++L + ++ P    S KD N   L V NL  +++++ L  IFG YG + +   
Sbjct: 66  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 307 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 335
           +R+  T   R   F+ +     A+ A+ +LN
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>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 = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 247
           +FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 248 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           AL N  +      +H  I   P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 78  ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 134
Query: 305 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
           +E R    P    R   F+ F     A+ A+K+++++
Sbjct: 135 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 171

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 247
           +FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 248 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           AL N  +      +H  I   P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 66  ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
Query: 305 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
           +E R    P    R   F+ F     A+ A+K+++++
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 22/161 (13%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 245
           L V  +  N+   E R+LF   G+I +    CK           G+  ++Y D + A  A
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIES----CKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           +  L    L+ + + + ++     PS   +    L V  L  +++ ++L Q+F  YG + 
Sbjct: 61  INTLNGLRLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
             R      T   R   FI F     AE A+K LN    +G
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 40/155 (25%), Positives = 64/155 (41%), Gaps = 22/155 (14%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 245
           L V  +  N+   E ++LF   GDI +    CK           G+  ++Y D   A  A
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIES----CKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           +  L    L+ + + + ++     PS   +    L V  L  ++S +++ Q+F  YG + 
Sbjct: 63  INTLNGLKLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRII 118
Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
             R      T   R   FI F     AE A+K LN
Sbjct: 119 TSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153

>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 = 46.2 bits (108), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 41/186 (22%), Positives = 85/186 (45%), Gaps = 28/186 (15%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+   
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQ-----GTLVVFNLDPSVSNEDLRQIFGAYG 302
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 75  NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIK-----------L 346
           ++K   +   P    HK   FIE+   ++++ A+ S N  D+ G+ ++           L
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Query: 347 EPSRPG 352
            P+ PG
Sbjct: 195 TPATPG 200

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           L V  +  +  D EL ALF   G I T      Y      G+  + +     ++ A++ L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 306
               +R ++L + ++ P    S KD N   L V NL  +++++ L  IFG YG + +   
Sbjct: 77  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 307 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 335
           +R+  T   R   F+ +     A+ A+ +LN
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 45/170 (26%), Positives = 74/170 (43%), Gaps = 19/170 (11%)
Query: 195 LFVRNINSNVEDSELRA----LFEQYG----DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           LFV N+N N    EL+     +F +      D+R   T    R F    Y D  +A    
Sbjct: 10  LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYVDFESAEDLE 62
Query: 247 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 306
           +AL+   L+    +I    PK   S K+ +  TL+  NL   V+ ++L+++F    E++ 
Sbjct: 63  KALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL----EPSRPG 352
           + +    +   +IEF     AE   +    ++I G+ I L    EP   G
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPKGEG 172

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 41/160 (25%), Positives = 74/160 (46%), Gaps = 15/160 (9%)
Query: 195 LFVRNINSNVEDSELR-ALFEQYG-------DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           LF+ N+N N   +EL+ A+ E +        D+RT      +R F    Y D  +A    
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 247 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 306
           +AL+   L+    +I    PK   S K     TL+  NL  +++ ++L+++F    E++ 
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           + +    +   +IEF     AE  L+    ++I G+ + L
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 243
            P+ T+++ N+N  ++  EL+    A+F Q+G I  +    + K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 244 TAMRALQNKPLRRRKLDIHFS 264
            A+R++Q  P   + + I ++
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/155 (21%), Positives = 74/155 (47%), Gaps = 12/155 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR------GFVMISYYDIRAAR 243
           +P  +L+V +++ +V ++ L   F   G I ++   C+        G+  +++     A 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
            A+  +    ++ + + I +S  + +PS +    G + + NLD S+ N+ L   F A+G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 304 V---KEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           +   K + +    + + F+ F    AAE A++ +N
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 36/153 (23%), Positives = 67/153 (43%), Gaps = 11/153 (7%)
Query: 196 FVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMRA 248
           FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  A
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           L N  +           P D+  +  +    L +  +    +  D+R  F ++G+++E R
Sbjct: 67  LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
Query: 309 --ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
               P    R   F+ F     A+ A+K+ +++
Sbjct: 127 ILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQA 159

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F Q+G I  +    + K RG   + + ++ +A  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 245 AMRALQNKPLRRRKLDIHFS 264
           A+R++Q  P   + + I ++
Sbjct: 68  ALRSMQGFPFYDKPMRIQYA 87

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVRAAEAALKSLNRS 337
           TLV+ NL  S + E L+++F     +K  +    K + + FIEF     A+ AL S N+ 
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 338 DIAGKRIKLEPSRPGGA 354
           +I G+ I+LE   P G+
Sbjct: 77  EIEGRAIRLELQGPRGS 93

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F Q+G I  +    + K RG   + + ++ +A  
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 245 AMRALQNKPLRRRKLDIHFS 264
           A+R++Q  P   + + I ++
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 86

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAA 330
           ++G L V  L    + + L Q+F  YG++ E+     RET   R   F+ F ++  A+ A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 331 LKSLNRSDIAGKRIKLE 347
           + ++N   + G++I+++
Sbjct: 71  MMAMNGKSVDGRQIRVD 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	780
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-32
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-32
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-29
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-29
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-26
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-24
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-25
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-24
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-04
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-21
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-21
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-20
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-20
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-19
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-15
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-19
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-16
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-17
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	4e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-12
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	9e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-14
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-15
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	9e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-14
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-08
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-14
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	9e-14
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-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	1e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-13
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-11
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-11
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	6e-09
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	7e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	8e-13
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-07
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-12
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-11
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-12
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	5e-12
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-12
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	6e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-06
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-08
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	8e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	9e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	5e-09
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05
2div_A	99	TRNA selenocysteine associated protein; structural	1e-08
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	6e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	9e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-08
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-06
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	9e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	9e-08
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	8e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	9e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-04
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	2e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	7e-04

>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 =  123 bits (310), Expect = 2e-32
 Identities = 33/196 (16%), Positives = 59/196 (30%), Gaps = 39/196 (19%)

Query: 191 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
            S  L V  ++ S +    +  +F  YG++  +       G  M+   D  A   A+  L
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 250 QNKPLRRRKLDIHFS------------IPKDNPSDKDLNQG------------------- 278
            N  +  +K+++  S            +   + S KD ++                    
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 279 --TLVVFNLDPSVSNEDLRQIFGAYG-----EVKEIRETPHKRHHKFIEFYDVRAAEAAL 331
              L  FN    V+ E+  +I    G      VK       +     +E+     A   L
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 332 KSLNRSDIAGKRIKLE 347
             LN   +        
Sbjct: 183 GFLNHYQMKNPNGPYP 198

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 69.3 bits (169), Expect = 1e-13
 Identities = 25/122 (20%), Positives = 46/122 (37%), Gaps = 1/122 (0%)

Query: 279 TLVVFNLDPSVSNED-LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
            L+V+ LD S  N D +  +F  YG V++++    K     +E  D  A + A+  LN +
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65

Query: 338 DIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPI 397
            + G+++ +  S+           L       +                  N +Q  S +
Sbjct: 66  FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV 125

Query: 398 EH 399
            H
Sbjct: 126 LH 127

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 50.9 bits (121), Expect = 3e-07
 Identities = 9/82 (10%), Positives = 27/82 (32%), Gaps = 5/82 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFVMISYYDIRAAR 243
           +HPS  L   N    V +     + ++ G      ++      +     ++ +     A 
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 244 TAMRALQNKPLRRRKLDIHFSI 265
             +  L +  ++       +++
Sbjct: 180 ETLGFLNHYQMKNPNGPYPYTL 201

>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 =  122 bits (308), Expect = 8e-32
 Identities = 49/226 (21%), Positives = 81/226 (35%), Gaps = 40/226 (17%)

Query: 166 GNGLLHYSVPNGAGTVAGEHPYGEHP------SRTLFVRNIN-SNVEDSELRALFEQYGD 218
           G+   H+   +G             P      +  L V N+N   V    L  LF  YGD
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61

Query: 219 IRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS------IPKDNPSD 272
           ++ +      +   ++   D   A+ AM  L    L  + + I  S      +P++   D
Sbjct: 62  VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQED 121

Query: 273 KDLNQG-------------------------TLVVFNLDPSVSNEDLRQIFGAYGE-VKE 306
           + L +                          TL + N+ PSVS EDL+ +F + G  VK 
Sbjct: 122 QGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKG 181

Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRP 351
            +     R    I+   V  A  AL  L+  D+     +++  S+ 
Sbjct: 182 FKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 227

>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 = 66.6 bits (162), Expect = 2e-12
 Identities = 31/131 (23%), Positives = 57/131 (43%), Gaps = 6/131 (4%)

Query: 270 PSDKDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE 328
           P         L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+
Sbjct: 27  PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQ 86

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDES-----RILQHQVGSPIT 383
            A+  LN   + GK I++  S+    +     Q +Q L +D       R  +    +   
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146

Query: 384 NSPPGNWVQFS 394
             PP   +  S
Sbjct: 147 IFPPSATLHLS 157

>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 = 1e-29
 Identities = 44/189 (23%), Positives = 72/189 (38%), Gaps = 34/189 (17%)

Query: 192 SRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           +  L V N+N   V    L  LF  YGD++ +      +   ++   D   A+ AM  L 
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 251 NKPLRRRKLDIHFS------IPKDNPSDKDLNQG-------------------------T 279
              L  + + I  S      +P++   D+ L +                          T
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L + N+ PSVS EDL+ +F + G  VK  +     R    I+   V  A  AL  L+  D
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182

Query: 339 IA-GKRIKL 346
           +     +++
Sbjct: 183 LGENHHLRV 191

>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 = 71.1 bits (174), Expect = 4e-14
 Identities = 44/215 (20%), Positives = 82/215 (38%), Gaps = 28/215 (13%)

Query: 275 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS 333
           +    L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 60

Query: 334 LNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQF 393
           LN   + GK I++  S+    +     Q +Q L +D      H               +F
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH---------------RF 105

Query: 394 SSPIEHNPLQTISKSPN--FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRG-- 449
             P   N       S      N+ P+ S     L  +       ++      KD+     
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEED--LKVLFSSNGGVVKGFKFFQKDRKMALI 163

Query: 450 --SLMEHALTNTISANGASFQQSN----SFSEPKI 478
               +E A+   I  +     +++    SFS+  I
Sbjct: 164 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198

>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 = 6e-09
 Identities = 28/101 (27%), Positives = 40/101 (39%), Gaps = 6/101 (5%)

Query: 166 GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYT 224
           GN  LH     G+       P    PS TL + NI  +V + +L+ LF   G + +    
Sbjct: 98  GNSPLHRFKKPGSKNFQNIFP----PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF 153

Query: 225 ACKHRGFVMISYYDIRAARTAMRALQNKPLRR-RKLDIHFS 264
             K R   +I    +  A  A+  L N  L     L + FS
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>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 =  117 bits (295), Expect = 2e-29
 Identities = 35/192 (18%), Positives = 68/192 (35%), Gaps = 11/192 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               L V N+  ++   +   L   +G +   +        + +G+    Y    +A  A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNED-LRQIFGAYGEV 304
              L  KPL  R L +H++      +   L+   L V  L P  ++ D L +   A    
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAG-QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 305 KEIRETPHKR-HHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360
              +    +    K    +E+     AE A +  +   + G  +++    PG   R+++ 
Sbjct: 213 TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLA 272

Query: 361 QLNQELEQDESR 372
            L        +R
Sbjct: 273 ALIAAQATALNR 284

>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 =  109 bits (274), Expect = 1e-26
 Identities = 29/169 (17%), Positives = 62/169 (36%), Gaps = 17/169 (10%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
            R + +R +  +V + E+  L   Y  ++  +   K++G   ++  +   A  A+ A   
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-KYKGTAFVTLLNGEQAEAAINAFHQ 79

Query: 252 KPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--E 309
             LR R+L +                  L V NL PS++ +   ++   +G ++      
Sbjct: 80  SRLRERELSVQLQPTDAL----------LCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

Query: 310 TPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 355
           +      K   F E+    +A  A   L    +  + + +  +  G   
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT 178

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 64.6 bits (158), Expect = 2e-11
 Identities = 15/104 (14%), Positives = 42/104 (40%), Gaps = 11/104 (10%)

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           L  + +R+R         +    ++      +++  L   V+N+++  +   Y  +K   
Sbjct: 3   LDPEEIRKR-----LEHTERQFRNR----RKILIRGLPGDVTNQEVHDLLSDYE-LKYCF 52

Query: 309 ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
              +K    F+   +   AEAA+ + ++S +  + + ++     
Sbjct: 53  VDKYKG-TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>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 = 53.1 bits (128), Expect = 1e-07
 Identities = 17/90 (18%), Positives = 25/90 (27%), Gaps = 13/90 (14%)

Query: 189 EHPSRTLFVRNINSNVEDSE-LRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 239
              SR L V  +     D + L              T C+         +GF ++ Y   
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSP----TFCQLACGQDGQLKGFAVLEYETA 236

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
             A  A +      L    L + F  P   
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266

>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 =  110 bits (276), Expect = 6e-28
 Identities = 30/169 (17%), Positives = 67/169 (39%), Gaps = 7/169 (4%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAART 244
                 LF+ N+N N   +EL+    +      L         +R F  + +        
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A+  L    +   ++ +     +D+   +     TL+  NL  +++ ++L+++F    E+
Sbjct: 70  AL-ELTGLKVFGNEIKLEKPKGRDSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEI 126

Query: 305 KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG 353
           + + +    +   +IEF     AE  L+    ++I G+ + L  +   G
Sbjct: 127 RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>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 = 69.6 bits (171), Expect = 6e-14
 Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDV 324
               +      L + NL+P+ S  +L+          ++         ++   +++F   
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
              E AL+ L    + G  IKLE  +   +++
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKPKGRDSKK 95

>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 =  108 bits (273), Expect = 2e-26
 Identities = 37/175 (21%), Positives = 67/175 (38%), Gaps = 16/175 (9%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LYTAC--KHRGFVMISYYDIRAA 242
                 TL++ N   +     +R L +    +     L +      R F  I       A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 243 RTAMRALQNKPLRRRKLDIHFSIP--KDNPSDKDLNQG-TLVVFNLDPSVSNED-LRQIF 298
           R  +  L    +    L    S P  K   +D    +G  +++ NL   + +E+ LR+ F
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232

Query: 299 GAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
             +G +++I       E        F+ F +  +AE AL+ +NRS +  + I + 
Sbjct: 233 EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS 286

>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 =  101 bits (255), Expect = 6e-24
 Identities = 31/182 (17%), Positives = 61/182 (33%), Gaps = 20/182 (10%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQ 250
           T+ V+N+  +   +++   F+  G I  +  A    K+  F  I +     A  A+    
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET 310
               +   +  H +            + TL + N  PS +  ++R +      V      
Sbjct: 103 KVVGQNEIIVSHLT------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150

Query: 311 PHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQE 365
           P  R +      +I+      A   ++ LN   I G  +  + S P    +       + 
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEG 210

Query: 366 LE 367
            E
Sbjct: 211 RE 212

>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 = 63.9 bits (156), Expect = 4e-11
 Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 4/85 (4%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYD 323
            +    ++    T++V NL  S +   + + F   G +  +      + +     IEF  
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR 90

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEP 348
              A AA+   ++  +    I +  
Sbjct: 91  YDGALAAITKTHKV-VGQNEIIVSH 114

>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 =  101 bits (255), Expect = 3e-25
 Identities = 35/171 (20%), Positives = 69/171 (40%), Gaps = 16/171 (9%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRGFVMISYYDIRAART 244
           +  +FV  +     + +LR LFEQYG +  +           + +G   +++Y  +AA  
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A  AL N  +           P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122

Query: 305 KEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           +E R         R   F+ F     A+ A+K+++       +     S P
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH-----QAQTMEGCSSP 168

>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 = 63.0 bits (154), Expect = 1e-11
 Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHK---FIEFYDVRAAE 328
           +   + V  +  + S +DLR++F  YG V EI      + +    K   F+ FY  +AA 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            A  +L+   +          +P  + +N
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKN 90

>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 = 99.2 bits (248), Expect = 2e-24
 Identities = 36/166 (21%), Positives = 68/166 (40%), Gaps = 16/166 (9%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAARTA 245
           +  L V  +  ++ D EL ALF   G       +R   T     G+  + +     ++ A
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTG-YSYGYAFVDFTSEMDSQRA 61

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           ++ L    +R ++L + ++     P  + +    L V NL  +++++ L  IFG YG + 
Sbjct: 62  IKVLNGITVRNKRLKVSYA----RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIV 117

Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           +        T   R   F+ +     A+ A+ +LN     G    L
Sbjct: 118 QKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL 163

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 67.2 bits (165), Expect = 4e-13
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAA 330
           +   L+V  L   +++ +L  +F A G +   R        +     F++F     ++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 331 LKSLNRSDIAGKRIKLEPSRPGGARRN 357
           +K LN   +  KR+K+  +RPGG    
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIK 88

>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 = 41.4 bits (98), Expect = 3e-04
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               L+V N+   + D +L  +F +YG I            + RG   + Y     A+ A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 246 MRALQNKPL 254
           + AL N   
Sbjct: 148 ISALNNVIP 156

>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 = 99.2 bits (248), Expect = 3e-24
 Identities = 26/169 (15%), Positives = 60/169 (35%), Gaps = 20/169 (11%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIRA 241
           +R L+V NI   + +  +   F     +  L  A           + + F  + +  +  
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY 301
              AM A      + + L I                  L +  L   ++++ ++++  ++
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLP----GAHKLFIGGLPNYLNDDQVKELLTSF 118

Query: 302 GEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           G +K         T   + + F E+ D+   + A+  LN   +  K++ 
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 46.8 bits (112), Expect = 4e-06
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 185 HPYGEHPS-RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYD 238
           H Y   P    LF+  + + + D +++ L   +G ++             +G+    Y D
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 239 IRAARTAMRALQNKPLRRRKLDI 261
           I     A+  L    L  +KL +
Sbjct: 146 INVTDQAIAGLNGMQLGDKKLLV 168

>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 = 97.0 bits (242), Expect = 3e-23
 Identities = 28/194 (14%), Positives = 65/194 (33%), Gaps = 32/194 (16%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIR 240
            +R L+V NI   + +  +   F     +  L  A           + + F  + +  + 
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG----------------TLVVFN 284
               AM A      + + L I              N                   L +  
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

Query: 285 LDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L   ++++ ++++  ++G +K         T   + + F E+ D+   + A+  LN   +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181

Query: 340 AGKRIKLEPSRPGG 353
             K++ ++ +  G 
Sbjct: 182 GDKKLLVQRASVGA 195

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 97.4 bits (243), Expect = 3e-23
 Identities = 33/176 (18%), Positives = 81/176 (46%), Gaps = 17/176 (9%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 242
                  ++V +I   + +  +R  F  +G I+++  +      KH+GF  + Y    AA
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPK-------DNPSDKDLNQGTLVVFNLDPSVSNEDLR 295
           + A+  + +  L  R + +             D  +++      + V ++   +S++D++
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143

Query: 296 QIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
            +F A+G++K         T   + + FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 67.7 bits (166), Expect = 5e-13
 Identities = 25/130 (19%), Positives = 48/130 (36%), Gaps = 12/130 (9%)

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
           + M ++       R                      + V ++   +  + +RQ F  +G 
Sbjct: 2   SHMASMTGGQQMGRG-------SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGP 54

Query: 304 VKEIR--ETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
           +K I          HK   F+E+    AA+ AL+ +N   + G+ IK+      G  + +
Sbjct: 55  IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPI 114

Query: 359 MLQLNQELEQ 368
           + QL +E   
Sbjct: 115 IDQLAEEARA 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 = 52.7 bits (127), Expect = 7e-08
 Identities = 16/86 (18%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               ++V +++ ++ D +++++FE +G I++   A      KH+G+  I Y   ++++ A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPS 271
           + ++    L  + L +  ++    P 
Sbjct: 184 VSSMNLFDLGGQYLRVGKAVTPPMPL 209

>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 = 96.2 bits (240), Expect = 8e-23
 Identities = 36/204 (17%), Positives = 85/204 (41%), Gaps = 10/204 (4%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 243
            +P  +L+V +++ +V ++ L   F   G I ++         +  G+  +++     A 
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
            A+  +    ++ + + I +S     PS +    G + + NLD S+ N+ L   F A+G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRD--PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129

Query: 304 VKEIR---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360
           +   +   +    + + F+ F    AAE A++ +N   +  +++ +   +    R   + 
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189

Query: 361 QLNQELEQDESRILQHQVGSPITN 384
              +E    +        G  +T+
Sbjct: 190 ARAKEFYPYDVPDYAGSSGRIVTD 213

>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 = 65.4 bits (160), Expect = 3e-12
 Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYD 323
           NPS       +L V +L P V+   L + F   G +  IR      T     + ++ F  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
              AE AL ++N   I GK +++  S+   + R
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQRDPSLR 99

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 94.6 bits (236), Expect = 1e-22
 Identities = 39/167 (23%), Positives = 67/167 (40%), Gaps = 16/167 (9%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDIRAARTA 245
              L V  +  N+   E R+LF   G+I +     +        G+  ++Y D + A  A
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESC-KLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           +  L    L+ + + + ++ P    S   +    L V  L  +++ ++L Q+F  YG + 
Sbjct: 61  INTLNGLRLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116

Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
             R      T   R   FI F     AE A+K LN    +G    + 
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163

>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 = 67.6 bits (166), Expect = 3e-13
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAA 330
           ++  L+V  L  +++ E+ R +FG+ GE++  +    K         F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 331 LKSLNRSDIAGKRIKLEPSRPGGAR 355
           + +LN   +  K IK+  +RP  A 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSAS 85

>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 = 94.0 bits (234), Expect = 1e-21
 Identities = 48/196 (24%), Positives = 75/196 (38%), Gaps = 19/196 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
            LFV N+ +++ + + + LFE+YG+   ++   + RGF  I       A  A   L    
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTI 82

Query: 254 LRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----E 309
           L+ R L I F+               L V NL P VSNE L Q F  +G V++      +
Sbjct: 83  LKSRPLRIRFATHGAA----------LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD 132

Query: 310 TPHKRHHKFIEFYDVRAAEAALKSLNRSDI----AGKRIKLEPSRPGGARRNLMLQLNQE 365
                   F+EF     A  AL+             + + +EP         L  +L Q+
Sbjct: 133 RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQK 192

Query: 366 LEQDESRILQHQVGSP 381
            +Q      Q    + 
Sbjct: 193 TQQYHKEREQPPRFAQ 208

>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 = 68.6 bits (168), Expect = 7e-13
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 266 PKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV 324
               P +K   Q   L V NL   ++ ED +++F  YGE  E+      R   FI     
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVF-INRDRGFGFIRLESR 68

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPG 352
             AE A   L+ + +  + +++  +  G
Sbjct: 69  TLAEIAKAELDGTILKSRPLRIRFATHG 96

>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 = 47.8 bits (114), Expect = 5e-06
 Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 4/67 (5%)

Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTA 245
                L V+N++  V +  L   F Q+G +           +  G   + +     AR A
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153

Query: 246 MRALQNK 252
           +    + 
Sbjct: 154 LERCGDG 160

>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 = 88.8 bits (221), Expect = 2e-21
 Identities = 19/85 (22%), Positives = 44/85 (51%), Gaps = 6/85 (7%)

Query: 189 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAA 242
             P+ T+++ N+N  ++  EL+    A+F ++G I    +  + K RG   + + ++ +A
Sbjct: 5   TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPK 267
             A+R++Q  P   + + I ++   
Sbjct: 65  TNALRSMQGFPFYDKPMRIQYAKTD 89

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 61.5 bits (150), Expect = 7e-12
 Identities = 19/94 (20%), Positives = 47/94 (50%), Gaps = 12/94 (12%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHK 317
           ++P+  P+       T+ + NL+  +  ++L++    IF  +G++ +I    +   R   
Sbjct: 1   AVPETRPNH------TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQA 54

Query: 318 FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           F+ F +V +A  AL+S+       K ++++ ++ 
Sbjct: 55  FVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88

>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 = 90.3 bits (225), Expect = 3e-21
 Identities = 34/167 (20%), Positives = 70/167 (41%), Gaps = 19/167 (11%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAART 244
           R L+V N++  + +  L+  F+  G I        +      K+  +  + Y+    A  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN----NKNVNYAFVEYHQSHDANI 56

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A++ L  K +    + I+++      S  D +   L V +L+ +V +E LR  F  +   
Sbjct: 57  ALQTLNGKQIENNIVKINWAFQ-SQQSSSD-DTFNLFVGDLNVNVDDETLRNAFKDFPSY 114

Query: 305 KEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
                    +T   R + F+ F     A+ A+ S+   D+ G+ +++
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>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 = 64.5 bits (158), Expect = 3e-12
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
            L V NLD +++ + L+Q F   G +  I+    +     ++ F+E++    A  AL++L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           N   I    +K+  +       +
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSS 84

>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 = 41.7 bits (99), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 13/78 (16%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRA 241
            +  LFV ++N NV+D  LR  F+ +    +                RG+  +S+     
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLS----GHVMWDMQTGSSRGYGFVSFTSQDD 141

Query: 242 ARTAMRALQNKPLRRRKL 259
           A+ AM ++Q + L  R L
Sbjct: 142 AQNAMDSMQGQDLNGRPL 159

>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 = 88.0 bits (219), Expect = 2e-20
 Identities = 31/174 (17%), Positives = 68/174 (39%), Gaps = 25/174 (14%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAA 242
           S  +F+  +N +  +  LR  F +YG +    T           + RGF  +S+    + 
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTV----TDLKIMKDPATGRSRGFGFLSFEKPSSV 58

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG 302
              ++      L  + +D   +IP+D         G + V  + P V  ++  + F  +G
Sbjct: 59  DEVVKTQHI--LDGKVIDPKRAIPRDEQD----KTGKIFVGGIGPDVRPKEFEEFFSQWG 112

Query: 303 EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            + +      ++T   R   F+ +    A +   +     D   ++I+++ + P
Sbjct: 113 TIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP 165

>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 = 48.3 bits (116), Expect = 1e-06
 Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 14/87 (16%)

Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIR 240
             +  +FV  I  +V   E    F Q+G I                + RGF  ++Y    
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTI----IDAQLMLDKDTGQSRGFGFVTYDSAD 140

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPK 267
           A        +    + RK++I  + P+
Sbjct: 141 AVDRVC-QNKFIDFKDRKIEIKRAEPR 166

>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 = 87.7 bits (218), Expect = 5e-20
 Identities = 39/196 (19%), Positives = 73/196 (37%), Gaps = 29/196 (14%)

Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMI 234
           E P      R LF+  ++    D  LR+ FEQ+G +    T C         + RGF  +
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVF--NLDPSVSNE 292
           +Y  +     AM A +   +  R ++   ++ +++      +     +F   +       
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 293 DLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI--- 344
            LR  F  YG+++ I     R +  KR   F+ F D  + +  +       + G      
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178

Query: 345 ----KLEPSRPGGARR 356
               K E +    ++R
Sbjct: 179 KALSKQEMASASSSQR 194

>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 = 51.9 bits (125), Expect = 1e-07
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYY 237
            + P      + +FV  I  + E+  LR  FEQYG I  +         K RGF  +++ 
Sbjct: 95  SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           D  +    +   +   +     ++  ++ K   +
Sbjct: 155 DHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMA 187

>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 = 49.2 bits (118), Expect = 8e-07
 Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 8/98 (8%)

Query: 265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFI 319
           + K     +      L +  L    ++E LR  F  +G + +        T   R   F+
Sbjct: 1   MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 320 EFYDVRAAEAALKSLNRSDIAGKRI--KLEPSRPGGAR 355
            +  V   +AA+ +     + G+ +  K   SR    R
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR 97

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 84.9 bits (210), Expect = 5e-20
 Identities = 25/103 (24%), Positives = 42/103 (40%), Gaps = 3/103 (2%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY 237
            G+    H     PSR + +R +  +V + E+ +L   +G + T     K +    I   
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV-TNLLMLKGKNQAFIEMN 60

Query: 238 DIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLNQG 278
              AA T +    +    LR + + I FS  K+  +D   NQ 
Sbjct: 61  TEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 103

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.5 bits (131), Expect = 2e-09
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 3/75 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNR 336
            + +  L   V+  ++  +   +G+V  +     K +  FIE     AA   +   +   
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVT 76

Query: 337 SDIAGKRIKLEPSRP 351
             + G+ I ++ S  
Sbjct: 77  PVLRGQPIYIQFSNH 91

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 83.8 bits (207), Expect = 2e-19
 Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 6/98 (6%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISY 236
           G  P    PS+ + + NIN  V   +L+    AL    GDI    +  +  + G   I +
Sbjct: 20  GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVF 79

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD 274
               +A+  + A Q  P +   L I FS    +   +D
Sbjct: 80  ATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAED 117

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 71.5 bits (175), Expect = 4e-15
 Identities = 15/92 (16%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHKFI 319
               P   + +Q  +++ N++P V  E L+     +  + G++ +I    +       +I
Sbjct: 19  LGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYI 77

Query: 320 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            F    +A+A +++       G  + +  S  
Sbjct: 78  VFATQESAQAFVEAFQGYPFQGNPLVITFSET 109

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 83.0 bits (205), Expect = 3e-19
 Identities = 26/113 (23%), Positives = 46/113 (40%), Gaps = 6/113 (5%)

Query: 171 HYSVPNGA---GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 227
           H+   +G    G+  G+      PSR + +R +  +V + E+ +L   +G +       K
Sbjct: 7   HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN-LLMLK 65

Query: 228 HRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLNQG 278
            +    I      AA T +    +    LR + + I FS  K+  +D   NQ 
Sbjct: 66  GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 118

>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 = 54.5 bits (131), Expect = 3e-09
 Identities = 18/112 (16%), Positives = 37/112 (33%), Gaps = 9/112 (8%)

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY 301
             +      +  L  R   +  S     PS        + +  L   V+  ++  +   +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR------VIHIRKLPIDVTEGEVISLGLPF 55

Query: 302 GEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNRSDIAGKRIKLEPSRP 351
           G+V  +     K +  FIE     AA   +   +     + G+ I ++ S  
Sbjct: 56  GKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>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 = 77.4 bits (191), Expect = 2e-17
 Identities = 20/89 (22%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
            L + NL   ++ E++  IFG YG +++IR   TP  R   ++ + D+  A+ A+  L+ 
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 337 SDIAGKRIKLEPSRPGGARRNLMLQLNQE 365
            +++ + + +       A + +  +  +E
Sbjct: 70  FNVSNRYLVVLYYNANRAFQKMDTKKKEE 98

>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 = 74.7 bits (184), Expect = 2e-16
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 4/88 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMR 247
            +R L++RN+   +   E+  +F +YG    IR   T  + RG   + Y DI  A+ A+ 
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP-ETRGTAYVVYEDIFDAKNAVD 65

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKDL 275
            L    +  R L + +          D 
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDT 93

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 76.9 bits (190), Expect = 2e-17
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 2/91 (2%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 325
           P  +   +     TL+  NL  +++ ++L+++F    E++ + +    +   +IEF    
Sbjct: 7   PCTSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
            AE  L+    ++I G+ + L  +   G  R
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 75.4 bits (186), Expect = 7e-17
 Identities = 18/83 (21%), Positives = 37/83 (44%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
              +RTL  +N++ N+ + EL+ +FE   +IR +    K +G   I +     A   +  
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 249 LQNKPLRRRKLDIHFSIPKDNPS 271
            Q   +  R + ++++  K    
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 75.0 bits (185), Expect = 1e-16
 Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN-RS 337
            L + NL P+V+ +DLRQ+FG         +   K  + F+++ D   A  A+++L+ + 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68

Query: 338 DIAGKRIKLEPSRPGGARR 356
           ++ GK ++++ S     R 
Sbjct: 69  ELHGKIMEVDYSVSKKLRS 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 = 59.2 bits (144), Expect = 4e-11
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 2/88 (2%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTA 245
             G      L++ N++  V   +LR LF                G+  + Y D   A  A
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRA 60

Query: 246 MRALQNKP-LRRRKLDIHFSIPKDNPSD 272
           +  L  K  L  + +++ +S+ K   S 
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRSS 88

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.9 bits (182), Expect = 3e-16
 Identities = 21/107 (19%), Positives = 44/107 (41%), Gaps = 4/107 (3%)

Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE 309
            +       L    S    +  + +L+   L V      V   +L +IFG +G +KE++ 
Sbjct: 5   HHHHHHSSGLVPRGS-HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

Query: 310 TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
                   F+EF +  +A  A++ ++    A + +++  S+    R 
Sbjct: 64  ---LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 62.3 bits (152), Expect = 4e-12
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           GE  +  LFVR    +V++SEL  +F  +G ++         GF  + + +  +A  A+ 
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMK---EVKILNGFAFVEFEEAESAAKAIE 83

Query: 248 ALQNKPLRRRKLDIHFSIPKDN 269
            +  K    + L++ +S     
Sbjct: 84  EVHGKSFANQPLEVVYSKLPAK 105

>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 = 75.3 bits (185), Expect = 3e-16
 Identities = 31/154 (20%), Positives = 53/154 (34%), Gaps = 17/154 (11%)

Query: 215 QYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN----------KPLRRRKLDIHFS 264
           QY  I    T     G       D   A    +   N              +       S
Sbjct: 2   QYKLILNGKTLK---GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGS 58

Query: 265 IPKDNPSDKD--LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY 322
               +   +D       + V NL  + +  +L + FG YG ++ +    +     F+EF 
Sbjct: 59  HHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFE 118

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
           D R A  A++ L+   + G R+++E S     +R
Sbjct: 119 DPRDAADAVRELDGRTLCGCRVRVELSNGE--KR 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 = 64.9 bits (158), Expect = 1e-12
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR 243
            H         ++V N+ +N   +EL   F  YG +R+++ A    GF  + + D R A 
Sbjct: 65  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAA 124

Query: 244 TAMRALQNKPLRRRKLDIHFSIPK 267
            A+R L  + L   ++ +  S  +
Sbjct: 125 DAVRELDGRTLCGCRVRVELSNGE 148

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 73.1 bits (180), Expect = 6e-16
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 1/81 (1%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 325
                        T  + N+    +  DL  +F  +G + + +    ++   FI++    
Sbjct: 16  VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEKGCCFIKYDTHE 74

Query: 326 AAEAALKSLNRSDIAGKRIKL 346
            A   + +L      G+ ++ 
Sbjct: 75  QAAVCIVALANFPFQGRNLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
             T ++ NI     +++L  LF+ +G I         +G   I Y     A   + AL N
Sbjct: 27  VTTAYIGNIPHFATEADLIPLFQNFGFILDFKH-YPEKGCCFIKYDTHEQAAVCIVALAN 85

Query: 252 KPLRRRKL 259
            P + R L
Sbjct: 86  FPFQGRNL 93

>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 = 71.8 bits (177), Expect = 1e-15
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALK 332
            + +  L  +V+ + + +IF  YG++K I            + + ++EF +   AE ALK
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 333 SLNRSDIAGKRIKLEPSRP 351
            ++   I G+ I       
Sbjct: 66  HMDGGQIDGQEITATAVLA 84

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 49.8 bits (120), Expect = 5e-08
 Identities = 9/85 (10%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRGFVMISYYDIRAART 244
               + +  +  NV    +  +F  YG I+ +            +G+  + + +   A  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDN 269
           A++ +    +  +++     +    
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWP 87

>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 = 72.3 bits (178), Expect = 1e-15
 Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 1/95 (1%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RETPHKRHHKFIEFY 322
           S      S       TLV+ NL  S + E L+++F     +K    +    + + FIEF 
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFA 61

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
               A+ AL S N+ +I G+ I+LE   P G+  +
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNS 96

>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 = 61.1 bits (149), Expect = 9e-12
 Identities = 18/97 (18%), Positives = 44/97 (45%), Gaps = 4/97 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIR--TLYTACKHRGFVMI 234
           G+   +G   +    S+TL + N++ +  +  L+ +FE+   I+        K +G+  I
Sbjct: 1   GSSGSSGNSTWSG-ESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNG-KSKGYAFI 58

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            +     A+ A+ +   + +  R + +    P+ +P+
Sbjct: 59  EFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 21/74 (28%), Positives = 34/74 (45%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
           NL       +L + F  YG ++ +    +     F+EF D R AE A++ L+   I G R
Sbjct: 7   NLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66

Query: 344 IKLEPSRPGGARRN 357
           +++E S     R  
Sbjct: 67  VRVELSTGMPRRSR 80

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 59.2 bits (144), Expect = 5e-11
 Identities = 22/80 (27%), Positives = 36/80 (45%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+ +     EL   F  YG +RT++ A    GF  + + D R A  A+R L  K +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 255 RRRKLDIHFSIPKDNPSDKD 274
              ++ +  S      S  D
Sbjct: 63  CGSRVRVELSTGMPRRSRFD 82

>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 = 72.4 bits (178), Expect = 1e-15
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALK 332
           N   + V NL P +  +D+  +F  YG +++I +  ++R      F+EF D R AE A+ 
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI-DLKNRRGGPPFAFVEFEDPRDAEDAVY 79

Query: 333 SLNRSDIAGKRIKLEPSRPGGARR 356
             +  D  G R+++E  R G    
Sbjct: 80  GRDGYDYDGYRLRVEFPRSGRGTG 103

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 56.6 bits (137), Expect = 5e-10
 Identities = 16/94 (17%), Positives = 34/94 (36%), Gaps = 2/94 (2%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH--RG 230
           S  +G            +    ++V N+  ++   ++  +F +YG IR +    +     
Sbjct: 3   SGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP 62

Query: 231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
           F  + + D R A  A+           +L + F 
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 96

>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 = 71.5 bits (176), Expect = 2e-15
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL  S S E + + F        +      R + F+ F +   A  A+K+LN   
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGA-VERVKKIRDYAFVHFSNREDAVEAMKALNGKV 75

Query: 339 IAGKRIKLEPSRP 351
           + G  I++  ++P
Sbjct: 76  LDGSPIEVTLAKP 88

>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 = 65.0 bits (159), Expect = 3e-13
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
             + L+VRN+  +  +  +   F             K R +  + + +   A  AM+AL 
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-KIRDYAFVHFSNREDAVEAMKALN 72

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
            K L    +++  + P D  S
Sbjct: 73  GKVLDGSPIEVTLAKPVDKDS 93

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 71.5 bits (176), Expect = 2e-15
 Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V NL    S + LR++F  YG V ++       T   R   F+ F+D R A+ A  +
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           ++ +++ G+ ++++ +R G    +
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLS 98

>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 = 57.2 bits (139), Expect = 2e-10
 Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 5/91 (5%)

Query: 182 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 236
           +G          TL V N+        LR +FE+YG +  +Y          RGF  + +
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           +D R A+ A  A+    L  R+L +  +   
Sbjct: 63  HDRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.7 bits (176), Expect = 3e-15
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK---FIEFYDVRAAEAALKS 333
            +    L+ +V    L+ +   YGEV+E+     P  R H     + F   R A+  +K+
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           L+ + + G  I  +    G  R 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRM 90

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.3 bits (170), Expect = 2e-14
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 242
           G+ P + +    +N NV ++ L+ +  +YG++  +         KH G   + +   R A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDN 269
           +  ++ L    +    +     I    
Sbjct: 62  KETVKNLHLTSVMGNIIHAQLDIKGQQ 88

>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 = 73.0 bits (179), Expect = 3e-15
 Identities = 28/143 (19%), Positives = 56/143 (39%), Gaps = 14/143 (9%)

Query: 229 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG---------T 279
           +G       D   A    +   N      +     +      ++   +           +
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS 72

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL    S + LR++F  YG V ++     R T   R   F+ F+D R AE A+ ++
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           + + + G+ ++++ +R G    +
Sbjct: 133 DGAVLDGRELRVQMARYGRPPDS 155

>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 = 56.4 bits (136), Expect = 2e-09
 Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHR 229
               G+    H        +L V N+        LR +FE+YG +  +Y        + R
Sbjct: 53  TVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 112

Query: 230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
           GF  + ++D R A  AM A+    L  R+L +  +     P
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 153

>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 = 71.1 bits (175), Expect = 3e-15
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 3/92 (3%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVR 325
              + D    TL V NL   V+   + Q+F   G  K  +       +    F+EFY+ R
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            A AAL ++N   I GK +K+  +    ++++
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 17/96 (17%), Positives = 45/96 (46%), Gaps = 4/96 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYTACKHRGFVM 233
           G+   +G     +   RTL+V N++ +V +  +  LF Q G     + +     +  +  
Sbjct: 1   GSSGSSGMME-DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF 59

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           + +Y+ R A  A+ A+  + +  +++ ++++    +
Sbjct: 60  VEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS 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 = 70.7 bits (174), Expect = 3e-15
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA 329
                  +  L V NL P ++ E++R++F  YG+  E+      +   FI       AE 
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEI 66

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARR 356
           A   L+   + GK++++  +    +  
Sbjct: 67  AKVELDNMPLRGKQLRVRFACHSASLT 93

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 60.7 bits (148), Expect = 1e-11
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
               LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L 
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELD 72

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
           N PLR ++L + F+    + +
Sbjct: 73  NMPLRGKQLRVRFACHSASLT 93

>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 = 71.2 bits (175), Expect = 4e-15
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 327
           D  +       T+    +   ++++ +RQ F  +G++ EIR  P K  + F+ F    +A
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-YSFVRFSTHESA 74

Query: 328 EAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
             A+ S+N + I G  +K    +      +
Sbjct: 75  AHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104

>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 = 54.3 bits (131), Expect = 3e-09
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           + T++   I S + D  +R  F  +G I  +      +G+  + +    +A  A+ ++  
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEI-RVFPEKGYSFVRFSTHESAAHAIVSVNG 83

Query: 252 KPLRRRKLDIHFSIPKDNPSD 272
             +    +  ++     + + 
Sbjct: 84  TTIEGHVVKCYWGKESPDMTS 104

>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 = 70.8 bits (174), Expect = 4e-15
 Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL  +V+ E L + F  +G+++ +++    + + FI F +   A  A++ +N  D
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKK---LKDYAFIHFDERDGAVKAMEEMNGKD 69

Query: 339 IAGKRIKLEPSRPGGARRN 357
           + G+ I++  ++P   +R 
Sbjct: 70  LEGENIEIVFAKPPDQKRK 88

>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 = 61.1 bits (149), Expect = 9e-12
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRAL 249
             + LFVRN+ + V +  L   F Q+G +       K  + +  I + +   A  AM  +
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKL----ERVKKLKDYAFIHFDERDGAVKAMEEM 65

Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
             K L    ++I F+ P D    +   Q
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQ 93

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 72.1 bits (177), Expect = 6e-15
 Identities = 25/118 (21%), Positives = 48/118 (40%), Gaps = 6/118 (5%)

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A+R+     L + + D HF    +          TL V NL    + E + ++F   G++
Sbjct: 8   ALRSDSYVELSQYR-DQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 305 KEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           K+I     +         F+E+Y    AE A++ +N + +  + I+ +        R 
Sbjct: 67  KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124

>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 = 56.7 bits (137), Expect = 1e-09
 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
            S TL+V N++    + ++  LF + GDI+ +            GF  + YY    A  A
Sbjct: 38  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           MR +    L  R +   +      
Sbjct: 98  MRYINGTRLDDRIIRTDWDAGFKE 121

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE- 328
            S +D    TL V  L  +++  DLR  F  +GE++ I     ++   FI+F   +AAE 
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQRQQCAFIQFATRQAAEV 63

Query: 329 AALKSLNRSDIAGKRIKL 346
           AA KS N+  + G+R+ +
Sbjct: 64  AAEKSFNKLIVNGRRLNV 81

>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 = 52.7 bits (127), Expect = 6e-09
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +GE         TL+V  +   + +++LR  F Q+G+IRT+ T  + +    I +
Sbjct: 1   GSSGSSGEDK----TITTLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQF 55

Query: 237 YDIRAARTAMRALQNK 252
              +AA  A     NK
Sbjct: 56  ATRQAAEVAAEKSFNK 71

>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 = 1e-14
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 4/91 (4%)

Query: 268 DNPSDKDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRA 326
            N +D       + + NL+ + V   D+  IF  YG V         + + F+++ + R 
Sbjct: 18  TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS---VHKGYAFVQYSNERH 74

Query: 327 AEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           A AA+   N   +AG+ + +  +      R+
Sbjct: 75  ARAAVLGENGRVLAGQTLDINMAGEPKPDRS 105

>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 = 56.2 bits (136), Expect = 7e-10
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 6/82 (7%)

Query: 191 PSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRA 248
            +  +F+ N+N+  V+ S++  +F +YG +      C  H+G+  + Y + R AR A+  
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVA----GCSVHKGYAFVQYSNERHARAAVLG 81

Query: 249 LQNKPLRRRKLDIHFSIPKDNP 270
              + L  + LDI+ +      
Sbjct: 82  ENGRVLAGQTLDINMAGEPKPD 103

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V  L P+ S   L + F  +G ++ I          +I++  + AA+AA   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 339 IAG--KRIKLEPSRPGGAR 355
           + G  +R++++ ++ G + 
Sbjct: 78  LGGPDRRLRVDFAKSGPSS 96

>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 = 67.3 bits (165), Expect = 6e-14
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           P+  L+V  +  N   + L   F+++G IRT+    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMR 74

Query: 251 NKPLRRRKLDIHFSIPKDNPSD 272
             PL      +     K  PS 
Sbjct: 75  GFPLGGPDRRLRVDFAKSGPSS 96

>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 = 67.6 bits (166), Expect = 4e-14
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V N+  + ++++LR +F   G V E       + + F+       A+AA+  LN  ++ G
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAAIAQLNGKEVKG 70

Query: 342 KRIKLEPSRPGGARR 356
           KRI +E S  G  + 
Sbjct: 71  KRINVELSTKGQKKS 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.8 bits (143), Expect = 5e-11
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            +  +FV N+++     ELR+LFE+ G +         + +  +       A+ A+  L 
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVI---ECDVVKDYAFVHMEKEADAKAAIAQLN 64

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
            K ++ +++++  S      S
Sbjct: 65  GKEVKGKRINVELSTKGQKKS 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 67.2 bits (165), Expect = 5e-14
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
           NL    + +++R +F  YG+V E       +++ F+   D  AAE A+++L+   + G  
Sbjct: 15  NLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71

Query: 344 IKLEPSRPGGARRN 357
           I +E S+      +
Sbjct: 72  INVEASKNKSKASS 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 56.1 bits (136), Expect = 5e-10
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G      LF+ N+     + E+R+LFEQYG +         + +  +   D  AA  A+R
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVL---ECDIIKNYGFVHIEDKTAAEDAIR 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
            L +  L    +++  S  K   S
Sbjct: 61  NLHHYKLHGVNINVEASKNKSKAS 84

>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 = 67.2 bits (165), Expect = 5e-14
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 334 LNRSDIAGKRIKLEPSRPG 352
            N  ++ G+RI++     G
Sbjct: 77  ANGMELDGRRIRVSGPSSG 95

>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 = 51.8 bits (125), Expect = 1e-08
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGF 231
           G+   +G     + P+  L V  ++    + +LR +F +YG I  +         + RGF
Sbjct: 1   GSSGSSGNRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 59

Query: 232 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
             + + ++  A+ A        L  R++ +   
Sbjct: 60  AFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 67.7 bits (166), Expect = 6e-14
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 6/96 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 320
           P DN S ++ +  T+    L   +   DL   F A G+V+++     R +   +   ++E
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
           F ++++   A+  L    + G  I ++ S+    R 
Sbjct: 74  FCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRL 108

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 48.5 bits (116), Expect = 3e-07
 Identities = 16/102 (15%), Positives = 37/102 (36%), Gaps = 6/102 (5%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 227
           S  +            E  +RT+F   + + +   +L   F   G +R +         +
Sbjct: 6   SGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRR 65

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
            +G   + + +I++   A+  L  + L    + +  S  + N
Sbjct: 66  SKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKN 106

>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 = 66.9 bits (164), Expect = 7e-14
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V N+ P+ +N++LR  F  YG V E       + + F+       A  A++ L+ ++  G
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIECDI---VKDYAFVHMERAEDAVEAIRGLDNTEFQG 71

Query: 342 KRIKLEPSRPGGARRN 357
           KR+ ++ S       +
Sbjct: 72  KRMHVQLSTSRLRTAS 87

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 58.0 bits (141), Expect = 8e-11
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            S  L V NI+    + ELRA FE+YG +         + +  +       A  A+R L 
Sbjct: 9   ASTKLHVGNISPTCTNQELRAKFEEYGPVI---ECDIVKDYAFVHMERAEDAVEAIRGLD 65

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
           N   + +++ +  S  +   +
Sbjct: 66  NTEFQGKRMHVQLSTSRLRTA 86

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 68.2 bits (167), Expect = 8e-14
 Identities = 27/129 (20%), Positives = 54/129 (41%), Gaps = 6/129 (4%)

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNED 293
           S++    +   +    +         +            D+   T L V NL    S + 
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDT 63

Query: 294 LRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
           LR++F  YG V ++     R T   R   F+ F+D R AE A+ +++ + + G+ ++++ 
Sbjct: 64  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

Query: 349 SRPGGARRN 357
           +R G    +
Sbjct: 124 ARYGRPPDS 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 = 56.3 bits (136), Expect = 1e-09
 Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 5/110 (4%)

Query: 163 SASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL 222
            +    +             G  P       +L V N+        LR +FE+YG +  +
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 223 YTAC-----KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           Y        + RGF  + ++D R A  AM A+    L  R+L +  +   
Sbjct: 78  YIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 66.5 bits (163), Expect = 9e-14
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 282 VFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 340
           + NL   +VS EDL +IF  YG + +I     K    FI+F + ++   A++  ++    
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 341 GKRIKLEPSRPGGARR 356
           GK++ LE S      +
Sbjct: 72  GKKLILEVSSSNARPQ 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 191 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRA 248
           P   LF+ N+   NV   +L  +F  YG I            F  I + + ++ R A+  
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM----QINIKNAFGFIQFDNPQSVRDAIEC 64

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
              +    +KL +  S     P     + GT
Sbjct: 65  ESQEMNFGKKLILEVSSSNARPQFDHGDHGT 95

>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 = 1e-13
 Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIR 240
           P+  ++V+N+  +V++ +L+ +F +Y D  +               + +G   I   + +
Sbjct: 44  PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 103

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           AA  A++      L  + + + F+       D 
Sbjct: 104 AAAKALKEANGYVLFGKPMVVQFARSARPKQDP 136

>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 = 60.6 bits (147), Expect = 4e-11
 Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 14/99 (14%)

Query: 267 KDNPSDKDLNQG----TLVVFNLDPSVSNEDLRQIFGAYGEVKE----------IRETPH 312
           +     +    G     + V NL   V  +DL+ IFG Y +             + +   
Sbjct: 31  ETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGR 90

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            +   FI   + +AA  ALK  N   + GK + ++ +R 
Sbjct: 91  MKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129

>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 = 66.8 bits (163), Expect = 1e-13
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 4/102 (3%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +G+   G  PSR L +R +   V ++E+ AL   +G +  +    K +    +  
Sbjct: 1   GSSGSSGDKMDGA-PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLEL 58

Query: 237 YDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLN 276
               AA T +         LR + + I +S  K+  +    +
Sbjct: 59  ATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSGPSS 100

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 267 KDNPSDKDLNQGTLVVF--NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV 324
             +  DK     + V+    L   V+  ++  +   +G+V  I     K +  F+E    
Sbjct: 3   SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATE 61

Query: 325 RAAEAALK--SLNRSDIAGKRIKLEPSR 350
            AA   +   S     +  + I ++ S 
Sbjct: 62  EAAITMVNYYSAVTPHLRNQPIYIQYSN 89

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 66.9 bits (164), Expect = 1e-13
 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L + NL P V+  DL  +F  + E K         T   R   FI F +   A  AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
           +N   + GK + +E  +    R
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQR 108

>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 = 65.0 bits (159), Expect = 6e-13
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG------DIRTLYTACKHRGFVMISYYDIRAART 244
           P++ L+++N++  V + +L +LF ++           + T  + RG   I++ +   A  
Sbjct: 24  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTG-RMRGQAFITFPNKEIAWQ 82

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSD 272
           A+  +    L  + L I F   K   S 
Sbjct: 83  ALHLVNGYKLYGKILVIEFGKNKKQRSS 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 = 67.1 bits (164), Expect = 1e-13
 Identities = 26/125 (20%), Positives = 57/125 (45%), Gaps = 10/125 (8%)

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA 300
           A    M+   +K +           P      K++++ ++ V N+D   + +DL   F +
Sbjct: 1   AIAPCMQTTHSK-MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 59

Query: 301 YGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR---PG 352
            G +  I     + + H + + +IEF +  + +AA+ +++ +   G+ IK+ P R   PG
Sbjct: 60  CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPG 118

Query: 353 GARRN 357
            +  +
Sbjct: 119 ISSTD 123

>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 = 45.9 bits (109), Expect = 3e-06
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 6/92 (6%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 227
           +   G           E   R+++V N++      +L A F   G I  +   C      
Sbjct: 17  AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGH 76

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKL 259
            +G+  I + +  +   A+ A+     R R +
Sbjct: 77  PKGYAYIEFAERNSVDAAV-AMDETVFRGRTI 107

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 66.5 bits (163), Expect = 2e-13
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V ++      +++++ F  YGE+K I     R T   + +  +E+   + A AA ++
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           LN ++I G+ I+++     G +R
Sbjct: 88  LNGAEIMGQTIQVDWCFVKGPKR 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 = 56.5 bits (137), Expect = 4e-10
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 5/103 (4%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 227
            V N         P        LFV +I+   ++ E++  F  YG+I+ ++         
Sbjct: 7   RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF 66

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
            +G+ ++ Y   + A  A  AL    +  + + + +   K   
Sbjct: 67  SKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 65.9 bits (161), Expect = 2e-13
 Identities = 10/79 (12%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            S  + +R +   V +++L    +++G I  +      +   ++ + D+  A  A+    
Sbjct: 20  ASPVVHIRGLIDGVVEADLVEALQEFGPISYV-VVMPKKRQALVEFEDVLGACNAVNYAA 78

Query: 251 NKP--LRRRKLDIHFSIPK 267
           +    +      +++S  +
Sbjct: 79  DNQIYIAGHPAFVNYSTSQ 97

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.0 bits (143), Expect = 4e-11
 Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 9/100 (9%)

Query: 253 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH 312
                 ++ +    K   S        + +  L   V   DL +    +G +  +   P 
Sbjct: 3   HHHHHHMENYDDPHKTPASP------VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSR 350
           KR    +EF DV  A  A+     +   IAG    +  S 
Sbjct: 57  KR-QALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>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 = 67.5 bits (165), Expect = 2e-13
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V ++      +++++ F  YGE+K I     R T   + +  +E+   + A AA ++
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           LN ++I G+ I+++     G +R 
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRV 157

>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 = 61.4 bits (149), Expect = 3e-11
 Identities = 20/108 (18%), Positives = 41/108 (37%), Gaps = 5/108 (4%)

Query: 171 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---- 226
           +  V N         P        LFV +I+   ++ E++  F  YG+I+ ++       
Sbjct: 51  YERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 110

Query: 227 -KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
              +G+ ++ Y   + A  A  AL    +  + + + +   K     K
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK 158

>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 = 66.7 bits (163), Expect = 2e-13
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 334 LNRSDIAGKRIKLEPSRP 351
            N  ++ G+RI+++ S  
Sbjct: 108 ANGMELDGRRIRVDFSIT 125

>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 = 55.5 bits (134), Expect = 2e-09
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
           P+  L V  ++    + +LR +F +YG I  +         + RGF  + + ++  A+ A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
                   L  R++ + FSI K
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 65.8 bits (161), Expect = 3e-13
 Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 15/96 (15%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH----HK-- 317
            +PK   + K      ++V N+    +  ++R++F  +GE+K +R  P K      H+  
Sbjct: 8   QVPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVR-LPKKMTGTGAHRGF 60

Query: 318 -FIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP 351
            F++F   + A+ A  +L + + + G+R+ LE +  
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 24/102 (23%), Positives = 46/102 (45%), Gaps = 8/102 (7%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY------TACKHRG 230
           G+   +G+ P  +  +  + VRNI       E+R LF  +G+++T+           HRG
Sbjct: 1   GSSGSSGQVPKKQ-TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59

Query: 231 FVMISYYDIRAARTAMRALQN-KPLRRRKLDIHFSIPKDNPS 271
           F  + +   + A+ A  AL +   L  R+L + ++  +    
Sbjct: 60  FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 = 65.6 bits (160), Expect = 3e-13
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G           +  +N+ +    +E++  F ++G +  +          ++ + +   A
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-GITAIVEFLEPLEA 59

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           R A R L         L + ++ P       
Sbjct: 60  RKAFRHLAYSKFHHVPLYLEWA-PIGVFGAA 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 = 63.3 bits (154), Expect = 2e-12
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            ++  NL       ++++ F  +G +  +   P       +EF +   A  A + L  S 
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVL-LPEGGITAIVEFLEPLEARKAFRHLAYSK 70

Query: 339 IAGKRIKLE 347
                + LE
Sbjct: 71  FHHVPLYLE 79

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 8/88 (9%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHK---FIEFYDVRAAEA 329
             L + NL+ S + E L+ +F   G +K       +            F+E+     A+ 
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           ALK L    + G ++++  S       +
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPAS 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 = 55.7 bits (135), Expect = 6e-10
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 8/92 (8%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDI 239
           G   S  LF++N+N +  +  L+ +F + G I        +         GF  + Y   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
             A+ A++ LQ   +   KL++  S     P+
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISERATKPA 92

>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 = 4e-13
 Identities = 13/89 (14%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            S  + VR +  +V +++L    E++G I  +      +   ++ + +I +A+  +    
Sbjct: 14  VSPVVHVRGLCESVVEADLVEALEKFGTICYV-MMMPFKRQALVEFENIDSAKECVTFAA 72

Query: 251 NKP--LRRRKLDIHFSIPKDNPSDKDLNQ 277
           + P  +  ++   ++S  K      +   
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITRPGNSGP 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 = 58.3 bits (141), Expect = 1e-10
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            + V  L  SV   DL +    +G +  +   P KR    +EF ++ +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-QALVEFENIDSAKECVTFAADVP 75

Query: 339 --IAGKRIKLEPSR 350
             IAG++     S 
Sbjct: 76  VYIAGQQAFFNYST 89

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 64.9 bits (158), Expect = 4e-13
 Identities = 17/87 (19%), Positives = 30/87 (34%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 325
           P   P +       + V NL       DL++     G V         R   F+ + D  
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSA 67

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPG 352
           AA+ A+  L    +    +++  +R  
Sbjct: 68  AAQQAVSCLQGLRLGTDTLRVALARQQ 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 60.6 bits (147), Expect = 1e-11
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 177 GAGTVAGEHP--YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMI 234
            +G+     P   G   +  ++V N+  +   S+L+    + G +    T    R    +
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
            Y D  AA+ A+  LQ   L    L +  +  + +
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96

>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 = 64.6 bits (158), Expect = 6e-13
 Identities = 18/92 (19%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
           P+ +  +  T+ V NL       DL+++F  +G +  I     + T   +   FI F+  
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
             A  A+  ++        + +E ++P     
Sbjct: 68  EDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
            + T+ V N++ +  +++L+ LF  +G I  +Y A      + +GF  IS++    A  A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +  +         L++ ++ P  N
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTN 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 = 64.3 bits (157), Expect = 7e-13
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 282 VFNLD-PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 340
           + NL   +VS EDL +IF  YG + +I     K    FI+F + ++   A++  ++    
Sbjct: 27  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIEXESQEMNF 83

Query: 341 GKRIKLEPSRPG 352
           GK++ LE S   
Sbjct: 84  GKKLILEVSSSN 95

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 182 AGEHPYGEHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDI 239
           +G  P G H    LF+ N+   NV   +L  +F  YG I            F  I + + 
Sbjct: 12  SGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM----QINIKNAFGFIQFDNP 67

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPK 267
           ++ R A+     +    +KL +  S   
Sbjct: 68  QSVRDAIEXESQEMNFGKKLILEVSSSN 95

>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 = 64.2 bits (157), Expect = 7e-13
 Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 5/95 (5%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFY 322
              S     +  L V  L   V ++ L   F  +G++ +I      ET   R   F+EF 
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
               A AA+ ++N S++ G+ I++  ++P   + +
Sbjct: 63  LAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 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 = 53.0 bits (128), Expect = 6e-09
 Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTA 245
             R L+V  +   V+D  L A F  +GDI        Y   KHRGF  + +     A  A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSD 272
           +  +    L  R + ++ + P      
Sbjct: 71  IDNMNESELFGRTIRVNLAKPMRIKES 97

>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 = 64.2 bits (157), Expect = 7e-13
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEF 321
           S     P+ +     TL V  L    + E L++ F      + +  RET   +   F++F
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDF 61

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
                A+AA +++   +I G ++ L+ ++P G   +
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGS 97

>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 = 54.6 bits (132), Expect = 2e-09
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMR 247
           PS+TLFV+ ++ +  +  L+  F+     R +    T    +GF  + +     A+ A  
Sbjct: 14  PSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETG-SSKGFGFVDFNSEEDAKAAKE 72

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
           A+++  +   K+ + ++ PK    
Sbjct: 73  AMEDGEIDGNKVTLDWAKPKGEGG 96

>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 = 64.2 bits (157), Expect = 8e-13
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
            P  +     T+ V  LD  VS   L ++F   G V        R T   + + F+EF  
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              A+ A+K ++   + GK I++  +  
Sbjct: 67  EEDADYAIKIMDMIKLYGKPIRVNKASA 94

>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 = 50.7 bits (122), Expect = 4e-08
 Identities = 15/98 (15%), Positives = 39/98 (39%), Gaps = 6/98 (6%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGF 231
           G+   +G      +   T++V  ++  V +  L  LF Q G +   +        +H+G+
Sbjct: 1   GSSGSSG-PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59

Query: 232 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
             + +     A  A++ +    L  + + ++ +   + 
Sbjct: 60  GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 97

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 64.2 bits (157), Expect = 8e-13
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 4/86 (4%)

Query: 274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEA 329
            L +  L +  L  S + E+L +I  A+G VK++R         +   ++E+ +   A  
Sbjct: 14  SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQ 73

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGAR 355
           A+  ++   I    IK+  S  G + 
Sbjct: 74  AVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAM 246
               LF+  +  +    EL  + + +G ++ L        K +G   + Y +   A  A+
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75

Query: 247 RALQNKPLRRRKLDIHFSIPKDN 269
             +    ++   + +  S    +
Sbjct: 76  MKMDGMTIKENIIKVAISNSGPS 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 = 63.8 bits (156), Expect = 9e-13
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALK 332
           G L V NL  + S EDL ++F AYG + E+       T   +   F+ F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            ++     G+ + + PS        
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 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 = 59.9 bits (146), Expect = 2e-11
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
            S  LFVRN++    + +L  LF  YG +  L+        K +GF  +++     A  A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSD 272
              +  +  + R L +  S  K   S 
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 63.8 bits (156), Expect = 1e-12
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAA 330
                   TL V+  D  ++   LR  F  +G + ++   P +    F+ +  + +A+ A
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNC-AFVTYEKMESADQA 65

Query: 331 LKSLNRSDIAGKRIKLEPSRP 351
           +  LN + +   ++K+  +R 
Sbjct: 66  VAELNGTQVESVQLKVNIARK 86

>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 = 47.7 bits (114), Expect = 4e-07
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 4/94 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +GE         TL+V   +  +  + LR  F  +G+I  L      R    ++Y
Sbjct: 1   GSSGSSGERR-APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTY 56

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
             + +A  A+  L    +   +L ++ +  +   
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVNIARKQPML 90

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 64.7 bits (158), Expect = 1e-12
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  +    + ED+   F  YGE+K I     R T + + +  +E+   + A+AA++ 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           LN  D+ G+ I ++     G  + 
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPKG 107

>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 = 57.8 bits (140), Expect = 2e-10
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 5/88 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               LFV  ++    + ++   F +YG+I+ ++          +G+ ++ Y   + A+ A
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           M  L  + L  + + + +   +  P  K
Sbjct: 81  MEGLNGQDLMGQPISVDWCFVRGPPKGK 108

>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 = 63.8 bits (156), Expect = 1e-12
 Identities = 21/97 (21%), Positives = 45/97 (46%), Gaps = 3/97 (3%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIE 320
           S      S+       L V N+     + DLRQ+FG +G++ ++    ++R  K   F+ 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           F +   A+ A + L+ + + G++I++  +       +
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 3/86 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAARTAMR 247
             + L V NI     D +LR +F Q+G I     ++     +GF  +++ +   A  A  
Sbjct: 14  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDK 273
            L    +  RK++++ +  +   +  
Sbjct: 74  KLHGTVVEGRKIEVNNATARVMTNSG 99

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.4 bits (155), Expect = 2e-12
 Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 5/94 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
             S    ++G L V  L    + + L Q+F  YG++ E+     RET   R   F+ F +
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           +  A+ A+ ++N   + G++I+++ +      R+
Sbjct: 64  IDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97

>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 = 49.9 bits (120), Expect = 7e-08
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 13/88 (14%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRA 241
               LFV  ++ +  +  L  +F +YG I    +             RGF  +++ +I  
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQI----SEVVVVKDRETQRSRGFGFVTFENIDD 66

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           A+ AM A+  K +  R++ +  +    +
Sbjct: 67  AKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

>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 = 62.0 bits (151), Expect = 3e-12
 Identities = 9/75 (12%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
               ++V NL    + +++  +   Y    +       +   F+   +   A+ A++  +
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD--LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 336 RSDIAGKRIKLEPSR 350
           +    GK + ++   
Sbjct: 62  QYSFRGKDLIVQLQP 76

>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 = 58.2 bits (141), Expect = 6e-11
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  + V+N+  +    E+  L + Y  ++  Y   +++    ++  +   A+ A++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-RNKRTAFVTLLNGEQAQNAIQ 58

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 278
                  R + L +        P+D  L  G
Sbjct: 59  MFHQYSFRGKDLIVQLQ-----PTDALLCSG 84

>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 = 63.0 bits (154), Expect = 3e-12
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSL 334
           G + + NLD S+ N+ L   F A+G +   K + +    + + F+ F    AAE A++ +
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 335 NRSDIAGKRIKLEPSRPGGARR 356
           N   +  +++ +   +    R 
Sbjct: 66  NGMLLNDRKVFVGRFKSRKERE 87

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 18/112 (16%), Positives = 43/112 (38%), Gaps = 15/112 (13%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIRAART 244
           S  +F++N++ ++++  L   F  +G+I     +CK        +G+  + +    AA  
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNI----LSCKVVCDENGSKGYGFVHFETQEAAER 60

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDN----PSDKDLNQGTLVVFNLDPSVSNE 292
           A+  +    L  RK+ +     +         +      + + N  P  +  
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  L   V ++ L   F  +G++ +I      ET   R   F+EF     A AA+ +
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 334 LNRSDIAGKRIK 345
           +N S++ G+ I+
Sbjct: 69  MNESELFGRTIR 80

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
             R L+V  +   V+D  L A F  +GDI  +         KHRGF  + +     A  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 246 MRALQNKPLRRRKL 259
           +  +    L  R +
Sbjct: 66  IDNMNESELFGRTI 79

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 63.6 bits (155), Expect = 4e-12
 Identities = 22/103 (21%), Positives = 40/103 (38%), Gaps = 6/103 (5%)

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQG-TLVVFNLDPSVSNEDLRQIFGAYGEVKEI 307
           +    +   +  +         S         L V  L   V ++ L   F  +G++ +I
Sbjct: 34  VAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 93

Query: 308 -----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
                 ET   R   F+EF     A AA+ ++N S++ G+ I+
Sbjct: 94  QIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 55.2 bits (133), Expect = 3e-09
 Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 5/90 (5%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHR 229
            +G    +G         R L+V  +   V+D  L A F  +GDI  +         KHR
Sbjct: 46  VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

Query: 230 GFVMISYYDIRAARTAMRALQNKPLRRRKL 259
           GF  + +     A  A+  +    L  R +
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTI 135

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 61.4 bits (150), Expect = 4e-12
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +  L P  +++DL ++   YG++        + T   + + F++F    AA+ A+ +L  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 337 SDIAGKRIKLEPSRPG 352
           S +  +  K      G
Sbjct: 70  SGVQAQMAKQSGPSSG 85

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYD 238
           G   S  L++R +     D +L  L + YG I     + K          +G+  + +  
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKI----VSTKAILDKTTNKCKGYGFVDFDS 56

Query: 239 IRAARTAMRALQNKPLRRRKL 259
             AA+ A+ AL+   ++ +  
Sbjct: 57  PSAAQKAVTALKASGVQAQMA 77

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 62.3 bits (152), Expect = 4e-12
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  +    + ED+   F  YGE+K I     R T + + +  +E+   + A+AA++ 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN  D+ G+ I ++    
Sbjct: 85  LNGQDLMGQPISVDWCFV 102

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               LFV  ++    + ++   F +YG+I+ ++          +G+ ++ Y   + A+ A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNP 270
           M  L  + L  + + + +   +  P
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVRGPP 106

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 63.2 bits (154), Expect = 4e-12
 Identities = 32/130 (24%), Positives = 57/130 (43%), Gaps = 13/130 (10%)

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 292
           ++S YD       ++ LQ +  +         IP    + +      L+V  +  +V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 293 DLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            LRQ+F  YG ++ +     RET   R + F++F    +A+ A+  LN  +I  KR+K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 348 PSRPGGARRN 357
            +  G  R  
Sbjct: 118 LAASGHQRPG 127

>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 = 46.7 bits (111), Expect = 2e-06
 Identities = 21/115 (18%), Positives = 39/115 (33%), Gaps = 13/115 (11%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK----- 227
                      +        R L V  I + V++ +LR LFE+YG I     + K     
Sbjct: 23  QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI----ESVKIVCDR 78

Query: 228 ----HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 278
                RG+  + +    +A+ A+  L    +  ++L +  +             G
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVG 133

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 62.8 bits (152), Expect = 5e-12
 Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 11/114 (9%)

Query: 262 HFSIPKDNPSDKDLNQGTLV-VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE 320
             + P +       N+  L+ + N    ++ + L  +    G+V+ I           +E
Sbjct: 9   RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVE 68

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKL--EPSRPGGARRNLMLQLNQELEQDESR 372
           F  V  A+ A  +LN +DI      L  E +RP         +LN     ++S 
Sbjct: 69  FESVLCAQKAKAALNGADIYAGCCTLKIEYARPT--------RLNVIRNDNDSW 114

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 50.1 bits (119), Expect = 1e-07
 Identities = 12/84 (14%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 189 EHPSRTLF--VRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM 246
              ++ L   ++N    +    L  +    G ++ +    ++    M+ +  +  A+ A 
Sbjct: 20  SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAK 79

Query: 247 RALQNKPL--RRRKLDIHFSIPKD 268
            AL    +      L I ++ P  
Sbjct: 80  AALNGADIYAGCCTLKIEYARPTR 103

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 5/85 (5%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 320
                     ++ T+ V NL  S++N DL +IF  YG+V ++     ++T   +   FI 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIK 345
           F D  +A+   +++N   + G+ IK
Sbjct: 65  FLDKDSAQNCTRAINNKQLFGRVIK 89

>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 = 50.7 bits (122), Expect = 4e-08
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRG 230
            +G+             T++V N+  ++ +++L  +F +YG +  +       T  K +G
Sbjct: 2   SSGSSGMSGGLAP-SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR-KSKG 59

Query: 231 FVMISYYDIRAARTAMRALQNKPLRRRKL 259
              I + D  +A+   RA+ NK L  R +
Sbjct: 60  VAFILFLDKDSAQNCTRAINNKQLFGRVI 88

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 61.4 bits (150), Expect = 5e-12
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAE 328
           + +  ++ V N+D   + E+L   F   G V  +     + + H +   +IEF D  +  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 329 AALKSLNRSDIAGKRIKLEPSRP 351
            +L  L+ S   G++IK+ P R 
Sbjct: 63  TSLA-LDESLFRGRQIKVIPKRT 84

>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 = 44.8 bits (107), Expect = 4e-06
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAAR 243
           E  +R+++V N++      EL A F   G +  +   C       +GF  I + D  + R
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 244 TAMRALQNKPLRRRKL 259
           T++ AL     R R++
Sbjct: 63  TSL-ALDESLFRGRQI 77

>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 = 63.6 bits (154), Expect = 5e-12
 Identities = 29/144 (20%), Positives = 60/144 (41%), Gaps = 12/144 (8%)

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLV-VFNLDPSVSN 291
           M  ++   +A+ A++A+ +       L    +      +    +    + V NL   V+ 
Sbjct: 1   MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTL 60

Query: 292 EDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSDI--AGKRIKLEP 348
           + L QIF  +G V +I         +  +++ D  +A+ A  SL+  +I  A   ++++ 
Sbjct: 61  DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

Query: 349 SRPGGARRNLMLQLNQELEQDESR 372
           S+           LN +   D+SR
Sbjct: 121 SKLT--------SLNVKYNNDKSR 136

>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 = 57.8 bits (139), Expect = 5e-10
 Identities = 28/129 (21%), Positives = 49/129 (37%), Gaps = 9/129 (6%)

Query: 172 YSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF 231
               + A   AG    G+ P   + V N+   V    L  +F ++G +  + T  K+  F
Sbjct: 26  ALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF 85

Query: 232 -VMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIPKD------NPSDKDLNQGTLVV 282
             ++ Y D  +A+ A  +L  + +      L I FS          N   +D  +  L  
Sbjct: 86  QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPS 145

Query: 283 FNLDPSVSN 291
            +  PS+  
Sbjct: 146 GDSQPSLDQ 154

>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 = 61.1 bits (149), Expect = 8e-12
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
           PSR +++ +I  +  + ++  L    G +  L         + +G+  I + D+ ++ +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSD 272
           +R L    L  R L   +S   D    
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGV 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 = 60.7 bits (148), Expect = 9e-12
 Identities = 14/89 (15%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           + ++    + E +  +    G V  +      +T   + + FIEF D+ ++ +A+++LN 
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66

Query: 337 SDIAGKRIKLEPSRPGGARRNLMLQLNQE 365
             +  + +K   S         +   +  
Sbjct: 67  YQLGSRFLKCGYSSNSDISGVSLEHHHHH 95

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 61.1 bits (149), Expect = 8e-12
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 5/91 (5%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHKFIEFYDVR 325
              +      L + NL+P+ S  +L+          ++      T   R   +++F    
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
             E AL+ L    + G  IKLE  +     R
Sbjct: 70  DLEKALE-LTGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 245
               LF+ N+N N   +EL+    +        +  + T   +R F  + +        A
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTG-TNRKFGYVDFESAEDLEKA 74

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +  L    +   ++ +     +D 
Sbjct: 75  L-ELTGLKVFGNEIKLEKPKGRDG 97

>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 = 60.6 bits (148), Expect = 1e-11
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V +L  +++ + LR IF  +G++  I      +T   + + FI F D   A  AL+ 
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           LN  ++AG+ +++          +
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGGS 90

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 5/90 (5%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 242
           G   S  L+V +++ N+ +  LR +FE +G I  +         + +G+  I++ D   A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSD 272
           R A+  L    L  R + +     + +   
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDGGS 90

>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 = 61.2 bits (149), Expect = 1e-11
 Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
           S     PSD      T+ + NL      E L ++   +G++K +      +T H +   F
Sbjct: 3   SGSSGLPSDVT-EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 319 IEFYDVRAAEAALKSLNRS------DIAGKRIKLEPSRPGGARRNL 358
            +F    AA+  L + +         + G+++K++ +       + 
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 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 = 54.7 bits (132), Expect = 2e-09
 Identities = 17/99 (17%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIR 240
           P      +T+F+RN++ + E+  L  + +Q+GD++ +           +G     +    
Sbjct: 9   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68

Query: 241 AARTAMRALQNKPLRR------RKLDIHFSIPKDNPSDK 273
           AA+  + A   +          R+L +  ++ +D  +  
Sbjct: 69  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 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 = 60.4 bits (147), Expect = 2e-11
 Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNRSD 338
           V N+     + DLRQ+FG +G++ ++    ++R  K   F+ F +   A+ A + L+ + 
Sbjct: 34  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTV 93

Query: 339 IAGKRIKLEPSRP 351
           + G++I++  +  
Sbjct: 94  VEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.3 bits (113), Expect = 8e-07
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAART 244
            +   + L V NI     D +LR +F Q+G I     ++     +GF  +++ +   A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84

Query: 245 AMRALQNKPLRRRKLDIHFSIPK 267
           A   L    +  RK++++ +  +
Sbjct: 85  AREKLHGTVVEGRKIEVNNATAR 107

>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 = 64.5 bits (156), Expect = 2e-11
 Identities = 21/93 (22%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F Q+G I    +  + K RG   + + ++ +A  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
           A+R++Q  P   + + I ++    +   K    
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT 100

>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 = 60.3 bits (145), Expect = 5e-10
 Identities = 27/160 (16%), Positives = 58/160 (36%), Gaps = 9/160 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALK 332
           T+ + NL+  +  ++L++    IF  +G++ +I    +   R   F+ F +V +A  AL+
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQ 392
           S+       K ++++ ++        M     E ++   +       +P T         
Sbjct: 71  SMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGA 130

Query: 393 FSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQ 432
                                 +P   +HMPG    + P 
Sbjct: 131 TPVVGAVQGPVP---GMPPMTQAPRIMHHMPGQPPYMPPP 167

>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 = 54.5 bits (130), Expect = 4e-08
 Identities = 14/91 (15%), Positives = 28/91 (30%)

Query: 168 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 227
           G +             +      P+  LF+ N+     +  L  LF Q+   + +     
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRK 258
                 + + +   A  A  ALQ   + +  
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNN 273

>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 = 52.6 bits (125), Expect = 2e-07
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L + NL    +   L  +F  +   KE+R  P +    F+EF +   A AA  +L    
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 339 I-AGKRIKLEPSR 350
           I     +K+  ++
Sbjct: 269 ITQNNAMKISFAK 281

>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 = 60.4 bits (147), Expect = 2e-11
 Identities = 23/93 (24%), Positives = 48/93 (51%), Gaps = 6/93 (6%)

Query: 271 SDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
           S K+  +G  L +++L     ++DL Q+F  +G V        ++T   +   F+ + + 
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            +A+AA++S+N   I  KR+K++  R     ++
Sbjct: 78  VSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>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 = 45.8 bits (109), Expect = 4e-06
 Identities = 19/116 (16%), Positives = 46/116 (39%), Gaps = 19/116 (16%)

Query: 163 SASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL 222
           S+  +GL   S+        G           LF+ ++     D +L  +F  +G++   
Sbjct: 2   SSGSSGLTQQSIGAAGSQKEGP------EGANLFIYHLPQEFGDQDLLQMFMPFGNV--- 52

Query: 223 YTACK---------HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
             + K          + F  +SY +  +A+ A++++    +  ++L +     K++
Sbjct: 53  -VSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 107

>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 = 60.2 bits (146), Expect = 2e-11
 Identities = 16/96 (16%), Positives = 36/96 (37%), Gaps = 9/96 (9%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-------IRTLYTACKHRGFVMISYYDIRAAR 243
            +  LF+  I    +  E+     +  +         +     K+RGF  + Y   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 244 TAMRALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQ 277
            A R L    ++    ++ + ++ P+ +  +  +  
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 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 = 56.3 bits (136), Expect = 6e-10
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 9/85 (10%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV-------KEIRETPHKRHHKFIEFYDVRAAE 328
               L +  +      E++ +      E            +    R   F+E+   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 329 AALKSLNRSD--IAGKRIKLEPSRP 351
            A + L      + G +I ++ + P
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEP 91

>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 = 60.0 bits (146), Expect = 3e-11
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 4/86 (4%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAAL 331
           + G L +  L+   + + L+ +FG +G + E+      T   R   FI F +   A+ A 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 332 KSLNRSDIAGKRIKLEPSRPGGARRN 357
           K +N   + GK IK+E ++    +  
Sbjct: 66  KDMNGKSLHGKAIKVEQAKKPSFQSG 91

>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 = 51.2 bits (123), Expect = 4e-08
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 12/89 (13%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAA 242
               LF+  +N    +  L+A+F ++G I        RT     K RGF  I++ +   A
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT----SKSRGFAFITFENPADA 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           + A + +  K L  + + +  +      S
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 60.0 bits (146), Expect = 3e-11
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V +L  +++ + LR IF  +G ++ I      ET   + + FI F D   A+ AL+ LN 
Sbjct: 31  VGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG 90

Query: 337 SDIAGKRIKLEPSRP 351
            ++AG+ +K+     
Sbjct: 91  FELAGRPMKVGHVTE 105

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 20/99 (20%), Positives = 43/99 (43%), Gaps = 5/99 (5%)

Query: 176 NGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRG 230
           + A  +A     G      L+V +++ N+ +  LR +FE +G I ++         + +G
Sbjct: 10  HMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG 69

Query: 231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           +  I++ D   A+ A+  L    L  R + +     + +
Sbjct: 70  YGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 59.5 bits (145), Expect = 4e-11
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           V NLD  + +E LR+ F  +G +   K + E    +   F+ F     A  A+  +N   
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI 79

Query: 339 IAGKRIKLEPSRPGGARRN 357
           +A K + +  ++    R++
Sbjct: 80  VATKPLYVALAQRKEERQS 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 = 47.6 bits (114), Expect = 6e-07
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 11/81 (13%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIRAARTAMR 247
           L+V+N++  ++D  LR  F  +G I    T+ K        +GF  + +     A  A+ 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTI----TSAKVMMEGGRSKGFGFVCFSSPEEATKAVT 73

Query: 248 ALQNKPLRRRKLDIHFSIPKD 268
            +  + +  + L +  +  K+
Sbjct: 74  EMNGRIVATKPLYVALAQRKE 94

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 59.7 bits (145), Expect = 4e-11
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 8/107 (7%)

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGE 303
           +  AL   PL    L    +       +    +G  L +++L    ++ DL   F  +G 
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEG--PEGCNLFIYHLPQEFTDTDLASTFLPFGN 66

Query: 304 VKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           V        ++T   +   F+ F +  +A+ A+K++N   +  KR+K
Sbjct: 67  VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK 113

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 44.7 bits (106), Expect = 7e-06
 Identities = 19/108 (17%), Positives = 47/108 (43%), Gaps = 14/108 (12%)

Query: 161 SDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIR 220
           + + S + L   ++   A   AG+   G      LF+ ++     D++L + F  +G++ 
Sbjct: 10  ASALSTSPLASVALSAAAAAAAGKQIEGPEGCN-LFIYHLPQEFTDTDLASTFLPFGNV- 67

Query: 221 TLYTACK---------HRGFVMISYYDIRAARTAMRALQNKPLRRRKL 259
               + K          + F  +S+ +  +A+ A++A+    +  ++L
Sbjct: 68  ---ISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL 112

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 58.9 bits (143), Expect = 4e-11
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 11/85 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRETPHKRHHK-----FIEFYDVRAAEAAL 331
           T+++ N+ P    + +      Y    V  IR    K+  +     F++      A   L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 332 KSLNRSD----IAGKRIKLEPSRPG 352
           + L        I GK I ++ ++  
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 15/94 (15%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD--------IRTLYTACKHRGFVMI 234
           G H    H   T+ +RNI  +     +      Y          I+   T  ++RGF  +
Sbjct: 2   GHHH--HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQ-QNRGFAFV 58

Query: 235 SYYDIRAARTAMRALQNKPLRR----RKLDIHFS 264
                  A   ++ LQ+         + + + F+
Sbjct: 59  QLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.9 bits (143), Expect = 5e-11
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           ++ V      V +  L + F A+G V  +     K     +E  DV A EA L   ++  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHS 68

Query: 339 IAGKRIKLEPSRP 351
           + G R+++ P   
Sbjct: 69  LGGHRLRVRPREQ 81

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G    R++FV      V+ ++L   F  +G + ++        F ++   D+ A    + 
Sbjct: 4   GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL- 62

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDK 273
           +     L   +L +     K+  S  
Sbjct: 63  SQSQHSLGGHRLRVRPREQKEFQSPA 88

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 58.6 bits (142), Expect = 6e-11
 Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 2/71 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK--FIEFYDVRAAEAALKSLNR 336
            L + N+ P +  E L  +   YG V+   +           + +     A  AL  LN 
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76

Query: 337 SDIAGKRIKLE 347
             +    +K+ 
Sbjct: 77  FQLENFTLKVA 87

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 52.1 bits (125), Expect = 1e-08
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 3/93 (3%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR--GFVMI 234
           G+   +G  P  +   R L +RNI  +++   L +L  QYG + +            V +
Sbjct: 1   GSSGSSGSVPKRQ-RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNV 59

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           +Y     AR A+  L    L    L + +   +
Sbjct: 60  TYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 3/83 (3%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSL 334
             + V NL    + + L+  F   G V       E    +    ++F     AE A + +
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           N   ++G+ I +   R      +
Sbjct: 69  NGMKLSGREIDVRIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 46.8 bits (112), Expect = 9e-07
 Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 11/91 (12%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIR 240
           G   +  +FVRN+  +     L+  F + G +                +G  ++ +    
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHV----LYADIKMENGKSKGCGVVKFESPE 59

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            A  A R +    L  R++D+        PS
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDRNASGPS 90

>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 = 57.7 bits (140), Expect = 2e-10
 Identities = 17/99 (17%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
           S           N   + V +L P ++ ED++  F  +G + +        T   + + F
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           + F++   AE A++ +    + G++I+   +        
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPK 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 = 47.7 bits (114), Expect = 6e-07
 Identities = 15/108 (13%), Positives = 44/108 (40%), Gaps = 7/108 (6%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGF 231
             + +            +FV +++  +   +++A F  +G       ++ + T  K +G+
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATG-KSKGY 59

Query: 232 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
             +S+++   A  A++ +  + L  R++  +++  K           T
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT 107

>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 = 56.4 bits (137), Expect = 2e-10
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           +L+ +V +E LR  F  +            +T   R + F+ F     A+ A+ S+   D
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 67

Query: 339 IAGKRIKLEPSRP 351
           + G+ +++  +  
Sbjct: 68  LNGRPLRINWAAK 80

>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 = 50.2 bits (121), Expect = 4e-08
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAARTA 245
           +  LFV ++N NV+D  LR  F+ +        +  + T    RG+  +S+     A+ A
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG-SSRGYGFVSFTSQDDAQNA 59

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           M ++Q + L  R L I+++   ++
Sbjct: 60  MDSMQGQDLNGRPLRINWAAKLEH 83

>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 = 57.3 bits (139), Expect = 2e-10
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           ++ V N+    + E L+ IF   G V        RET   + + F E+ D   A +A+++
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           LN  + +G+ ++++ +     + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKE 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 = 56.1 bits (136), Expect = 6e-10
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 6/99 (6%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIR 240
           P  +   R++FV NI     + +L+ +F + G + +          K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDN-PSDKDLNQG 278
            A +AMR L  +    R L +  +  + N    K L  G
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 56.5 bits (137), Expect = 3e-10
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR--HHK---FIEFYDVRAAEAALKS 333
           T+ V NL+  V  E L ++F   G + ++      R    K   F+ F    +   A+  
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVT-ICKDREGKPKSFGFVCFKHPESVSYAIAL 76

Query: 334 LNRSDIAGKRIK 345
           LN   + G+ I 
Sbjct: 77  LNGIRLYGRPIN 88

>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 = 55.7 bits (135), Expect = 6e-10
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFV 232
           G+   +G  P  E   RT+FV N+ + V +  L  LF Q G +  +        K + F 
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKL 259
            + +    +   A+  L    L  R +
Sbjct: 61  FVCFKHPESVSYAIALLNGIRLYGRPI 87

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 57.0 bits (138), Expect = 4e-10
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 13/86 (15%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKFIEFYDVR 325
           T+ V  L  +V+ E +   F   G +K               RET   +    + F D  
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRP 351
           +A+AA+   +  + +G  IK+  +  
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATR 94

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.6 bits (137), Expect = 6e-10
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 13/96 (13%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRT----------LYT---ACKHRGFVMISYY 237
            + T+FV+ +  NV    +   F+Q G I+T          LYT     K +G   +S+ 
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           D  +A+ A+     K      + + F+  + + +  
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101

>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 = 56.0 bits (136), Expect = 4e-10
 Identities = 13/73 (17%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           +L P ++   +   F  +G + + R      T   + + F+ F++   AE A++ +    
Sbjct: 13  DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72

Query: 339 IAGKRIKLEPSRP 351
           + G++I+   +  
Sbjct: 73  LGGRQIRTNWATR 85

>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 = 46.0 bits (110), Expect = 1e-06
 Identities = 14/83 (16%), Positives = 40/83 (48%), Gaps = 7/83 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAART 244
               +FV +++  +  + + A F  +G       ++ + T  K +G+  +S+++   A  
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATG-KSKGYGFVSFFNKWDAEN 63

Query: 245 AMRALQNKPLRRRKLDIHFSIPK 267
           A++ +  + L  R++  +++  K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 56.7 bits (137), Expect = 4e-10
 Identities = 11/89 (12%), Positives = 33/89 (37%), Gaps = 5/89 (5%)

Query: 273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDVRAAE 328
            D+   ++ +       + +D+++     G+V  I+      +  K   F+ F  + +A+
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARRN 357
             ++           + +       A++N
Sbjct: 67  KFVE-TPGQKYKETDLLILFKDDYFAKKN 94

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 8/77 (10%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAART 244
           +  +R+++++   ++    +++   E  G +  +          +G + + +  I +A+ 
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 245 AMRALQNKPLRRRKLDI 261
            +     +  +   L I
Sbjct: 68  FV-ETPGQKYKETDLLI 83

>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 = 56.5 bits (137), Expect = 5e-10
 Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 277 QGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAAL 331
             T L + NL  S+  ++L  +   +G+V   R     +   R   F         EA +
Sbjct: 24  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 332 KSLNRSDIAGKRIKLEPSRP 351
              N   I        P+ P
Sbjct: 84  GHFNGKFIKTPPGVSAPTEP 103

>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 = 44.9 bits (107), Expect = 6e-06
 Identities = 10/90 (11%), Positives = 27/90 (30%), Gaps = 17/90 (18%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDIRAARTAM 246
           L++ N+  ++++ EL  + + +G +     + +         RG               +
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQV----ISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 247 RALQNKPLRRRKLDIHFSIPK-----DNPS 271
                K ++        + P         S
Sbjct: 84  GHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113

>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 = 56.3 bits (136), Expect = 7e-10
 Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 13/101 (12%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RET 310
           S       D+D +   + V  L+ SV+ +DL   F   G VK               +ET
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 311 PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              +    + + D   A+AA++  +  D  G ++K+  +R 
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

>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 = 49.3 bits (118), Expect = 2e-07
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 13/93 (13%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-------------RGFVMISYYD 238
           +  ++V+ +N +V   +L   F+Q G ++      +              +G   +SY D
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

Query: 239 IRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
              A+ A+     K  +  KL +  +  K   +
Sbjct: 75  PPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>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 = 54.9 bits (133), Expect = 1e-09
 Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V NL  S ++E ++++F  +G+V  +     RET   +   F+E  +  +   A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           L+ +D  G+ I++  + P  +  +
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEH 85

>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 = 45.6 bits (109), Expect = 2e-06
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 247
           R ++V N+  +    +++ LF Q+G +  +         K +GF  +   +  +   A+ 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKD 274
            L N     R + +  + PK +     
Sbjct: 61  KLDNTDFMGRTIRVTEANPKKSLEHHH 87

>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 = 54.9 bits (133), Expect = 1e-09
 Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEA 329
               + + NLDP +  + L   F A+G + +        +T + + + FI F    A++A
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           A++++N   +  + I +  +    ++ +
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDSKGS 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 = 46.4 bits (111), Expect = 1e-06
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 14/92 (15%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----------RGFVMISYY 237
           G   S  +F+ N++  +++  L   F  +G I                   +G+  I++ 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFA 56

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
              A+  A+ A+  + L  R + + ++  KD+
Sbjct: 57  SFDASDAAIEAMNGQYLCNRPITVSYAFKKDS 88

>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 = 54.6 bits (132), Expect = 2e-09
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 5/91 (5%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
                S        + V N+  +VS +++   F  Y  +       +           + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           F     A AA+  LN   I  +++KL     
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 5/94 (5%)

Query: 179 GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVM 233
            + +     G+     + V+N+   V   E+   F  Y  I        +      G  M
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           +++     A  A+  L ++P+  RK+ +      
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 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 = 54.6 bits (132), Expect = 2e-09
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 13/95 (13%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH---------- 316
             +      +  T+ V  L  +V+ E +   F   G +K  ++T     +          
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 317 K---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
           K    + F D  +A+AA+   +  + +G  IK+  
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 13/82 (15%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-------------RGFVMISYY 237
            + T+FV+ +  NV    +   F+Q G I+T     +              +G   +S+ 
Sbjct: 12  DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71

Query: 238 DIRAARTAMRALQNKPLRRRKL 259
           D  +A+ A+     K      +
Sbjct: 72  DPPSAKAAIDWFDGKEFSGNPI 93

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 54.3 bits (130), Expect = 2e-09
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           S  L ++N+ + ++   LR L  Q+G + + +      G  +  Y     A  A  AL N
Sbjct: 7   SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-GIALCKYTTREEANKAQMALNN 65

Query: 252 KPLRRRKLDIHFSIPKDNPSDKDLNQ 277
             L    +          PS+ ++  
Sbjct: 66  CVLANTTIFAES------PSENEVQS 85

>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 = 54.2 bits (131), Expect = 2e-09
 Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 5/92 (5%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
                S        + V N+  +VS +++   F  Y  +       +           + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
           F     A AA+  LN   I  +++KL     G
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>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 = 50.4 bits (121), Expect = 5e-08
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFV 232
             + +     G+     + V+N+   V   E+   F  Y  I        +      G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
           M+++     A  A+  L ++P+  RK+ +   
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 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 = 54.5 bits (131), Expect = 3e-09
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 3/69 (4%)

Query: 279 TLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +LVV N  L   VS   L  +    G V  +   P+K  + F  +     ++ A  +LN 
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNG 85

Query: 337 SDIAGKRIK 345
            ++     +
Sbjct: 86  KEVVDDLGQ 94

>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 = 53.0 bits (127), Expect = 8e-09
 Identities = 13/90 (14%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 189 EHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM 246
            + +++L V N  + + V  ++L  + E+ G +  L     ++ +    Y     ++ A 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAY 80

Query: 247 RALQNK---PLRRRKLDIHFSIPKDNPSDK 273
             L  K       +K+ ++ +  +      
Sbjct: 81  VTLNGKEVVDDLGQKITLYLNFVEKVQWSG 110

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 55.6 bits (134), Expect = 4e-09
 Identities = 20/122 (16%), Positives = 41/122 (33%), Gaps = 5/122 (4%)

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
                     + KPL  +     F          +     L+V NLD  VS+ D++++F 
Sbjct: 52  GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVE-TGAKLLVSNLDFGVSDADIQELFA 110

Query: 300 AYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 355
            +G +K+       +        + F     A  A+K      + G+ + ++        
Sbjct: 111 EFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170

Query: 356 RN 357
            +
Sbjct: 171 EH 172

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 46.0 bits (109), Expect = 8e-06
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LYTAC-KHRGFVMISYYDIRA 241
             G      L V N++  V D++++ LF ++G ++     Y    +  G   + +     
Sbjct: 82  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 141

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
           A  AM+  +  PL  R +DI     + +      + 
Sbjct: 142 ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>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 = 53.4 bits (129), Expect = 4e-09
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 284 NLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           NL    ++EDL +   + G  ++ EI     R     +    +      +++  +  L +
Sbjct: 8   NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK 67

Query: 337 SDIAGKRIKLEPSRPGGARRN 357
            ++ G+   + PS       +
Sbjct: 68  RELHGQNPVVTPSNKLEHHHH 88

>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 = 42.6 bits (101), Expect = 3e-05
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 195 LFVRNINSNVEDSELRALFEQYG-----DIRTLY---TACKHRGFVMISYYDIRAARTAM 246
           L++ N+     D +L       G     +I+         + +GF ++      +++  M
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG-QSKGFALVGVGSEASSKKLM 62

Query: 247 RALQNKPLRRRKLDIHFSIPKD 268
             L  + L  +   +  S   +
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLE 84

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 54.3 bits (131), Expect = 4e-09
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
            L+V NLD  VS+ D++++F  +G +K+       +        + F     A  A+K  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96

Query: 335 NRSDIAGKRIKLEPSRPGGARR 356
               + G+ + ++         
Sbjct: 97  KGVPLDGRPMDIQLVASQIDLE 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 = 48.1 bits (115), Expect = 5e-07
 Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 12/98 (12%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 239
           G      L V N++  V D++++ LF ++G +                  G   + +   
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVDYDRSGRSLGTADVHFERR 86

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
             A  AM+  +  PL  R +DI     + +      + 
Sbjct: 87  ADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 54.3 bits (130), Expect = 4e-09
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSD 338
           ++V NL   V+ + L QIF  +G V +I         +  +++ D  +A+ A  SL+  +
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90

Query: 339 I--AGKRIKLEPSRP 351
           I  A   ++++ S+ 
Sbjct: 91  IYNACCTLRIDFSKL 105

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 50.8 bits (121), Expect = 9e-08
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 7/102 (6%)

Query: 172 YSVPNGAGTVAGEHPYGEHPSRTLF--VRNINSNVEDSELRALFEQYGDIRTLYTACKHR 229
               + A   AG        S  L   V N+   V    L  +F ++G +  + T  K+ 
Sbjct: 8   ALAASAAAVDAGMAM--AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN 65

Query: 230 GF-VMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIPKD 268
            F  ++ Y D  +A+ A  +L  + +      L I FS    
Sbjct: 66  QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 56.7 bits (136), Expect = 5e-09
 Identities = 21/113 (18%), Positives = 43/113 (38%), Gaps = 11/113 (9%)

Query: 256 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSN---------EDLRQIFGAYGEVKE 306
           R K   +        S +  N+ TL V  +D ++++           +R +F   G++  
Sbjct: 114 REKFADYREDMGGIGSFRKKNK-TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDR 172

Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
           IR     ++  F++F     AE A ++++   +     K    R  G    + 
Sbjct: 173 IR-YVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVK 224

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 50.2 bits (119), Expect = 8e-07
 Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 12/98 (12%)

Query: 183 GEHPYGEHPSRTLFVRNINSNV---------EDSELRALFEQYGDIRTL-YTACKHRGFV 232
           G        ++TL+V  I+  +          +S +R +F + GDI  + Y   K+ GFV
Sbjct: 125 GGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFV 184

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
              +     A  A  A+ N+ L            +   
Sbjct: 185 --KFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>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 = 53.4 bits (129), Expect = 5e-09
 Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 5/102 (4%)

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 308
           ++P +      H            +  G  L+V NLD  VS+ D++++F  +G +K+   
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 309 ---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
               +        + F     A  A+K  N   + G+ + ++
Sbjct: 62  HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 103

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 45.0 bits (107), Expect = 6e-06
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 239
           G      L V N++  V D++++ LF ++G +                  G   + +   
Sbjct: 25  GVETGGKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVHYDRSGRSLGTADVHFERK 80

Query: 240 RAARTAMRALQNKPLRRRKLDIHF 263
             A  AM+     PL  R ++I  
Sbjct: 81  ADALKAMKQYNGVPLDGRPMNIQL 104

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.8 bits (127), Expect = 9e-09
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 11/88 (12%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNE-------DLRQIFGAYGEVKEI---RETPHKRHH 316
           KD P + D     +VV N+ P V  +        + +IF  +G++       E    + +
Sbjct: 5   KDRPQEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGY 63

Query: 317 KFIEFYDVRAAEAALKSLNRSDIAGKRI 344
            F+E+     A  A+K+ +   +  +  
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQHT 91

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 9/75 (12%)

Query: 189 EHPSRTLFVRNINSNVEDSE------LRALFEQYGDIRTLYTAC---KHRGFVMISYYDI 239
           +     + V N+     D        +  +F ++G I   +      K +G++ + Y   
Sbjct: 12  DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASP 71

Query: 240 RAARTAMRALQNKPL 254
             A  A++      L
Sbjct: 72  AHAVDAVKNADGYKL 86

>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 = 57.9 bits (139), Expect = 1e-08
 Identities = 54/517 (10%), Positives = 130/517 (25%), Gaps = 181/517 (35%)

Query: 9   SGPPKIPQLNIPKE---------------------VGGGSCGRIAGSDSYLASDDASLFS 47
           +      + N+ +                       G    G+     +++A D     S
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK-----TWVALD--VCLS 173

Query: 48  SSLPVLPHEKLNLNA--MGLGR-QSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPD 104
             +      K++     + L    S + +   L K+ + +  +            +++  
Sbjct: 174 YKV----QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN----WTSRSDHSSNIKL 225

Query: 105 DEDELLAGIMDDFDLRGLPSSLEDLED------YDIFGSGGGMELEGEPQESLSMSMSKI 158
               + A +      +   + L  L +      ++ F                     KI
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS-----------------CKI 268

Query: 159 -------SISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRA 211
                   ++D  S     H S+                  ++L ++ ++   +D     
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISL------DHHSMTLTPDEVKSLLLKYLDCRPQD----- 317

Query: 212 LFEQYGDIRTLYTACKHRGFV--MIS--------------YYDIRAARTAMRA-LQN-KP 253
           L  +                   +I+              + +     T + + L   +P
Sbjct: 318 LPRE---------VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368

Query: 254 LRRRKLDIHFSI-PKDN--PSDKDLNQGTLVVF--NLDPSV-----------------SN 291
              RK+    S+ P     P+        L +   ++  S                    
Sbjct: 369 AEYRKMFDRLSVFPPSAHIPTI------LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422

Query: 292 EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV--------------------------R 325
           E    I   Y E+K   E  +  H   ++ Y++                          +
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLK 482

Query: 326 AAEAALKS-------LNRSDIAGK-RIKLEPSRPGGARRNLMLQLN------QELEQDES 371
             E   +        L+   +  K R         G+  N + QL        + +    
Sbjct: 483 NIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYE 542

Query: 372 RILQ------HQVGSPITNSPPGNWVQFSSPIEHNPL 402
           R++        ++   +  S   + ++ +   E   +
Sbjct: 543 RLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAI 579

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 6e-05
 Identities = 41/348 (11%), Positives = 90/348 (25%), Gaps = 116/348 (33%)

Query: 498 VETLSGP--QFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQ 555
           VE +     +FL    S        P+  T                 Y  ++      +Q
Sbjct: 83  VEEVLRINYKFLM---SPIKTEQRQPSMMTRM---------------YIEQRDRLYNDNQ 124

Query: 556 ---HHHVGSAPSGVPLER-RFGFLPESPETSFMNPVAFCGM-GIG--------------- 595
               ++V       P  + R   L   P  +    V   G+ G G               
Sbjct: 125 VFAKYNV---SRLQPYLKLRQALLELRPAKN----VLIDGVLGSGKTWVALDVCLSYKVQ 177

Query: 596 --QNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPAN 653
              +   F +N+ +  S    + + + L             ++ P +     +       
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLY-----------QIDPNWTSRSDHSSNIKLR 226

Query: 654 IEGLYERGR----SRRIEN------------------------------NNGNQLDSKKQ 679
           I  +    R    S+  EN                                 + L +   
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286

Query: 680 FQLELEKIRSGEDTRTTLMI---------KNIPN--KYTSKMLLAAIDE---NHKGTYDF 725
             + L+             +         +++P     T+   L+ I E   +   T+D 
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN 346

Query: 726 LYLPIDFKNKCNVGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNNN 773
            +  ++      +  + +N+L P      ++     ++    F  + +
Sbjct: 347 -WKHVNCDKLTTIIESSLNVLEPAEYRKMFD---RLSV----FPPSAH 386

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 10/78 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE----VKEIR--ETPHKRHHKFIEFYDVRAAEAALK 332
           +L + +L+P +    + + F   GE    VK IR   T     + F+EF D+  AE  L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 333 SLNRSDIAG----KRIKL 346
            +N   + G    KR KL
Sbjct: 71  KINGKPLPGATPAKRFKL 88

>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 = 43.1 bits (102), Expect = 2e-05
 Identities = 13/82 (15%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-------IRTLYTACKHRGFVMISYYDIRAAR 243
            + +L++ ++   ++++ +   F   G+       IR   T     G+  + + D+  A 
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTG-IPAGYCFVEFADLATAE 66

Query: 244 TAMRALQNKPLRRRKLDIHFSI 265
             +  +  KPL        F +
Sbjct: 67  KCLHKINGKPLPGATPAKRFKL 88

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.6 bits (126), Expect = 1e-08
 Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 12/83 (14%)

Query: 277 QGTLV-VFNLDPSVSNEDL---RQIFGAYGEVKEI-----RETPHKRHHK---FIEFYDV 324
           Q  LV V  L   +++ ++    + FG +G++ ++           +      ++ +   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 325 RAAEAALKSLNRSDIAGKRIKLE 347
             A  A++ +N   + G+ +K  
Sbjct: 74  EDALRAIQCVNNVVVDGRTLKAS 96

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.1 bits (91), Expect = 6e-04
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 11/85 (12%)

Query: 194 TLFVRNINSNVEDSEL---RALFEQYGDI-------RTLYTACK-HRGFVMISYYDIRAA 242
            +FV  ++  + D E+      F ++G I        T Y   +       ++Y     A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPK 267
             A++ + N  +  R L       K
Sbjct: 77  LRAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 52.4 bits (126), Expect = 1e-08
 Identities = 11/93 (11%), Positives = 30/93 (32%), Gaps = 6/93 (6%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----F 318
           S       D +  +    + N+  S++  D+ Q        +         + +      
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           ++F +   A  + + L+R  + G+   +     
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFVHVVTL 93

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.6 bits (98), Expect = 9e-05
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 6/86 (6%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYG----DIRTLYTAC-KHRGFVMISYYDIRAA 242
                    + NI  ++   ++    E        +  L     +  G  ++ + +   A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKD 268
           R + R L  K L  R+  +H    +D
Sbjct: 71  RKSER-LHRKKLNGREAFVHVVTLED 95

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           T+ V NLD  V  + L+++F   G V        +    R    + F     A  A+   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           N   +  + + ++       + +
Sbjct: 77  NGQLLFDRPMHVKMDERALPKGD 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 = 45.4 bits (108), Expect = 4e-06
 Identities = 17/100 (17%), Positives = 33/100 (33%), Gaps = 13/100 (13%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------H 228
           G+   +G    G     T+FV N++  V   +L+ +F   G +                 
Sbjct: 1   GSSGSSGALQAGR-LGSTVFVANLDYKVGWKKLKEVFSMAGVV----VRADILEDKDGKS 55

Query: 229 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
           RG   +++     A  A+     + L  R + +       
Sbjct: 56  RGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL 95

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
            +D  +   ++R  F  YG VKE++     T   + + F+ FY+    +  ++  ++ + 
Sbjct: 16  GIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINF 73

Query: 340 AGKRIKLEPSRP 351
            GK++KL P+  
Sbjct: 74  HGKKLKLGPAIR 85

>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 = 49.9 bits (120), Expect = 8e-08
 Identities = 23/103 (22%), Positives = 48/103 (46%), Gaps = 7/103 (6%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRA 241
           P G+    T+FV  I+  ++++E+R+ F +YG ++ +          +G+  +S+Y+   
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFN 284
            +  +          +KL +  +I K N S     Q   ++FN
Sbjct: 63  VQKIVE--SQINFHGKKLKLGPAIRKQNLSTYH-VQPRPLIFN 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 = 56.4 bits (135), Expect = 2e-08
 Identities = 25/113 (22%), Positives = 47/113 (41%), Gaps = 7/113 (6%)

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
              +   +  + +     +L +    P ++P+ +     TL V  ++   +   LR+ F 
Sbjct: 67  MERKRREKIERRQQEVETELKMW--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124

Query: 300 AYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            YG +K I     KR  K     FIE+   R   +A K  +   I G+R+ ++
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177

>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 = 49.1 bits (116), Expect = 4e-06
 Identities = 28/133 (21%), Positives = 48/133 (36%), Gaps = 7/133 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
             +TLFV  +N +  +S+LR  FE YG I+ ++        K RG+  I Y   R   +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

Query: 246 MRALQNKPL--RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
            +    K +  RR  +D+           + L  G          V+     +   +  +
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220

Query: 304 VKEIRETPHKRHH 316
            +        R  
Sbjct: 221 ERPGPSPLPHRDR 233

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 52.1 bits (125), Expect = 2e-08
 Identities = 14/98 (14%), Positives = 33/98 (33%), Gaps = 6/98 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
            +            + +  L     N+ +   F     V++     +  + K     F+E
Sbjct: 14  KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 73

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
           F +    +AAL   ++  +  + I++ P    G    +
Sbjct: 74  FRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKI 110

>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 = 39.4 bits (92), Expect = 7e-04
 Identities = 16/106 (15%), Positives = 38/106 (35%), Gaps = 15/106 (14%)

Query: 177 GAGTVAGEHPYGEHPSR---------TLFVRNINSNVEDSELRALFEQYG----DIRTLY 223
           G+   +G+ P G+  SR          ++++ +    E+  +   F++       I   Y
Sbjct: 1   GSSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY 60

Query: 224 TAC-KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
               K  G   + + +    + A+     + +  R + +H    K 
Sbjct: 61  GPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKG 105

>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 = 51.2 bits (123), Expect = 3e-08
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 8/94 (8%)

Query: 182 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 236
           +G     +H +  LF+  I  N+++ +L+ LFE++G I  L          H+G   ++Y
Sbjct: 3   SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

Query: 237 YDIRAARTAMRALQNK---PLRRRKLDIHFSIPK 267
            +  +A  A  AL  +   P   R + +  +  +
Sbjct: 63  CERESALKAQSALHEQKTLPGMNRPIQVKPADSE 96

>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 = 46.6 bits (111), Expect = 1e-06
 Identities = 14/71 (19%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
              KD +   L +  +  ++  +DL+ +F  +G++ E+     R T   +   F+ + + 
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 325 RAAEAALKSLN 335
            +A  A  +L+
Sbjct: 66  ESALKAQSALH 76

>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 = 50.7 bits (122), Expect = 4e-08
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK------FIEFYDVRAAEAALK 332
           T  + NL   V+ E +++ F     +  +R      + +      + EF D+ +  +AL 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            LN   +  KRI+++ +     + +
Sbjct: 76  -LNEESLGNKRIRVDVADQAQDKDS 99

>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 = 46.9 bits (112), Expect = 1e-06
 Identities = 13/97 (13%), Positives = 37/97 (38%), Gaps = 6/97 (6%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFV 232
             + +      + P  T F+ N+  +V +  ++  F           R      + +GF 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
              + D+ +  +A+ +L  + L  +++ +  +    +
Sbjct: 61  YAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD 96

>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 = 50.7 bits (122), Expect = 4e-08
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 10/88 (11%)

Query: 269 NPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYD 323
           + S+    +   L V  L+   S ED+ ++F  +G + E           +   F++F  
Sbjct: 6   SGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSS 65

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              A+AA+ +L+     G +     S  
Sbjct: 66  HTEAQAAIHALH-----GSQTMPGASSS 88

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 50.7 bits (122), Expect = 5e-08
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 10/97 (10%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAART 244
               R LFV  +N    + ++  LF+ +G I             +G   + +     A+ 
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71

Query: 245 AMRALQNK---PLRRRKLDIHFSIPKDNPSDKDLNQG 278
           A+ AL      P     L + F+   D   +   + G
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFA---DTDKESGPSSG 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 = 51.8 bits (124), Expect = 4e-08
 Identities = 17/97 (17%), Positives = 33/97 (34%), Gaps = 4/97 (4%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFY 322
                + +      + +  L    +  D+   F     V+  I   P  R      +EF 
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFA 94

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
               A AA+   +R+++  + I+L  +   GA     
Sbjct: 95  THEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAY 130

>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 = 51.1 bits (122), Expect = 4e-08
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 189 EHPSRTLFVRNI-NSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           +   R + + N+ +S   DS +  L E YG I+      + +    I       A   + 
Sbjct: 22  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVD 80

Query: 248 ALQNKP--LRRRKLDIHFS 264
               K    + R + +  S
Sbjct: 81  HCLKKALWFQGRCVKVDLS 99

>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 = 41.5 bits (97), Expect = 9e-05
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 4/75 (5%)

Query: 279 TLVVFNL-DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLN 335
            + + NL     S+  + ++   YG++K       K    FIE      A A +      
Sbjct: 27  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS-QAFIEMETREDAMAMVDHCLKK 85

Query: 336 RSDIAGKRIKLEPSR 350
                G+ +K++ S 
Sbjct: 86  ALWFQGRCVKVDLSE 100

>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 = 51.4 bits (123), Expect = 4e-08
 Identities = 19/93 (20%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----F 318
            + + + S    N G + +  L    + E++ Q F     V      P     K     F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           ++F     AE AL   ++  I  + I++  S  
Sbjct: 89  VQFASQELAEKALG-KHKERIGHRYIEVFKSSQ 120

>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 = 41.4 bits (97), Expect = 1e-04
 Identities = 12/101 (11%), Positives = 30/101 (29%), Gaps = 6/101 (5%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-----LYTACK 227
           S+  G     G +         + +R +       E+   F     +       +    K
Sbjct: 23  SMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK 82

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
             G   + +     A  A+     + +  R +++  S  ++
Sbjct: 83  ITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQEE 122

>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 = 50.8 bits (122), Expect = 7e-08
 Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 6/97 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 320
              + S KD     + V  L    ++  LR+ F  +G+++E      R+T   R + F+ 
Sbjct: 6   SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
             D  AAE A K  N   I G++  +  +  G   R+
Sbjct: 66  MADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRS 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 = 50.4 bits (121), Expect = 7e-08
 Identities = 25/121 (20%), Positives = 43/121 (35%), Gaps = 17/121 (14%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------K 227
            +G+        +     +FV  +  +  D+ LR  FE +GDI                K
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDI----EEAVVITDRQTGK 57

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 287
            RG+  ++  D  AA  A +   N  +  RK +++ +     P      Q    +    P
Sbjct: 58  SRGYGFVTMADRAAAERACKDP-NPIIDGRKANVNLAYLGAKPRS---LQTGFAIGVSGP 113

Query: 288 S 288
           S
Sbjct: 114 S 114

>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 = 50.1 bits (120), Expect = 7e-08
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 6/91 (6%)

Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVR 325
           S    N G + +  L    S E++ Q F     V      P     +     F++F    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
            AE ALK  ++  I  + I++  S     R 
Sbjct: 69  IAEKALK-KHKERIGHRYIEIFKSSRAEVRT 98

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.5 bits (123), Expect = 7e-08
 Identities = 11/80 (13%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAAL 331
            + V +     +++ L Q+  + G  +V E+     R     + +  +      +    L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 332 KSLNRSDIAGKRIKLEPSRP 351
           + L    + G+++ + P+  
Sbjct: 117 ELLPGKVLNGEKVDVRPATR 136

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 46.5 bits (110), Expect = 4e-06
 Identities = 11/104 (10%), Positives = 32/104 (30%), Gaps = 7/104 (6%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-------K 227
            N    +   +    +    ++V + +    D +L  +    G    +           +
Sbjct: 38  NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQ 97

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            +G+  +      +    +  L  K L   K+D+  +  ++   
Sbjct: 98  SKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141

>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 = 9e-08
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQI----FGAYGEVKEIRETPHKRHHK--FIEFYDVRAAEAALK 332
            + V N+D  +S ++L+Q+    F  +G+VK +  +PH  +     ++  +++ A  A+ 
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70

Query: 333 SLNRSDIAGKRIKLEPSRPGGAR 355
           SL+R  I  K+I +  +      
Sbjct: 71  SLHRYKIGSKKILVSLATGASGP 93

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 5/72 (6%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALK 332
           G  V+ +    V  + L  +F   G+V  +       T   +   F+E   +  A+  +K
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 333 SLNRSDIAGKRI 344
           S +   +  K  
Sbjct: 73  SFHGKRLDLKHR 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 196 FVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRALQ 250
            + +    V    L +LF + G +  +         K +GF+ +    +  A+  +++  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 251 NKPL 254
            K L
Sbjct: 76  GKRL 79

>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 = 48.6 bits (116), Expect = 2e-07
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            +VV  L PS S +DL+      G+V       ++     +EF        A++ L+ + 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADV--YRDGTGVVEFVRKEDMTYAVRKLDNTK 74

Query: 339 IAGKRIKLEPSRP 351
                 +    R 
Sbjct: 75  FRSHEGETAYIRV 87

>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 = 43.6 bits (103), Expect = 1e-05
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 5/82 (6%)

Query: 185 HPYGEHPSRT---LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRA 241
              G    R+   + V  +  +    +L+    + GD+   Y      G  ++ +     
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKED 62

Query: 242 ARTAMRALQNKPLRRRKLDIHF 263
              A+R L N   R  + +  +
Sbjct: 63  MTYAVRKLDNTKFRSHEGETAY 84

>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 = 48.0 bits (115), Expect = 4e-07
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 11/85 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK------FIEFYDVRAAEAALK 332
           T  + NL   V+ E +++ F     +  +R      + +      + EF D+ +  +AL 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            LN   +  +RI+++ +      ++
Sbjct: 80  -LNEESLGNRRIRVDVADQ---AQD 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 = 47.6 bits (114), Expect = 5e-07
 Identities = 14/92 (15%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG--DIRTLY---TACKHRGFVMISYY 237
                 + P  T F+ N+  +V +  ++  F       +R         + +GF    + 
Sbjct: 10  HRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFE 69

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           D+ +  +A+ +L  + L  R++ +  +    +
Sbjct: 70  DLDSLLSAL-SLNEESLGNRRIRVDVADQAQD 100

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 48.3 bits (115), Expect = 4e-07
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            +VV  L PS S +DL+      G+V       ++     +EF        A++ L+ + 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD--VYRDGTGVVEFVRKEDMTYAVRKLDNTK 75

Query: 339 IAGKRIKLEPSRP 351
                 +    R 
Sbjct: 76  FRSHEGETAYIRV 88

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 46.7 bits (111), Expect = 2e-06
 Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 2/87 (2%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G        P        + V  +  +    +L+    + GD+   Y      G  ++ +
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEF 58

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHF 263
                   A+R L N   R  + +  +
Sbjct: 59  VRKEDMTYAVRKLDNTKFRSHEGETAY 85

>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 = 50.5 bits (120), Expect = 5e-07
 Identities = 18/152 (11%), Positives = 43/152 (28%), Gaps = 13/152 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAAL 331
            L + NL    ++EDL +   + G  ++ EI     R     +    +      +++  +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 332 KSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWV 391
             L + ++ G+   + P       +       +   +  ++  Q             +  
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQ------FEMQSRKTTQSGQMSGEGKAGPPGGSSRA 183

Query: 392 QFSSPIEHNPLQTISKSPNFRNMSPTTSNHMP 423
            F            +     R   P      P
Sbjct: 184 AFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPP 215

>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 = 47.4 bits (112), Expect = 5e-06
 Identities = 14/111 (12%), Positives = 33/111 (29%), Gaps = 7/111 (6%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYTAC-----K 227
             G G               L++ N+     D +L       G  DI  +         +
Sbjct: 51  DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ 110

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 278
            +GF ++      +++  M  L  + L  +   +     +     +  ++ 
Sbjct: 111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

>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 = 47.1 bits (112), Expect = 1e-06
 Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK--FIEF 321
               P   + +   + V  +  S    D+R  F     V  +   +    R++    ++F
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKF 63

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              +    ALK  NR  +  + +++ P+  
Sbjct: 64  LSPQDTFEALK-RNRMLMIQRYVEVSPATE 92

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           T  V NL  +    D+  IF     ++ +R     +T   +   ++EF +V + + AL  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
            + + +  + ++++ +      ++
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKS 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLY---TACKHRGFVMISYYDIRAARTA 245
           P  T +V N+  N    ++ A+F+      +R +    T  K +GF  + + ++ + + A
Sbjct: 14  PPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTD-KFKGFCYVEFDEVDSLKEA 72

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +       L  R L +  +  +  
Sbjct: 73  L-TYDGALLGDRSLRVDIAEGRKQ 95

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 11/76 (14%)

Query: 279 TLVVFNLDPSVSNE-------DLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAE 328
            +VV N+ P V  +        + +IF  +G++       E    + + F+E+     A 
Sbjct: 3   VIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 329 AALKSLNRSDIAGKRI 344
            A+K+ +   +  +  
Sbjct: 62  DAVKNADGYKLDKQHT 77

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 9/70 (12%)

Query: 194 TLFVRNINSNVED------SELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAART 244
            + V N+     D      + +  +F ++G I   +      K +G++ + Y     A  
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

Query: 245 AMRALQNKPL 254
           A++      L
Sbjct: 63  AVKNADGYKL 72

>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 = 46.4 bits (111), Expect = 1e-06
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            +  +    +LR+ F  +G V E+      E    R   FI F D ++ + A+ +++  D
Sbjct: 17  GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHD 75

Query: 339 IAGKRI 344
           I GK++
Sbjct: 76  IMGKKV 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 = 42.6 bits (101), Expect = 3e-05
 Identities = 22/98 (22%), Positives = 44/98 (44%), Gaps = 14/98 (14%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVM 233
           G        S  +FV  I  N  ++ELR  F+++G +    T           + RGF  
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVV----TEVVMIYDAEKQRPRGFGF 56

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           I++ D ++   A+  +    +  +K+++  + P+D+ S
Sbjct: 57  ITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSKS 93

>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 = 45.8 bits (109), Expect = 2e-06
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFYDVRAAEAALKSLN 335
           T+ +     +V+ +++ +       V   I    H       F++F +    + ALK  N
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN 70

Query: 336 RSDIAGKRIKLEPSRPG 352
           R  + G+ I++   + G
Sbjct: 71  REYMGGRYIEVFREKSG 87

>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 = 45.9 bits (109), Expect = 2e-06
 Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 4/93 (4%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFYD 323
               S +      + +  L    +  D+   F     ++  I   P  R      +EF  
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFAT 64

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
              A AA+   +++++  + ++L  +   G   
Sbjct: 65  HEDAVAAMA-KDKANMQHRYVELFLNSTAGTSG 96

>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 = 45.3 bits (108), Expect = 3e-06
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  +FV     ++ + ELR  F QYGD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
                ++ ++LR+ F  YG+V ++      R   F+ F D + A++         I G  
Sbjct: 12  RCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGIS 69

Query: 344 IKLEPSRP 351
           + +  + P
Sbjct: 70  VHISNAEP 77

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 44.3 bits (105), Expect = 5e-06
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 13/78 (16%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHK-------RHHK---FIEFYDVRAAEAALKS 333
           N+   ++ E +   F A   +  + + P            K   F+EF  V     A+ +
Sbjct: 13  NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A 71

Query: 334 LNRSDIAGKRIKLEPSRP 351
            +     G+ +K+   RP
Sbjct: 72  FDGIIFQGQSLKI--RRP 87

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 11/80 (13%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA----------CKHRGFVMISYYDIRA 241
           +R L+V NI   + +  +   F     +  L  A           + + F  + +  +  
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65

Query: 242 ARTAMRALQNKPLRRRKLDI 261
              AM A      + + L I
Sbjct: 66  TTQAM-AFDGIIFQGQSLKI 84

>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 = 44.1 bits (105), Expect = 5e-06
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
           N S  + + G + V  L    S +DL+  F  +GEV +        T   R   FI F D
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 324 VRAAEAALKSLNRSDIAGKRI 344
             + E  L       + G+ I
Sbjct: 63  AASVEKVLDQKEH-RLDGRVI 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 = 39.1 bits (92), Expect = 3e-04
 Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 13/72 (18%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISY 236
              E  +  +FV  ++ +    +L+  F ++G++      C         + RGF  I +
Sbjct: 5   SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV----VDCTIKMDPNTGRSRGFGFILF 60

Query: 237 YDIRAARTAMRA 248
            D  +    +  
Sbjct: 61  KDAASVEKVLDQ 72

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 44.4 bits (105), Expect = 9e-06
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 2/79 (2%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRS 337
           + + NL    S +DL+ +               +       +EF        AL+ LN  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 338 DIAGKRIKLEPSRPGGARR 356
           +  G  I +E        R
Sbjct: 91  EFRGSVITVERDDNPPPIR 109

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 39.4 bits (92), Expect = 5e-04
 Identities = 11/98 (11%), Positives = 27/98 (27%), Gaps = 2/98 (2%)

Query: 166 GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD--IRTLY 223
           G+   H+   +G                 + ++N+       +L+ L  +       +  
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61

Query: 224 TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI 261
                 G   + +        A+  L N   R   + +
Sbjct: 62  NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
                        L+V  L    + +DL++ F  +GEV  +      +T H +   F+ F
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 322 YDVRAAEAALKSLNRSDIAGKRI 344
            +       +   +   I G+  
Sbjct: 65  TEYETQVKVMSQRH--MIDGRWC 85

>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 = 39.5 bits (93), Expect = 4e-04
 Identities = 11/95 (11%), Positives = 25/95 (26%), Gaps = 15/95 (15%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISY 236
                 +  L V  +     + +L+  F  +G++                  +GF  + +
Sbjct: 9   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEV----LMVQVKKDLKTGHSKGFGFVRF 64

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            +       M       +  R  D      K +  
Sbjct: 65  TEYETQVKVMSQRHM--IDGRWCDCKLPNSKQSQD 97

>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 = 42.9 bits (102), Expect = 1e-05
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 285 LDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L P    E +R+ FG +GEV+ I      +T  +R   FI F +    +  ++     ++
Sbjct: 7   LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNV 65

Query: 340 AGKRI 344
              + 
Sbjct: 66  GLSKC 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 = 40.9 bits (97), Expect = 5e-05
 Identities = 11/63 (17%), Positives = 26/63 (41%), Gaps = 13/63 (20%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 245
           +FV  ++ +  + ++R  F  +G++     +          K RGF  I++ +    +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEV----ESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 246 MRA 248
           M  
Sbjct: 58  MEK 60

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.5 bits (105), Expect = 1e-05
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 9/91 (9%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK--------FIEFYDVRAA 327
           NQ  + +  L  + + E++   FG +  +   +E      +         F+ F     A
Sbjct: 22  NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYA 81

Query: 328 EAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
           + AL+  ++  +  + I+L  S     ++ L
Sbjct: 82  QNALR-KHKDLLGKRYIELFRSTAAEVQQVL 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 = 43.8 bits (104), Expect = 1e-05
 Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 12/103 (11%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
           ++P +    +      L +  L    + E LR  +  +G++ +        +   R   F
Sbjct: 14  TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKL------EPSRPGGAR 355
           + F  +   +AA+ +     I G+ ++       E S  G + 
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESGSGPSS 115

>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 = 40.0 bits (94), Expect = 4e-04
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 14/98 (14%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVM 233
                 +   R LF+  ++    +  LR  +EQ+G +    T C         + RGF  
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKL----TDCVVMRDPASKRSRGFGF 73

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           +++  +     AM A +   +  R ++   ++ ++   
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESG 110

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 12/80 (15%), Positives = 23/80 (28%), Gaps = 4/80 (5%)

Query: 191 PSRTLFVRNI-NSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
             R + + +         +L  L E +G I              I       A+ A+   
Sbjct: 14  TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYY 72

Query: 250 QNKP--LRRRKLDIHFSIPK 267
              P  +  + + +H S   
Sbjct: 73  TTTPALVFGKPVRVHLSQKY 92

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
                ++ E+L+Q F  YGEV ++      R   F+ F D + A++         I G  
Sbjct: 18  RCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCG--EDLIIKGIS 75

Query: 344 IKLEPSRPGGARRN 357
           + +  + P   + N
Sbjct: 76  VHISNAEPKHNKLN 89

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G H +  H S+ +FV     ++   EL+  F QYG++  ++     R F  +++ D + A
Sbjct: 3   GSHHHHHHGSK-VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDN 269
           ++     ++  ++   + I  + PK N
Sbjct: 62  QSLCG--EDLIIKGISVHISNAEPKHN 86

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 44.8 bits (105), Expect = 3e-05
 Identities = 8/75 (10%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDVRAAEAALKSL 334
           ++ +       + +D+++     G+V  I+      +  K   F+ F  + +A+  +++ 
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170

Query: 335 NRSDIAGKRIKLEPS 349
            +       + +   
Sbjct: 171 GQK-YKETDLLILFK 184

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 43.0 bits (101), Expect = 3e-05
 Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 8/93 (8%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY---GEVKEIRETPHKRHHK----F 318
                  +      + +  L  S S ED++           V  +     +   +    F
Sbjct: 6   SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAF 65

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           +E       + ALK  +R  +  + I++  S  
Sbjct: 66  VELESEDDVKLALK-KDRESMGHRYIEVFKSHR 97

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.1 bits (95), Expect = 1e-04
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 285 LDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L  + + ED++  F  +G+V +      + T   R   F+ F      E   +  +  +I
Sbjct: 7   LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEI 65

Query: 340 AGKRI 344
             K +
Sbjct: 66  NNKMV 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 = 40.1 bits (95), Expect = 1e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 245
           +FV  ++ N    +++  FEQ+G +                +HRGF  +++         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKV----DDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 246 MRA 248
              
Sbjct: 58  CEI 60

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 11/68 (16%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRGFVMISYYDIR 240
           G   SR +FV  +  ++++ E+ A F ++G +   +       +    +G+  + + +  
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 241 AARTAMRA 248
           + +  + A
Sbjct: 64  SVQALIDA 71

>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 = 13/85 (15%), Positives = 32/85 (37%), Gaps = 15/85 (17%)

Query: 282 VF--NLDPSVSNEDLRQIFGAYGEVKEI-------RETPHKRHHKFIEFYDVRAAEAALK 332
           VF   L P +  +++   F  +G +          +     + + F+ F +  + +A + 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 333 SLNRSD------IAGKRIKLEPSRP 351
           +    D      ++   IK +P + 
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDKPVQI 95

>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 = 41.1 bits (97), Expect = 1e-04
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 10/92 (10%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
            +P+ +          + +  L    + E LR+ FG +GEVKE        T   R   F
Sbjct: 14  LVPRGSHMGSS--GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
           + F D    +  L   +R ++  K I  +P  
Sbjct: 72  VTFMDQAGVDKVLAQ-SRHELDSKTI--DPKV 100

>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 = 41.0 bits (96), Expect = 1e-04
 Identities = 11/89 (12%), Positives = 29/89 (32%), Gaps = 8/89 (8%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY---GEVKEIRETPHKRHHK----FIE 320
               ++  +   +    L  S + ED+   F           I    ++   +     IE
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPS 349
               +  + AL+  +R  +  + +++   
Sbjct: 62  MESEQDVQKALE-KHRMYMGQRYVEVYEI 89

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           + +  L    + E LR+ FG +GEVKE        T   R   F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 335 NRSDIAGKRIKLEPSR 350
           +R ++  K I  +P  
Sbjct: 62  SRHELDSKTI--DPKV 75

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 38.6 bits (91), Expect = 4e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 245
           +F+  ++       LR  F Q+G++      C         + RGF  +++ D       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV----KECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 246 MRA 248
           +  
Sbjct: 59  LAQ 61

>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 = 40.3 bits (95), Expect = 2e-04
 Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 14/101 (13%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------K 227
           G+   +G +  G      LFV  ++ +     LR+ F QYG++      C         +
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEV----VDCVIMKDKTTNQ 56

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
            RGF  + + D     T + + +   L  R +D     P+ 
Sbjct: 57  SRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRG 96

>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 = 39.5 bits (93), Expect = 4e-04
 Identities = 24/89 (26%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
               +      G L V  LD S + E LR  F  YGEV +      + T   R   F++F
Sbjct: 6   SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
            D       L S     + G+ I  +P  
Sbjct: 66  KDPNCVGTVLAS-RPHTLDGRNI--DPKP 91

>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 Length = 104

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 6/86 (6%)

Query: 188 GEHPSRTLFVRNINSNV-----EDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G   S  L     N +V       ++  +LF  Y    T +   K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTT-FQYFKSFKRVRINFSNPLSA 59

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKD 268
             A   L       +++ ++F+    
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLH 85

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 284 NLDPSVSNEDLRQIFGA-YGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN-RS 337
           +L P V +  L + F   Y   +  +    +T   + + F++F D    + AL       
Sbjct: 16  DLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAV 75

Query: 338 DIAGKRIKLEPSRPGGARR 356
            +  K ++L  + P  +R 
Sbjct: 76  GLGSKPVRLSVAIPKASRV 94

>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 = 41.7 bits (97), Expect = 7e-04
 Identities = 28/140 (20%), Positives = 43/140 (30%), Gaps = 28/140 (20%)

Query: 256 RRKLDIHFSI-PKDNPSDKDLNQGTLVVFNLDPS--VSNEDLRQIFGAYGEVKEIRETPH 312
           +  L  H  I      +        LVV N      VS   L  +    G V  +   P+
Sbjct: 2   KHTLLRHEGIETVSYATQS------LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 55

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           K  + F  +     ++ A  +LN           E     G +  L L   ++++  E R
Sbjct: 56  KP-YSFARYRTTEESKRAYVTLNGK---------EVVDDLGQKITLYLNFVEKVQWKELR 105

Query: 373 ILQHQVGSPITNSPPGNWVQ 392
                        PPG  V 
Sbjct: 106 ---------PQALPPGLMVV 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	780
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.98
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.95
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.94
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.8
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.79
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.79
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.77
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.77
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.77
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.77
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.75
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.72
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.72
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.7
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.65
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.65
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.64
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.64
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.63
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.62
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.6
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.6
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.59
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.59
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.58
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.58
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.58
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.58
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.57
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.57
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.57
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.56
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.56
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.56
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.56
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.56
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.56
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.56
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.56
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.56
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.56
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.56
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.56
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.56
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.55
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.55
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.55
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.55
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.55
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.55
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.55
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.55
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.55
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.54
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.54
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.54
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.54
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.54
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.54
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.54
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.54
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.54
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.54
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.54
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.54
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.54
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.54
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.54
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.54
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.54
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.54
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.54
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.53
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.53
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.53
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.53
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.53
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.53
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.53
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.53
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.53
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.53
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.53
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.53
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.53
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.53
2div_A	99	TRNA selenocysteine associated protein; structural	99.53
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.53
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.52
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.52
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.52
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.52
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.52
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.52
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.52
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.52
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.52
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.52
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.52
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.52
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.52
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.52
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.52
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.52
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.52
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.52
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.52
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.52
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.52
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.52
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.52
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.52
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.52
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.52
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.51
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.51
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.51
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.51
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.51
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.51
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.51
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.51
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.51
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.51
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.51
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.51
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.51
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.51
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.51
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.51
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.51
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.51
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.51
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.5
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.5
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.5
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.5
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.5
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.5
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.5
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.5
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.5
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.5
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.5
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.5
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.5
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.5
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.5
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.5
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.5
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.5
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.5
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.5
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.5
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.5
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.5
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.5
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.49
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.49
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.49
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.49
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.49
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.49
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.49
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.49
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.49
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.49
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.49
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.49
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.49
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.49
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.49
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.49
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.49
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.48
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.48
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.48
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.48
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.48
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.48
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.48
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.48
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.48
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.48
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.48
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.48
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.48
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.48
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.48
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.48
2div_A	99	TRNA selenocysteine associated protein; structural	99.48
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.48
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.48
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.48
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.48
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.48
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.48
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.48
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.47
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.47
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.47
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.47
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.47
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.47
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.47
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.47
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.47
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.47
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.47
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.47
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.47
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.47
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.47
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.47
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.47
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.47
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.47
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.47
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.47
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.47
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.46
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.46
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.46
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.46
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.46
1x5p_A	97	Negative elongation factor E; structure genomics,	99.46
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.46
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.46
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.46
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.46
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.46
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.46
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.46
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.46
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.46
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.46
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.46
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.46
1x5p_A	97	Negative elongation factor E; structure genomics,	99.45
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.45
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.45
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.45
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.45
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.45
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.45
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.45
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.45
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.45
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.44
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.44
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.44
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.44
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.44
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.43
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.43
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.43
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.43
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.43
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.43
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.42
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.42
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.42
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.42
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.42
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.42
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.42
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.42
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.42
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.42
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.41
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.41
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.41
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.41
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.41
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.4
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.4
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.4
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.4
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.4
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.4
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.39
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.39
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.39
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.38
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.38
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.38
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.38
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.37
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.37
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.37
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.37
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.37
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.37
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.37
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.37
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.37
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.36
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.36
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.36
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.35
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.35
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.35
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.34
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.34
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.34
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.34
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.33
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.33
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.33
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.33
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.33
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.32
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.32
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.32
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.31
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.31
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.3
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.3
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.28
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.28
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.27
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.26
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.24
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.24
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.24
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.23
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.23
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.23
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.2
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.16
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.15
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.12
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.11
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.11
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.06
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.05
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.03
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.02
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.01
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.97
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.95
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.94
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.79
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.72
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.64
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.48
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.42
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.37
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.35
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.33
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	98.32
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.19
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.15
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.0
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.55
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.55
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.3
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.97
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.51
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.44
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.67
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.62
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.94
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	93.58
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	92.92
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	92.53
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.14
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	91.57
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.55
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	90.14
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	88.13

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=1.7e-32  Score=290.10  Aligned_cols=238  Identities=16%  Similarity=0.231  Sum_probs=199.6

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcEEEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHPYGE  189 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~~~~e  189 (780)
                      .+.++|++||.++++.+++++|+.+|-+.+..    ...+|++++.|.+...|..    +++..+.+....+..     .
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~Gi~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~-----~   92 (284)
T 3smz_A           22 RRKILIRGLPGDVTNQEVHDLLSDYELKYCFV----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL-----Q   92 (284)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTSCEEEEEE----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE-----C
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCEEEEE----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe-----c
Confidence            46899999999999999999999999334443    4567899999998766642    233334433333222     2


Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||+++|+++|+++|++||.|..++     .+++++|||||+|.+.++|.+|++.|+|..+.|++|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            3568999999999999999999999999999886     26789999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCccceeecCCCCCC-ChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 004002          265 IPKDNPSDKDLNQGTLVVFNLDPSV-SNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (780)
Q Consensus       265 ~pk~~~s~~~~~~~~L~V~NLp~~v-teedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i  339 (780)
                      .++.... ......+|||+|||.++ ++++|+++|++||.|..|++    ++.++|+|||+|.+.++|.+|++.|||..+
T Consensus       173 ~~~~~~~-~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  251 (284)
T 3smz_A          173 DAGQLTP-ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSL  251 (284)
T ss_dssp             CGGGCCT-TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCc-ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Confidence            8765432 33456789999999996 99999999999999999875    456789999999999999999999999999


Q ss_pred             CCceEEEEecCCCchhhhHhhh
Q 004002          340 AGKRIKLEPSRPGGARRNLMLQ  361 (780)
Q Consensus       340 ~Gr~L~V~~a~~k~~r~~~l~q  361 (780)
                      .|++|+|.++.++..++..+.+
T Consensus       252 ~g~~l~v~~a~~~~~~~~~~~~  273 (284)
T 3smz_A          252 GGSHLRVSFCAPGPPGRSMLAA  273 (284)
T ss_dssp             TTEECEEEECCSSSCHHHHHHH
T ss_pred             CCeEEEEEEecCCCcccchhhh
Confidence            9999999999999877654443

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.98  E-value=6.4e-32  Score=286.85  Aligned_cols=230  Identities=18%  Similarity=0.287  Sum_probs=188.3

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCccc---ccccCCCCcccCCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGLL---HYSVPNGAGTVAGEHPY  187 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~~---~~~l~n~~~k~~g~~~~  187 (780)
                      .+.++|++||.++++.+++++|+.+|.|   .|..+...  .++++++.|.+...|..+.   +..+.+....+..    
T Consensus        41 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~----  114 (292)
T 2ghp_A           41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSH----  114 (292)
T ss_dssp             -CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEE----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEE----
Confidence            4789999999999999999999999997   44444432  4799999999887665332   2223222222221    


Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCC-CEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG-~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                        ...++|||+|||+++++++|+++|++|| +|..|+.    .++++|||||+|.+.++|++|++.|+|..|.|++|.|.
T Consensus       115 --~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  192 (292)
T 2ghp_A          115 --LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK  192 (292)
T ss_dssp             --CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             --CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence              2578999999999999999999999999 9999873    36789999999999999999999999999999999999


Q ss_pred             cCCCCCCCCC---CCCCccceeecCCCCC-CChhHHHHHhcccCCeeEEEeC------CCcccEEEEEEcCHHHHHHHHH
Q 004002          263 FSIPKDNPSD---KDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALK  332 (780)
Q Consensus       263 ~a~pk~~~s~---~~~~~~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~------g~srG~aFV~F~~~e~A~~Ai~  332 (780)
                      ++.+......   ......+|||+|||.+ +++++|+++|++||.|..|++.      +.++|||||+|.+.++|.+|+ 
T Consensus       193 ~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-  271 (292)
T 2ghp_A          193 VSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-  271 (292)
T ss_dssp             ECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-
T ss_pred             ECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-
Confidence            9987654332   2334579999999999 9999999999999999999862      677899999999999999999 


Q ss_pred             HhCCCccCCceEEEEecCCC
Q 004002          333 SLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       333 ~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      .|||..+.|++|+|.+++++
T Consensus       272 ~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          272 QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             GGTTEEETTEEEEEEECCCC
T ss_pred             HhcCCEECCcEEEEEEecCC
Confidence            99999999999999999886

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=8.6e-31  Score=267.03  Aligned_cols=165  Identities=19%  Similarity=0.351  Sum_probs=147.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||+++|+++|+++|++||+|.+|+.     +++++|||||+|.+.++|++|++.+++..+.|+.|++.++
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            46789999999999999999999999999999872     5889999999999999999999999999999999999988


Q ss_pred             CCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 004002          265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (780)
Q Consensus       265 ~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G  341 (780)
                      ......  ......+|||+|||.++|+++|+++|++||.|+.|++   .+.++|||||+|.+.++|++||+.|||..|.|
T Consensus        93 ~~~~~~--~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g  170 (213)
T 4f02_A           93 QRDPSL--RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLND  170 (213)
T ss_dssp             CCCTHH--HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             cccccc--cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            654321  2224568999999999999999999999999999976   34578999999999999999999999999999


Q ss_pred             ceEEEEecCCCchhh
Q 004002          342 KRIKLEPSRPGGARR  356 (780)
Q Consensus       342 r~L~V~~a~~k~~r~  356 (780)
                      ++|+|.+++++.++.
T Consensus       171 ~~i~V~~a~~~~~~~  185 (213)
T 4f02_A          171 RKVFVGRFKSRKERE  185 (213)
T ss_dssp             EECEEEECCCHHHHH
T ss_pred             EEEEEEEcCCCcccc
Confidence            999999999876544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.96  E-value=2.4e-29  Score=242.70  Aligned_cols=157  Identities=20%  Similarity=0.361  Sum_probs=143.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      |+|||+|||.++|+++|+++|++||+|.+++.    .++++|||||+|.+.++|++|++.|+|..+.|++|.|.++.+..
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            68999999999999999999999999999873    47789999999999999999999999999999999999987665


Q ss_pred             CCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce
Q 004002          269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  343 (780)
Q Consensus       269 ~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~  343 (780)
                      ..  ......+|||+|||.++++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.|++
T Consensus        81 ~~--~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  158 (166)
T 3md3_A           81 QS--SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP  158 (166)
T ss_dssp             CC--CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CC--CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Confidence            42  3345679999999999999999999999999999876     4667899999999999999999999999999999


Q ss_pred             EEEEecCC
Q 004002          344 IKLEPSRP  351 (780)
Q Consensus       344 L~V~~a~~  351 (780)
                      |+|.+|++
T Consensus       159 i~v~~a~~  166 (166)
T 3md3_A          159 LRINWAAK  166 (166)
T ss_dssp             CEEEESCC
T ss_pred             EEEEecCC
Confidence            99999864

>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=7.9e-29  Score=240.15  Aligned_cols=155  Identities=23%  Similarity=0.431  Sum_probs=142.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ++++|||+|||+++++++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
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            568999999999999999999999999999987     267789999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~  340 (780)
                      +...    .....+|||+|||.++++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.
T Consensus        82 ~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  157 (168)
T 1b7f_A           82 PGGE----SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE  157 (168)
T ss_dssp             CCSS----TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCcc----cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEec
Confidence            7543    335679999999999999999999999999999875     4566899999999999999999999999998


Q ss_pred             C--ceEEEEec
Q 004002          341 G--KRIKLEPS  349 (780)
Q Consensus       341 G--r~L~V~~a  349 (780)
                      |  ++|+|++|
T Consensus       158 g~~~~l~V~~A  168 (168)
T 1b7f_A          158 GGSQPLSVRLA  168 (168)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCCeEEEEEeC
Confidence            8  99999886

>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=9.9e-29  Score=238.55  Aligned_cols=155  Identities=25%  Similarity=0.441  Sum_probs=141.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ++++|||+|||+++|+++|+++|++||+|.+++.     +++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
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            3689999999999999999999999999999872     67889999999999999999999999999999999999988


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~  340 (780)
                      +...    .....+|||+|||..+++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.
T Consensus        81 ~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  156 (167)
T 1fxl_A           81 PSSA----SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS  156 (167)
T ss_dssp             CCCG----GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCcc----cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccC
Confidence            6542    335578999999999999999999999999999876     4556899999999999999999999999999


Q ss_pred             Cce--EEEEec
Q 004002          341 GKR--IKLEPS  349 (780)
Q Consensus       341 Gr~--L~V~~a  349 (780)
                      |+.  |+|++|
T Consensus       157 g~~~~i~v~~A  167 (167)
T 1fxl_A          157 GATEPITVKFA  167 (167)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCccceEEEeC
Confidence            964  888875

>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=2.1e-28  Score=247.15  Aligned_cols=163  Identities=20%  Similarity=0.387  Sum_probs=144.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      +.++|||+|||.++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4589999999999999999999999999999984     67799999999999999999999999999999999998876


Q ss_pred             CCCCCC-------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 004002          266 PKDNPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       266 pk~~~s-------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                      ......       .......+|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|.+|++.
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH
Confidence            543211       01234579999999999999999999999999999976     456789999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCCc
Q 004002          334 LNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       334 LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      |||..|.|+.|+|.++.++.
T Consensus       187 l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          187 MNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HTTCBCSSSBCEEEECSSCS
T ss_pred             ccCCEeCCcEEEEEEecCCC
Confidence            99999999999999998764

>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=2.8e-28  Score=242.50  Aligned_cols=167  Identities=19%  Similarity=0.370  Sum_probs=140.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      .....++|||+|||+++|+++|+++|++||+|.+|+.     +++++|||||+|.+.++|++|++. ++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            3446799999999999999999999999999999872     577899999999999999999985 8999999999999


Q ss_pred             cCCCCCCCCC--CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhC
Q 004002          263 FSIPKDNPSD--KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN  335 (780)
Q Consensus       263 ~a~pk~~~s~--~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~Ln  335 (780)
                      ++.+......  ......+|||+|||.++|+++|+++|++||.|+.|++     ++.++|||||+|.+.++|.+||.. +
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~  166 (196)
T 1l3k_A           88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-K  166 (196)
T ss_dssp             ECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-S
T ss_pred             cccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-C
Confidence            9876543321  2234579999999999999999999999999999976     466799999999999999999986 8


Q ss_pred             CCccCCceEEEEecCCCchhh
Q 004002          336 RSDIAGKRIKLEPSRPGGARR  356 (780)
Q Consensus       336 G~~i~Gr~L~V~~a~~k~~r~  356 (780)
                      |..+.|+.|.|.++.++.+..
T Consensus       167 ~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          167 YHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             CCEETTEECEEEECC------
T ss_pred             CcEECCEEEEEEecCChhHhc
Confidence            999999999999999876543

>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=5.7e-29  Score=243.69  Aligned_cols=161  Identities=19%  Similarity=0.279  Sum_probs=144.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE----EeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv----~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+.++|||+|||.++|+++|+++|++||.|..+    ..+++++|||||+|.+.++|++|++ |++..+.|++|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            3467999999999999999999999999864331    1468899999999999999999995 9999999999999999


Q ss_pred             CCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 004002          265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (780)
Q Consensus       265 ~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L  344 (780)
                      .++...  ......+|||+|||.++++++|+++|++||.|..+..++.++|+|||+|.+.++|.+|++.|||..+.|++|
T Consensus        89 ~~~~~~--~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  166 (175)
T 1fje_B           89 KGRDSK--KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV  166 (175)
T ss_dssp             CCSSCS--TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEE
T ss_pred             CCcccc--ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            876532  334567999999999999999999999999999996678889999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 004002          345 KLEPSRPG  352 (780)
Q Consensus       345 ~V~~a~~k  352 (780)
                      +|.+++++
T Consensus       167 ~v~~a~~k  174 (175)
T 1fje_B          167 SLYYTGEK  174 (175)
T ss_dssp             EEEECSSC
T ss_pred             EEEecCCC
Confidence            99999876

>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=8.5e-28  Score=253.84  Aligned_cols=163  Identities=23%  Similarity=0.449  Sum_probs=145.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HHhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr----~lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ..++++|||+|||.++|+++|+    ++|++||+|.+|+.  +++++|||||+|.+.++|++|++.|+|..|.|++|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   85 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   85 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            3578999999999999999977    89999999999883  78899999999999999999999999999999999999


Q ss_pred             cCCCCCCCC-----------------------------------------------------------------------
Q 004002          263 FSIPKDNPS-----------------------------------------------------------------------  271 (780)
Q Consensus       263 ~a~pk~~~s-----------------------------------------------------------------------  271 (780)
                      |+..+....                                                                       
T Consensus        86 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  165 (282)
T 3pgw_A           86 YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMP  165 (282)
T ss_pred             EeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCC
Confidence            986544200                                                                       


Q ss_pred             ------------------------------------CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCccc
Q 004002          272 ------------------------------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH  315 (780)
Q Consensus       272 ------------------------------------~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG  315 (780)
                                                          .......+|||+|||.++++++|+++|++||.|+.|++....+|
T Consensus       166 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g  245 (282)
T 3pgw_A          166 PPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD  245 (282)
T ss_pred             CCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCc
Confidence                                                01113467999999999999999999999999999998766679


Q ss_pred             EEEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecCC
Q 004002          316 HKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRP  351 (780)
Q Consensus       316 ~aFV~F~~~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~~  351 (780)
                      +|||+|.+.++|++|++.|||..+. |+.|+|.|+++
T Consensus       246 ~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          246 IAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             EEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence            9999999999999999999999999 99999999863

>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=1.4e-27  Score=245.98  Aligned_cols=163  Identities=26%  Similarity=0.359  Sum_probs=146.1

Q ss_pred             CCCcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          190 HPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       190 ~~s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      .++++|||+|||+ ++++++|+++|++||+|.+|+.....+|||||+|.+.++|++|++.|+|..+.|++|.|.++.++.
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  111 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN  111 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCcc
Confidence            4679999999999 999999999999999999998655568999999999999999999999999999999999987552


Q ss_pred             CCCCC-------------------------------CCCccceeecCCCCCCChhHHHHHhcccC-CeeEEEeCCCcccE
Q 004002          269 NPSDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHH  316 (780)
Q Consensus       269 ~~s~~-------------------------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG-~I~~v~~~g~srG~  316 (780)
                      ....+                               .....+|||+|||.++++++|+++|++|| .|..|++....+|+
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~  191 (229)
T 2adc_A          112 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM  191 (229)
T ss_dssp             CCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTC
T ss_pred             ccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcE
Confidence            11100                               11246899999999999999999999999 99999997777999


Q ss_pred             EEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecCCC
Q 004002          317 KFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRPG  352 (780)
Q Consensus       317 aFV~F~~~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~~k  352 (780)
                      |||+|.+.++|.+|++.|||..+. |++|+|.+++++
T Consensus       192 afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          192 ALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999999999999999999999999 999999999874

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.95  E-value=1.8e-28  Score=237.66  Aligned_cols=155  Identities=20%  Similarity=0.434  Sum_probs=140.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ++++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
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            468999999999999999999999999999998     2578999999999999999999994  678999999999886


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~  340 (780)
                      ++.    ......+|||+|||.++++++|+++|++||.|..|++     ++.++|+|||+|.+.++|.+|++ ++|..+.
T Consensus        80 ~~~----~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~  154 (167)
T 2cjk_A           80 PRD----EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFK  154 (167)
T ss_dssp             CHH----HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSS
T ss_pred             chh----hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeC
Confidence            543    2234568999999999999999999999999999975     46678999999999999999998 8999999


Q ss_pred             CceEEEEecCCC
Q 004002          341 GKRIKLEPSRPG  352 (780)
Q Consensus       341 Gr~L~V~~a~~k  352 (780)
                      |++|+|.++.++
T Consensus       155 g~~i~V~~a~pk  166 (167)
T 2cjk_A          155 DRKIEIKRAEPR  166 (167)
T ss_dssp             SSCEEEEECCCC
T ss_pred             CeEEEEeecCCC
Confidence            999999999886

>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=99.95  E-value=1e-27  Score=233.54  Aligned_cols=157  Identities=20%  Similarity=0.405  Sum_probs=137.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CC--CcceEEEEEEecHHHHHHHHHHccCcccc---ccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----AC--KHRGFVMISYYDIRAARTAMRALQNKPLR---RRKLD  260 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tg--kskG~aFV~F~~~e~A~~Al~~Lng~~l~---gr~I~  260 (780)
                      ..++|||+|||+++|+++|+++|++||+|.+|+.     ++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            4689999999999999999999999999999872     22  79999999999999999999999998875   56777


Q ss_pred             cccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCC
Q 004002          261 IHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  336 (780)
Q Consensus       261 V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG  336 (780)
                      +.++.+...   ......+|||+|||.++|+++|+++|++||.|+.|++    ++.++|||||+|.+.++|.+|++.|||
T Consensus        82 ~~~~~~~~~---~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           82 MKPADSEKN---NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEECGGGCC---SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             Ecccccccc---ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            776654432   2335679999999999999999999999999999976    455789999999999999999999999


Q ss_pred             CccC---CceEEEEecC
Q 004002          337 SDIA---GKRIKLEPSR  350 (780)
Q Consensus       337 ~~i~---Gr~L~V~~a~  350 (780)
                      ..+.   |++|+|++|.
T Consensus       159 ~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 AQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCCCTTCSSCCEEEECC
T ss_pred             CcccCCCCCCeEEEecC
Confidence            8776   4999999974

>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=5.9e-28  Score=235.24  Aligned_cols=153  Identities=16%  Similarity=0.345  Sum_probs=139.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcC----C-------CEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~y----G-------~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I  259 (780)
                      +.++|||+|||+++|+++|+++|++|    |       .|.+++ .++++|||||+|.+.++|++|+ .|++..+.|++|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i   80 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEE-EETTTTEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeE-ecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCcee
Confidence            46899999999999999999999999    7       788776 4678999999999999999999 899999999999


Q ss_pred             ccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHh
Q 004002          260 DIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL  334 (780)
Q Consensus       260 ~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~L  334 (780)
                      .|.++.+....    ....+|||+|||.++++++|+++|++||.|..|++     ++.++|+|||+|.+.++|++|++.|
T Consensus        81 ~v~~~~~~~~~----~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  156 (172)
T 2g4b_A           81 KIRRPHDYQPL----PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             EEECCSSCCCC----TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             eecCCcccCCC----CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence            99987654322    24678999999999999999999999999999976     5667899999999999999999999


Q ss_pred             CCCccCCceEEEEec
Q 004002          335 NRSDIAGKRIKLEPS  349 (780)
Q Consensus       335 nG~~i~Gr~L~V~~a  349 (780)
                      ||..+.|++|+|++|
T Consensus       157 ~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          157 NGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTCEETTEECEEEEC
T ss_pred             CCCEECCeEEEEEeC
Confidence            999999999999987

>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=243.78  Aligned_cols=159  Identities=18%  Similarity=0.230  Sum_probs=136.9

Q ss_pred             CCcEEEEeCCC-CCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          191 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       191 ~s~tLfVgNLp-~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      ++++|||+||| .++|+++|+++|++||+|.+|+.....+|||||+|.+.++|++|++.|||..|.|++|.|.++..+..
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~   82 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI   82 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCcc
Confidence            46899999999 89999999999999999999997666799999999999999999999999999999999999864321


Q ss_pred             CC-C--------------------C------------CCCccceeecCCCCCCChhHHHHHhcccCCe--eEEEeCC---
Q 004002          270 PS-D--------------------K------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV--KEIRETP---  311 (780)
Q Consensus       270 ~s-~--------------------~------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I--~~v~~~g---  311 (780)
                      .. .                    +            .....+|||+|||.++|+++|+++|++||.|  +.|++..   
T Consensus        83 ~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~  162 (205)
T 3tyt_A           83 MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKS  162 (205)
T ss_dssp             CCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCS
T ss_pred             CCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCC
Confidence            00 0                    0            0123579999999999999999999999999  8887632   


Q ss_pred             CcccEEEEEEcCHHHHHHHHHHhCCCccCCc----eEEEEec
Q 004002          312 HKRHHKFIEFYDVRAAEAALKSLNRSDIAGK----RIKLEPS  349 (780)
Q Consensus       312 ~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr----~L~V~~a  349 (780)
                      .++|+|||+|.+.++|.+||..|||..+.|+    ++.|+++
T Consensus       163 ~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          163 ERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            4569999999999999999999999999885    5666654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.95  E-value=1.1e-27  Score=239.85  Aligned_cols=161  Identities=26%  Similarity=0.368  Sum_probs=144.6

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCC
Q 004002          192 SRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP  270 (780)
Q Consensus       192 s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~  270 (780)
                      +++|||+|||+ ++++++|+++|++||.|..|+.....+|||||+|.+.++|++|++.|+|..+.|++|.|.++.+....
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~   82 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ   82 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcC
Confidence            58999999999 99999999999999999999865555899999999999999999999999999999999998754211


Q ss_pred             CCC-------------------------------CCCccceeecCCCCCCChhHHHHHhcccC-CeeEEEeCCCcccEEE
Q 004002          271 SDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHKF  318 (780)
Q Consensus       271 s~~-------------------------------~~~~~~L~V~NLp~~vteedL~~~Fs~yG-~I~~v~~~g~srG~aF  318 (780)
                      ..+                               .....+|||+|||..+++++|+++|++|| .|..|++....+|+||
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~af  162 (198)
T 1qm9_A           83 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMAL  162 (198)
T ss_dssp             CSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEE
T ss_pred             CCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEE
Confidence            100                               12256899999999999999999999999 9999999777799999


Q ss_pred             EEEcCHHHHHHHHHHhCCCccC-CceEEEEecCCC
Q 004002          319 IEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRPG  352 (780)
Q Consensus       319 V~F~~~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~~k  352 (780)
                      |+|.+.++|.+|++.|||..+. |++|+|.+++++
T Consensus       163 V~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          163 IQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9999999999999999999999 999999999874

>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=237.83  Aligned_cols=162  Identities=16%  Similarity=0.323  Sum_probs=142.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcC----C-------CEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~y----G-------~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I  259 (780)
                      .+++|||+|||+++|+++|+++|++|    |       .|..++ .++++|||||+|.+.++|++|+ .|+|..|.|++|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~-~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i   80 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEE-EETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeE-ecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceE
Confidence            46899999999999999999999999    5       677776 4778999999999999999999 799999999999


Q ss_pred             ccccCCCCCCCCC----------------CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEE
Q 004002          260 DIHFSIPKDNPSD----------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKF  318 (780)
Q Consensus       260 ~V~~a~pk~~~s~----------------~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aF  318 (780)
                      .|.++.+......                ......+|||+|||.++++++|+++|++||.|..|++     ++.++||||
T Consensus        81 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~af  160 (198)
T 2yh0_A           81 KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF  160 (198)
T ss_dssp             EEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEE
T ss_pred             EEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEE
Confidence            9999876532110                1134579999999999999999999999999999876     556689999


Q ss_pred             EEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       319 V~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      |+|.+.++|++|++.|||..+.|+.|+|.+++++..
T Consensus       161 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999999998753

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.95  E-value=3e-27  Score=249.89  Aligned_cols=178  Identities=19%  Similarity=0.320  Sum_probs=161.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP  270 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~  270 (780)
                      ++++|||+|||+++|+++|+++|++|| |..|+. ++++|||||+|.+.++|++|++.|+|..+.|++|.|.++.     
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            568999999999999999999999999 999876 7899999999999999999999999999999999999864     


Q ss_pred             CCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       271 s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                           ...+|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++.|+|..+.|+.|.
T Consensus        94 -----~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~  168 (284)
T 3smz_A           94 -----TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY  168 (284)
T ss_dssp             -----CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             -----CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence                 2358999999999999999999999999999875     566789999999999999999999999999999999


Q ss_pred             EEecCCCch-------hhhHhhhhchhc-cHHHHHHHHhhhCC
Q 004002          346 LEPSRPGGA-------RRNLMLQLNQEL-EQDESRILQHQVGS  380 (780)
Q Consensus       346 V~~a~~k~~-------r~~~l~ql~~~~-~~~~~~~~~~~~Gs  380 (780)
                      |.++.++..       +..++.++...+ +++++..+|..+|.
T Consensus       169 v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~  211 (284)
T 3smz_A          169 VHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHS  211 (284)
T ss_dssp             EEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSC
T ss_pred             EEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCC
Confidence            999987653       234678888886 88999999887753

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.94  E-value=2.2e-26  Score=244.16  Aligned_cols=182  Identities=19%  Similarity=0.260  Sum_probs=155.3

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       187 ~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.+.++|||+|||+++|+++|+++|++||+|..|+.   ...++|||||+|.+.++|++|++ +++..+.|++|.|.+
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~  114 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH  114 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEE
Confidence            34567899999999999999999999999999999873   23368999999999999999995 999999999999988


Q ss_pred             CCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccC-CeeEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       264 a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG-~I~~v~~~----g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      +           ...+|||+|||.++++++|+++|++|| .|..|++.    +.++|||||+|.+.++|.+|++.|||..
T Consensus       115 ~-----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~  183 (292)
T 2ghp_A          115 L-----------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK  183 (292)
T ss_dssp             C-----------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             C-----------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            6           256899999999999999999999999 99999863    4578999999999999999999999999


Q ss_pred             cCCceEEEEecCCCchh-----------hhHhhhhchh-ccHHHHHHHHhhhCC
Q 004002          339 IAGKRIKLEPSRPGGAR-----------RNLMLQLNQE-LEQDESRILQHQVGS  380 (780)
Q Consensus       339 i~Gr~L~V~~a~~k~~r-----------~~~l~ql~~~-~~~~~~~~~~~~~Gs  380 (780)
                      +.|+.|.|.++.+....           ..++.++... +++++++.+|.++|.
T Consensus       184 ~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~  237 (292)
T 2ghp_A          184 IEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGS  237 (292)
T ss_dssp             ETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSC
T ss_pred             eCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCC
Confidence            99999999998875432           3457788888 999999999998863

>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=1.5e-25  Score=235.42  Aligned_cols=155  Identities=28%  Similarity=0.423  Sum_probs=140.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      ...++|||+|||+++|+++|+++|++||.|..|+. .+++|||||+|.+.++|++|++.|+|..|.|++|.|.++.+   
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~~---   95 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH---   95 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC---
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc---
Confidence            45689999999999999999999999999999985 56799999999999999999999999999999999999864   


Q ss_pred             CCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCC-CccC---C
Q 004002          270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR-SDIA---G  341 (780)
Q Consensus       270 ~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG-~~i~---G  341 (780)
                             ..+|||+|||..+|+++|+++|++||.|..|++    ++.++|||||+|.+.++|.+|+..||+ ..+.   +
T Consensus        96 -------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~  168 (261)
T 3sde_A           96 -------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTP  168 (261)
T ss_dssp             -------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSC
T ss_pred             -------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCC
Confidence                   358999999999999999999999999999875    567799999999999999999999954 4444   8


Q ss_pred             ceEEEEecCCCchh
Q 004002          342 KRIKLEPSRPGGAR  355 (780)
Q Consensus       342 r~L~V~~a~~k~~r  355 (780)
                      ++|.|.++.+....
T Consensus       169 r~i~v~~~~~~~~~  182 (261)
T 3sde_A          169 RPVIVEPMEQFDDE  182 (261)
T ss_dssp             CBCEEEECCCEESS
T ss_pred             ceEEEeeccccCcc
Confidence            99999999876543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.80  E-value=9.4e-20  Score=185.39  Aligned_cols=155  Identities=13%  Similarity=0.236  Sum_probs=125.1

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCcc----cccccCCCCcccCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL----LHYSVPNGAGTVAGEHP  186 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~----~~~~l~n~~~k~~g~~~  186 (780)
                      .+.+||++||.+++|.+|+++|+.+|.|   .|..|..+...+|++++.|.+...+..+    +...+.+...++.....
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~   94 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   94 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccc
Confidence            4689999999999999999999999997   6777888888999999999987665422    22222222222211111


Q ss_pred             ---CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCccccccccc
Q 004002          187 ---YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (780)
Q Consensus       187 ---~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~  260 (780)
                         ......++|||+|||+++|+++|+++|++||.|..|+   ..+.++|||||+|.+.++|++|++.|+|..|.|++|.
T Consensus        95 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~  174 (213)
T 4f02_A           95 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF  174 (213)
T ss_dssp             CTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence               1122457999999999999999999999999999987   3566899999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 004002          261 IHFSIPKD  268 (780)
Q Consensus       261 V~~a~pk~  268 (780)
                      |.++.++.
T Consensus       175 V~~a~~~~  182 (213)
T 4f02_A          175 VGRFKSRK  182 (213)
T ss_dssp             EEECCCHH
T ss_pred             EEEcCCCc
Confidence            99998753

>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=99.80  E-value=1.3e-19  Score=174.50  Aligned_cols=127  Identities=19%  Similarity=0.244  Sum_probs=113.1

Q ss_pred             CCcceEEEEEEecHHHHHHHHHHc-cCccccccccccccCCCCC------------CCCCCCCCccceeecCCCCCCChh
Q 004002          226 CKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIHFSIPKD------------NPSDKDLNQGTLVVFNLDPSVSNE  292 (780)
Q Consensus       226 gkskG~aFV~F~~~e~A~~Al~~L-ng~~l~gr~I~V~~a~pk~------------~~s~~~~~~~~L~V~NLp~~vtee  292 (780)
                      .+.+|+++|+|.+.++|++|++++ +|..+.| .+.+.++..+.            .........++|||+|||.+++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            467899999999999999999999 9999999 99999876521            112233456799999999999999


Q ss_pred             HHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          293 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       293 dL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      +|+++|++||.|+.|++...++|||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            9999999999999999977789999999999999999999999999999999999998764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.79  E-value=7.4e-19  Score=177.08  Aligned_cols=157  Identities=13%  Similarity=0.224  Sum_probs=125.9

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHP  186 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~~  186 (780)
                      .+.++|++||.++++.+++++|+.+|.|   .|..+..+...++++++.|.+...+..    ++...+.+....+.....
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            5789999999999999999999999987   555566677889999999998776652    333334444333322211


Q ss_pred             C------------CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHc
Q 004002          187 Y------------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRAL  249 (780)
Q Consensus       187 ~------------~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~L  249 (780)
                      .            .....++|||+|||.++|+++|+++|++||.|..|+.     +++++|||||+|.+.++|.+|++.|
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l  187 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM  187 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHc
Confidence            1            1234589999999999999999999999999999873     5788999999999999999999999


Q ss_pred             cCccccccccccccCCCCCCC
Q 004002          250 QNKPLRRRKLDIHFSIPKDNP  270 (780)
Q Consensus       250 ng~~l~gr~I~V~~a~pk~~~  270 (780)
                      +|..|.|++|.|.|+.++..+
T Consensus       188 ~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          188 NLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             TTCBCSSSBCEEEECSSCSST
T ss_pred             cCCEeCCcEEEEEEecCCCCC
Confidence            999999999999999876543

>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=99.79  E-value=6.8e-19  Score=170.43  Aligned_cols=130  Identities=21%  Similarity=0.281  Sum_probs=103.6

Q ss_pred             CCCcceEEEEEEecHHHHHHHHHHccCcccc-------ccccccccCCCCC--CCCCCCCCccceeecCCCCCCChhHHH
Q 004002          225 ACKHRGFVMISYYDIRAARTAMRALQNKPLR-------RRKLDIHFSIPKD--NPSDKDLNQGTLVVFNLDPSVSNEDLR  295 (780)
Q Consensus       225 tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~-------gr~I~V~~a~pk~--~~s~~~~~~~~L~V~NLp~~vteedL~  295 (780)
                      ..+++|||||+|.+.++|++|++.+++....       +............  ..........+|||+|||.++++++|+
T Consensus         9 ~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~   88 (158)
T 2kn4_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLR   88 (158)
T ss_dssp             CSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHH
T ss_pred             CccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHH
Confidence            4578999999999999999999988764322       2222222111111  111223446799999999999999999


Q ss_pred             HHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          296 QIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       296 ~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      ++|++||.|..|++     ++.++|||||+|.+.++|++||+.|||..+.|+.|+|.+++++..
T Consensus        89 ~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           89 RVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             HHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             HHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999986     567899999999999999999999999999999999999987653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.78  E-value=1.1e-18  Score=167.91  Aligned_cols=150  Identities=19%  Similarity=0.290  Sum_probs=120.9

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccC---CC
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVA---GE  184 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~---g~  184 (780)
                      +.++|++||.++++.++.++|+.+|.|   .+..+. .+..++++++.|.+...+.    .+++..+.+....+.   ..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            368999999999999999999999997   444443 4668899999999876654    223333443322221   11


Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccc
Q 004002          185 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (780)
Q Consensus       185 ~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I  259 (780)
                      ......+.++|||+|||.++|+++|+++|++||.|..++.     +++++|||||+|.+.++|++|++.|+|..+.|++|
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            1233456789999999999999999999999999999873     57889999999999999999999999999999999


Q ss_pred             ccccCC
Q 004002          260 DIHFSI  265 (780)
Q Consensus       260 ~V~~a~  265 (780)
                      .|.|+.
T Consensus       160 ~v~~a~  165 (166)
T 3md3_A          160 RINWAA  165 (166)
T ss_dssp             EEEESC
T ss_pred             EEEecC
Confidence            999986

>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=99.77  E-value=1.2e-18  Score=168.38  Aligned_cols=150  Identities=21%  Similarity=0.331  Sum_probs=122.5

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCCC-
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHP-  186 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~~-  186 (780)
                      +.++|++||.++++.+++++|+.+|.|   .+..+..++..+|++++.|.+...|..    +.+..+.+....+....+ 
T Consensus         4 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   83 (168)
T 1b7f_A            4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG   83 (168)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCC
Confidence            679999999999999999999999987   444555677889999999998876652    333344443333322222 


Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccc--ccc
Q 004002          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKL  259 (780)
Q Consensus       187 ~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~I  259 (780)
                      ....+.++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|++|++.|+|..+.|  ++|
T Consensus        84 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l  163 (168)
T 1b7f_A           84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL  163 (168)
T ss_dssp             SSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             cccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEE
Confidence            23346789999999999999999999999999998872     67789999999999999999999999999977  999


Q ss_pred             ccccC
Q 004002          260 DIHFS  264 (780)
Q Consensus       260 ~V~~a  264 (780)
                      .|.||
T Consensus       164 ~V~~A  168 (168)
T 1b7f_A          164 SVRLA  168 (168)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99875

>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=99.77  E-value=2.2e-19  Score=173.63  Aligned_cols=152  Identities=18%  Similarity=0.281  Sum_probs=121.6

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCcccc--cccCCCCcccCCCCC-CC
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGLLH--YSVPNGAGTVAGEHP-YG  188 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~~~--~~l~n~~~k~~g~~~-~~  188 (780)
                      +.++|++||.++++.+++++|+.+|.|   .|..+..++..+|++++.|.+...+..+..  ..+.+....+....+ ..
T Consensus         4 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~~   83 (167)
T 2cjk_A            4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDE   83 (167)
T ss_dssp             GEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchhh
Confidence            689999999999999999999999997   455565678889999999998766543221  112222222211111 11


Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||.++|+++|+++|++||.|..++     .+++++|||||+|.+.++|++|++ +++..+.|++|.|.|
T Consensus        84 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~  162 (167)
T 2cjk_A           84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKR  162 (167)
T ss_dssp             HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEE
T ss_pred             ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEee
Confidence            23457999999999999999999999999999987     257899999999999999999998 899999999999999


Q ss_pred             CCCC
Q 004002          264 SIPK  267 (780)
Q Consensus       264 a~pk  267 (780)
                      +.|+
T Consensus       163 a~pk  166 (167)
T 2cjk_A          163 AEPR  166 (167)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=99.77  E-value=1.4e-18  Score=172.28  Aligned_cols=157  Identities=17%  Similarity=0.278  Sum_probs=120.3

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCcc---cccccCCCCcccCC----
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAGTVAG----  183 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~---~~~~l~n~~~k~~g----  183 (780)
                      ...++|++||.++++.+++++|+.+|.|   .|..+..++..+|++++.|.+...|..+   .+..+.+....+..    
T Consensus        13 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~   92 (196)
T 1l3k_A           13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   92 (196)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC-
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCc
Confidence            4789999999999999999999999987   6666777788899999999987665532   22222222111111    


Q ss_pred             ---CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          184 ---EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       184 ---~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                         ..+....+.++|||+|||.++|+++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++. ++..|.
T Consensus        93 ~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~  171 (196)
T 1l3k_A           93 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVN  171 (196)
T ss_dssp             ----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEET
T ss_pred             ccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEEC
Confidence               11112235589999999999999999999999999999872     578899999999999999999996 799999


Q ss_pred             ccccccccCCCCCCCC
Q 004002          256 RRKLDIHFSIPKDNPS  271 (780)
Q Consensus       256 gr~I~V~~a~pk~~~s  271 (780)
                      |+.|.|.++.++....
T Consensus       172 G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          172 GHNCEVRKALSKQEMA  187 (196)
T ss_dssp             TEECEEEECC------
T ss_pred             CEEEEEEecCChhHhc
Confidence            9999999998876543

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.77  E-value=1.8e-18  Score=168.10  Aligned_cols=152  Identities=15%  Similarity=0.263  Sum_probs=119.3

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccC--cccceEEEeecCccccCc----ccccccCCC---Cccc
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQES--LSMSMSKISISDSASGNG----LLHYSVPNG---AGTV  181 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~es--a~~g~~~v~~~~~~~a~~----~~~~~l~n~---~~k~  181 (780)
                      .++++|++||.++++.+++++|+.+|.|   .|..+....  ..++++++.|.+...|..    +++..+...   ...+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            3689999999999999999999999997   555565554  788999999998766542    222222211   1111


Q ss_pred             --CCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          182 --AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       182 --~g~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                        ...........++|||+|||.++|+++|+++|++||.|..++    ..++++|||||+|.+.++|++|++.|+|..+.
T Consensus        83 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  162 (175)
T 3nmr_A           83 KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTM  162 (175)
T ss_dssp             EECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCC
T ss_pred             ccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCccc
Confidence              111122233568999999999999999999999999999987    35778999999999999999999999998876


Q ss_pred             ---ccccccccCC
Q 004002          256 ---RRKLDIHFSI  265 (780)
Q Consensus       256 ---gr~I~V~~a~  265 (780)
                         +++|.|.|+.
T Consensus       163 ~g~~~~l~V~~ad  175 (175)
T 3nmr_A          163 EGCSSPMVVKFAD  175 (175)
T ss_dssp             TTCSSCCEEEECC
T ss_pred             CCCCCCeEEEecC
Confidence               4999999873

>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=99.77  E-value=2e-18  Score=166.12  Aligned_cols=150  Identities=21%  Similarity=0.297  Sum_probs=121.5

Q ss_pred             ceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCCCC
Q 004002          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHPY  187 (780)
Q Consensus       115 ~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~~~  187 (780)
                      +.++|++||.++++.+++++|+.+|.|   .+..+..++..+|++++.|.+...|..    +++..+.+....+....+.
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   82 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCC
Confidence            579999999999999999999999997   566666678888999999998876652    3334444433333222222


Q ss_pred             -CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccc--c
Q 004002          188 -GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK--L  259 (780)
Q Consensus       188 -~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~--I  259 (780)
                       .....++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|++|++.|+|..+.|+.  |
T Consensus        83 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i  162 (167)
T 1fxl_A           83 SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPI  162 (167)
T ss_dssp             CGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             cccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccce
Confidence             2345689999999999999999999999999999873     5778999999999999999999999999999975  6


Q ss_pred             ccccC
Q 004002          260 DIHFS  264 (780)
Q Consensus       260 ~V~~a  264 (780)
                      .|.||
T Consensus       163 ~v~~A  167 (167)
T 1fxl_A          163 TVKFA  167 (167)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            66664

>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=99.76  E-value=8.2e-19  Score=161.85  Aligned_cols=103  Identities=16%  Similarity=0.317  Sum_probs=72.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ..++|||+|||+++|+++|+++|++||.|.+|+   ..+.+||||||+|.+.++|++|++.|++..|.|++|.|.++.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            357999999999999999999999999999987   35668999999999999999999999999999999999999876


Q ss_pred             CCCCC----CCCCccceeecCCCCCCChhH
Q 004002          268 DNPSD----KDLNQGTLVVFNLDPSVSNED  293 (780)
Q Consensus       268 ~~~s~----~~~~~~~L~V~NLp~~vteed  293 (780)
                      .....    ......+|||+|||+++|++.
T Consensus        84 ~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           84 KEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CC----------------------------
T ss_pred             cccccccccccCCCCceEeCCCCCCccccc
Confidence            54322    223346899999999999874

>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=99.75  E-value=4.8e-19  Score=173.01  Aligned_cols=154  Identities=14%  Similarity=0.132  Sum_probs=125.0

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE--EEeccCccCcccceEEEeecCccccCc---ccccccCCCCcccCCCC---
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM--ELEGEPQESLSMSMSKISISDSASGNG---LLHYSVPNGAGTVAGEH---  185 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i--~V~~d~~esa~~g~~~v~~~~~~~a~~---~~~~~l~n~~~k~~g~~---  185 (780)
                      ...++|++||.++++.+++++|+.+|.+  .+..+...+..+|++++.|.+...|..   +++..+.+....+....   
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~   92 (175)
T 1fje_B           13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRD   92 (175)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSS
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCcc
Confidence            4789999999999999999999999875  133455667788999999998766543   33333444333332222   


Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       186 ~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .....+.++|||+|||.++|+++|+++|++||+|..+..+++++|||||+|.+.++|.+|++.|+|..|.|++|.|.|+.
T Consensus        93 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           93 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             CSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             ccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            12334568999999999999999999999999999886678899999999999999999999999999999999999998


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      ++
T Consensus       173 ~k  174 (175)
T 1fje_B          173 EK  174 (175)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>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=99.72  E-value=1.2e-17  Score=162.21  Aligned_cols=148  Identities=14%  Similarity=0.263  Sum_probs=116.5

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCC----C-------cEEEeccCccCcccceEEEeecCccccCcc---cccccCCCCc
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSG----G-------GMELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAG  179 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~----G-------~i~V~~d~~esa~~g~~~v~~~~~~~a~~~---~~~~l~n~~~  179 (780)
                      ..+++|++||.++++.+++++|+.+    |       .|.   +......++++++.|.+...|..+   ++..+.+...
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~---~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i   80 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVL---AVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   80 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEE---EEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCcee---eeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCcee
Confidence            3689999999999999999999999    5       331   112234579999999987666533   2333333333


Q ss_pred             ccCCCCCC-CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcc
Q 004002          180 TVAGEHPY-GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKP  253 (780)
Q Consensus       180 k~~g~~~~-~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~  253 (780)
                      .+...... .....++|||+|||.++|+++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|+|..
T Consensus        81 ~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (172)
T 2g4b_A           81 KIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ  160 (172)
T ss_dssp             EEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCE
T ss_pred             eecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCE
Confidence            33222221 2234689999999999999999999999999999873     67889999999999999999999999999


Q ss_pred             ccccccccccC
Q 004002          254 LRRRKLDIHFS  264 (780)
Q Consensus       254 l~gr~I~V~~a  264 (780)
                      +.|++|.|.||
T Consensus       161 ~~g~~l~V~~A  171 (172)
T 2g4b_A          161 LGDKKLLVQRA  171 (172)
T ss_dssp             ETTEECEEEEC
T ss_pred             ECCeEEEEEeC
Confidence            99999999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.72  E-value=1.5e-17  Score=165.13  Aligned_cols=156  Identities=12%  Similarity=0.202  Sum_probs=118.1

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---E-----EeccCccCcccceEEEeecCccccCcc---cccccCCCCcccC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---E-----LEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAGTVA  182 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~-----V~~d~~esa~~g~~~v~~~~~~~a~~~---~~~~l~n~~~k~~  182 (780)
                      .++++|++||.++++.+++++|+.+|.+   .     ...+......++++++.|.+...|..+   ++..+.+....+.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v~   83 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR   83 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEEE
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEEe
Confidence            5789999999999999999999999421   0     011222345678999999887655432   2222222211111


Q ss_pred             CCC---------------------CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEE
Q 004002          183 GEH---------------------PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISY  236 (780)
Q Consensus       183 g~~---------------------~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F  236 (780)
                      ...                     .....+.++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f  163 (198)
T 2yh0_A           84 RPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY  163 (198)
T ss_dssp             CCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEE
T ss_pred             CCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEE
Confidence            100                     011245689999999999999999999999999999872     677899999999


Q ss_pred             ecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       237 ~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      .+.++|++|++.|+|..|.|++|.|.|+.++..
T Consensus       164 ~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          164 VDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             SSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999987653

>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=99.70  E-value=9.7e-17  Score=164.88  Aligned_cols=149  Identities=19%  Similarity=0.217  Sum_probs=117.5

Q ss_pred             CceeeeccCCC-CCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCC
Q 004002          114 MDDFDLRGLPS-SLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEH  185 (780)
Q Consensus       114 ~~el~V~~Lp~-s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~  185 (780)
                      ...++|++||. ++++.+++++|+.+|.|   .|..+.     ++++++.|.+...|..    +++..+.+....+....
T Consensus        34 ~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  108 (229)
T 2adc_A           34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK  108 (229)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            47899999999 99999999999999997   333332     6889999988765542    33333333322221000


Q ss_pred             C------------------------------------CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCC-CEEEEEeCCCc
Q 004002          186 P------------------------------------YGEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYTACKH  228 (780)
Q Consensus       186 ~------------------------------------~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG-~I~sv~~tgks  228 (780)
                      .                                    ....+.++|||+|||.++++++|+++|++|| +|..++...+.
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~  188 (229)
T 2adc_A          109 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD  188 (229)
T ss_dssp             CCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSS
T ss_pred             CccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECC
Confidence            0                                    0123468999999999999999999999999 99999876667


Q ss_pred             ceEEEEEEecHHHHHHHHHHccCcccc-ccccccccCCCC
Q 004002          229 RGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSIPK  267 (780)
Q Consensus       229 kG~aFV~F~~~e~A~~Al~~Lng~~l~-gr~I~V~~a~pk  267 (780)
                      +|||||+|.+.++|++|++.|+|..+. |++|.|.|+.++
T Consensus       189 ~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          189 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999999999999999999999999999 999999999764

>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=99.69  E-value=1.2e-16  Score=168.28  Aligned_cols=75  Identities=20%  Similarity=0.347  Sum_probs=69.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccc-ccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~-gr~I~V~~a~  265 (780)
                      +.++|||+|||.++|+++|+++|++||.|..|+.....+|||||+|.+.++|++|++.|+|..|. |++|+|.|++
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            56889999999999999999999999999999865545799999999999999999999999999 9999999985

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=1.4e-16  Score=158.96  Aligned_cols=150  Identities=19%  Similarity=0.218  Sum_probs=115.8

Q ss_pred             ceeeeccCCC-CCChHHHHHHhcCCCcE-EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCC---
Q 004002          115 DDFDLRGLPS-SLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEH---  185 (780)
Q Consensus       115 ~el~V~~Lp~-s~~E~el~dlFs~~G~i-~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~---  185 (780)
                      ..++|++||. ++++.+++++|+.+|.| .|.+-...   ++++++.|.+...|..    +++..+.+....+....   
T Consensus         4 ~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~---~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A            4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC---SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            6799999999 99999999999999987 33222211   6788888887665541    22333333322111000   


Q ss_pred             ---------------------------------CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCC-CEEEEEeCCCcceE
Q 004002          186 ---------------------------------PYGEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYTACKHRGF  231 (780)
Q Consensus       186 ---------------------------------~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG-~I~sv~~tgkskG~  231 (780)
                                                       .....+.++|||+|||.++++++|+++|++|| .|..++.....+||
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~  160 (198)
T 1qm9_A           81 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM  160 (198)
T ss_dssp             CCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSC
T ss_pred             cCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcE
Confidence                                             00123478999999999999999999999999 99999876667999


Q ss_pred             EEEEEecHHHHHHHHHHccCcccc-ccccccccCCCC
Q 004002          232 VMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSIPK  267 (780)
Q Consensus       232 aFV~F~~~e~A~~Al~~Lng~~l~-gr~I~V~~a~pk  267 (780)
                      |||+|.+.++|.+|++.|+|..+. |++|.|.|+.++
T Consensus       161 afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          161 ALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            999999999999999999999999 999999998764

>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=99.65  E-value=1.9e-16  Score=142.43  Aligned_cols=76  Identities=22%  Similarity=0.478  Sum_probs=71.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|.||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            357999999999999999999999999999987     358899999999999999999999999999999999999997


Q ss_pred             C
Q 004002          266 P  266 (780)
Q Consensus       266 p  266 (780)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>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=99.65  E-value=2.8e-16  Score=141.29  Aligned_cols=75  Identities=28%  Similarity=0.488  Sum_probs=70.9

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++|+|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            468999999999999999999999999999975     577899999999999999999999999999999999999986

>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=99.65  E-value=2.8e-16  Score=159.66  Aligned_cols=147  Identities=12%  Similarity=0.134  Sum_probs=108.0

Q ss_pred             ceeeeccCC-CCCChHHHHHHhcCCCcE-EEeccCccCcccceEEEeecCccccC----cccccccCCCCcccCC-----
Q 004002          115 DDFDLRGLP-SSLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAG-----  183 (780)
Q Consensus       115 ~el~V~~Lp-~s~~E~el~dlFs~~G~i-~V~~d~~esa~~g~~~v~~~~~~~a~----~~~~~~l~n~~~k~~g-----  183 (780)
                      ..++|++|+ .++++.+|+++|+.+|.| .|.+-. .  .+|++++.|.+...|.    .+++..+.+..+.+..     
T Consensus         5 ~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~-~--~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMK-S--KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             SEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECT-T--STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEec-C--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            579999999 899999999999999998 232221 1  3688999998876554    2233333222111100     


Q ss_pred             ----C-------------------CC----------CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCE--EEEEe---C
Q 004002          184 ----E-------------------HP----------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDI--RTLYT---A  225 (780)
Q Consensus       184 ----~-------------------~~----------~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I--~sv~~---t  225 (780)
                          .                   ..          ....+.++|||+|||+++|+++|+++|++||.|  .+++.   .
T Consensus        82 ~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~  161 (205)
T 3tyt_A           82 IMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK  161 (205)
T ss_dssp             CCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC
T ss_pred             cCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC
Confidence                0                   00          011356799999999999999999999999998  77763   2


Q ss_pred             CCcceEEEEEEecHHHHHHHHHHccCcccccc----ccccccC
Q 004002          226 CKHRGFVMISYYDIRAARTAMRALQNKPLRRR----KLDIHFS  264 (780)
Q Consensus       226 gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr----~I~V~~a  264 (780)
                      ++.+|||||+|.+.++|.+||..|||..|.|+    ++.|+++
T Consensus       162 ~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          162 SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            45679999999999999999999999999876    5555554

>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=99.64  E-value=1.1e-16  Score=146.77  Aligned_cols=102  Identities=25%  Similarity=0.405  Sum_probs=91.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      .+.++|||+|||.++|+++|+++|++||.|..|+.  .++++|||||+|.+.++|++|++.|+|..+.|+.|.|.|+.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   85 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNAN   85 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            46789999999999999999999999999999873  5778999999999999999999999999999999999998764


Q ss_pred             CCCCCCCCCccceeecCCCCCCChhHHHHHhcccCC
Q 004002          268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE  303 (780)
Q Consensus       268 ~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~  303 (780)
                      ...            .+++...++++|+++|++||.
T Consensus        86 ~~~------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           86 RAF------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHT------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             hhh------------hhhhHhHhHHHHHHHHHHhCC
Confidence            321            567778899999999999985

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.64  E-value=2.1e-16  Score=150.17  Aligned_cols=120  Identities=22%  Similarity=0.333  Sum_probs=77.6

Q ss_pred             eEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe
Q 004002          230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  309 (780)
Q Consensus       230 G~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~  309 (780)
                      -++|++|.+...|..|+..++|....++. .+.+..+.    ......++|||+|||.++++++|+++|++||.|+.|++
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~~----~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i   79 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRPP----PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI   79 (135)
T ss_dssp             -------------------------------CCSCCSC----SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEEC
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCCC----CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE
Confidence            47889999999999999999888776654 33343332    23345679999999999999999999999999999986


Q ss_pred             -----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          310 -----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       310 -----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                           ++.++|||||+|.+.++|++||+.|||..+.|++|+|++++++..
T Consensus        80 ~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           80 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence                 456789999999999999999999999999999999999987654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.63  E-value=1e-15  Score=140.40  Aligned_cols=84  Identities=21%  Similarity=0.294  Sum_probs=76.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|++|++     +++++|||||+|.+.++|++||+.|||..+.|+.|+|.++.
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            4568999999999999999999999999999976     57789999999999999999999999999999999999998


Q ss_pred             CCchhhhHh
Q 004002          351 PGGARRNLM  359 (780)
Q Consensus       351 ~k~~r~~~l  359 (780)
                      .+..++.+.
T Consensus        85 ~~~~~~~~~   93 (110)
T 3s8s_A           85 KGQQRMKYY   93 (110)
T ss_dssp             TTHHHHHHH
T ss_pred             CCcHHHHHH
Confidence            876655433

>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=99.62  E-value=1e-15  Score=160.40  Aligned_cols=146  Identities=15%  Similarity=0.117  Sum_probs=116.0

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE-EEeccCccCcccceEEEeecCccccCc----ccccccCCCCcccCCCCCCC
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHPYG  188 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i-~V~~d~~esa~~g~~~v~~~~~~~a~~----~~~~~l~n~~~k~~g~~~~~  188 (780)
                      .+.++|++||.++++.+++++|+.+|.| .|.+.    ..+|++++.|.+...|..    +++..+.+....+..     
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~----~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~-----   92 (261)
T 3sde_A           22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN----RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF-----   92 (261)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE-----
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEe----CCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee-----
Confidence            3689999999999999999999999997 33321    347899999998766542    333334433333322     


Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCc-ccc---ccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNK-PLR---RRKLD  260 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~-~l~---gr~I~  260 (780)
                      ..+.++|||+|||.++|+++|+++|++||.|..|+    .+++++|||||+|.+.++|.+|++.|++. .+.   +++|.
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence            23568999999999999999999999999999987    36789999999999999999999999554 433   89999


Q ss_pred             cccCCCCC
Q 004002          261 IHFSIPKD  268 (780)
Q Consensus       261 V~~a~pk~  268 (780)
                      |.++.+..
T Consensus       173 v~~~~~~~  180 (261)
T 3sde_A          173 VEPMEQFD  180 (261)
T ss_dssp             EEECCCEE
T ss_pred             EeeccccC
Confidence            99987654

>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=99.60  E-value=1.3e-15  Score=140.24  Aligned_cols=80  Identities=23%  Similarity=0.390  Sum_probs=72.2

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..+|||+|||.++|+++|+++|++||.|++|++   .+.++|||||+|.+.++|++||+.|||..+.|++|+|.+++++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~   84 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   84 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc
Confidence            468999999999999999999999999999876   34568999999999999999999999999999999999998876


Q ss_pred             hhh
Q 004002          354 ARR  356 (780)
Q Consensus       354 ~r~  356 (780)
                      .+.
T Consensus        85 ~~~   87 (115)
T 4f25_A           85 ERE   87 (115)
T ss_dssp             C--
T ss_pred             ccc
Confidence            543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.60  E-value=1e-15  Score=137.02  Aligned_cols=95  Identities=24%  Similarity=0.357  Sum_probs=81.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD  272 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~  272 (780)
                      ++|||+|||+++|+++|+++|++||+|..|+....++|||||+|.+.++|++|++.|++..+.|++|.|.++.++.....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   80 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSR   80 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCccc
Confidence            58999999999999999999999999999885333899999999999999999999999999999999999987654322


Q ss_pred             C------CCCccceeecCCCC
Q 004002          273 K------DLNQGTLVVFNLDP  287 (780)
Q Consensus       273 ~------~~~~~~L~V~NLp~  287 (780)
                      .      .....+|||+||+.
T Consensus        81 ~~~~~~~~~~~~~ifvg~L~h  101 (101)
T 2hvz_A           81 FDRPPARRKLLEVLFNGPLEH  101 (101)
T ss_dssp             CCSCCCSCCCCSCCCSCCCCC
T ss_pred             CCCCCccccCCCceecCCCCC
Confidence            1      12246899999973

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.59  E-value=6.1e-16  Score=136.79  Aligned_cols=80  Identities=21%  Similarity=0.419  Sum_probs=71.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCC-CEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHcc-CccccccccccccC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYG-DIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQ-NKPLRRRKLDIHFS  264 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG-~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Ln-g~~l~gr~I~V~~a  264 (780)
                      +++|||+|||+++|+++|+++|++|| +|.+|+     .++++||||||+|.+.++|++|++.++ +..+.|++|.|.|+
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            47999999999999999999999999 788876     358899999999999999999999874 56799999999999


Q ss_pred             CCCCCCC
Q 004002          265 IPKDNPS  271 (780)
Q Consensus       265 ~pk~~~s  271 (780)
                      .|+....
T Consensus        81 ~~~~~~~   87 (91)
T 2lxi_A           81 DPKPKIN   87 (91)
T ss_dssp             CSCCCCS
T ss_pred             CCCCCCC
Confidence            8876543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.59  E-value=2.9e-15  Score=137.43  Aligned_cols=78  Identities=18%  Similarity=0.383  Sum_probs=72.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|||..|.|++|.|.++
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            46799999999999999999999999999999873     5889999999999999999999999999999999999998


Q ss_pred             CCC
Q 004002          265 IPK  267 (780)
Q Consensus       265 ~pk  267 (780)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            643

>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=99.58  E-value=6.8e-15  Score=134.80  Aligned_cols=103  Identities=20%  Similarity=0.400  Sum_probs=90.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||..+++++|+++|++||.|..|++  ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.+++++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR   86 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCh
Confidence            3468999999999999999999999999999987  56678999999999999999999999999999999999998765


Q ss_pred             hhhhHhhhhchhccHHHHHHHHhhhCCCC
Q 004002          354 ARRNLMLQLNQELEQDESRILQHQVGSPI  382 (780)
Q Consensus       354 ~r~~~l~ql~~~~~~~~~~~~~~~~Gsp~  382 (780)
                      ..    +++....+++++..++.++|...
T Consensus        87 ~~----~~~~~~~~~~~l~~~~~~~g~~~  111 (115)
T 3lqv_A           87 AF----QKMDTKKKEEQLKLLKEKYGINT  111 (115)
T ss_dssp             HT----TTSCHHHHHHHHHHHHHHHCCCC
T ss_pred             hh----hhhhHhHhHHHHHHHHHHhCCCC
Confidence            43    44555667788888899887553

>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=99.58  E-value=2.9e-15  Score=146.58  Aligned_cols=122  Identities=18%  Similarity=0.274  Sum_probs=73.3

Q ss_pred             EEEecHHHHHHHHHHccCcccc--ccccccccCCCCC----------------CCCCCCCCccceeecCCCCCCChhHHH
Q 004002          234 ISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIPKD----------------NPSDKDLNQGTLVVFNLDPSVSNEDLR  295 (780)
Q Consensus       234 V~F~~~e~A~~Al~~Lng~~l~--gr~I~V~~a~pk~----------------~~s~~~~~~~~L~V~NLp~~vteedL~  295 (780)
                      .+|.+.++|+.|+..|++....  |+.....+.....                ..........+|||+|||..+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6889999999999999887665  5555555422110                001122345689999999999999999


Q ss_pred             HHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchh
Q 004002          296 QIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (780)
Q Consensus       296 ~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r  355 (780)
                      ++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..|.|+.|.|.++.++..+
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            99999999999976     4557899999999999999999999999999999999999877654

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=6.9e-15  Score=131.03  Aligned_cols=81  Identities=26%  Similarity=0.399  Sum_probs=75.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.++
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            46799999999999999999999999999999984     6788999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      .++...
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            887654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.58  E-value=8.7e-15  Score=128.45  Aligned_cols=81  Identities=20%  Similarity=0.314  Sum_probs=74.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .+.++|||+|||.++++++|+++|++||+|..++   .+++++|||||+|.+.++|++|++.|++..+.|++|.|.++.+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   85 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRN   85 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            4679999999999999999999999999999887   3677899999999999999999999999999999999999987


Q ss_pred             CCCC
Q 004002          267 KDNP  270 (780)
Q Consensus       267 k~~~  270 (780)
                      ...+
T Consensus        86 ~~~~   89 (92)
T 2dgv_A           86 ASGP   89 (92)
T ss_dssp             CSSC
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=99.57  E-value=8.3e-15  Score=130.50  Aligned_cols=80  Identities=28%  Similarity=0.401  Sum_probs=74.5

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++
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            35679999999999999999999999999999987     5667899999999999999999999999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            98764

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=1.2e-14  Score=130.84  Aligned_cols=82  Identities=16%  Similarity=0.314  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3456799999999999999999999999999999983     67899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 004002          263 FSIPKDN  269 (780)
Q Consensus       263 ~a~pk~~  269 (780)
                      ++.++..
T Consensus        91 ~a~~~~~   97 (105)
T 1x5u_A           91 KASAHNK   97 (105)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCc
Confidence            9987654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1e-14  Score=130.36  Aligned_cols=82  Identities=16%  Similarity=0.295  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ...+.++|||+|||.++|+++|+++|++||+|..|+.    +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999873    478899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          264 SIPKDN  269 (780)
Q Consensus       264 a~pk~~  269 (780)
                      +.++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            987653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=7.2e-15  Score=133.87  Aligned_cols=83  Identities=25%  Similarity=0.348  Sum_probs=73.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccC--ccccccccccccCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIHFSIP  266 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng--~~l~gr~I~V~~a~p  266 (780)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|++. +.||||||+|.+.++|++|++.|++  ..|.|++|+|.|+.+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~-~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH   91 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCC
Confidence            3467999999999999999999999999999999853 3489999999999999999998864  789999999999987


Q ss_pred             CCCCCC
Q 004002          267 KDNPSD  272 (780)
Q Consensus       267 k~~~s~  272 (780)
                      +.....
T Consensus        92 ~~~~~~   97 (105)
T 1sjq_A           92 KELKTD   97 (105)
T ss_dssp             SSCCCT
T ss_pred             CCCCcc
Confidence            665443

>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=99.57  E-value=6.1e-15  Score=126.81  Aligned_cols=77  Identities=27%  Similarity=0.458  Sum_probs=71.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      +.+|||+|||.++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|..+.|++|.|.++.+
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            36899999999999999999999999999987     2578899999999999999999999999999999999999987


Q ss_pred             CC
Q 004002          267 KD  268 (780)
Q Consensus       267 k~  268 (780)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1e-14  Score=128.76  Aligned_cols=81  Identities=23%  Similarity=0.444  Sum_probs=74.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.++
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            35789999999999999999999999999999873     5778999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.3e-14  Score=129.45  Aligned_cols=81  Identities=23%  Similarity=0.474  Sum_probs=74.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++ |++..|.|++|.|.+
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            346799999999999999999999999999999983     47789999999999999999999 999999999999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++...
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9887654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=8.1e-15  Score=131.64  Aligned_cols=83  Identities=27%  Similarity=0.407  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456799999999999999999999999999999983     47889999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      ++.+....
T Consensus        89 ~a~~~~~~   96 (103)
T 2dnm_A           89 VARYGRRD   96 (103)
T ss_dssp             ECSSCCSC
T ss_pred             ECCcCCCC
Confidence            99876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.3e-14  Score=129.71  Aligned_cols=81  Identities=25%  Similarity=0.356  Sum_probs=74.2

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++
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            345679999999999999999999999999999976    3567899999999999999999999999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            98753

>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=99.56  E-value=6.9e-15  Score=130.57  Aligned_cols=78  Identities=23%  Similarity=0.444  Sum_probs=73.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ++++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|+|..+.|++|.|.++.
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            4689999999999999999999999999999983     47889999999999999999999999999999999999998


Q ss_pred             CCC
Q 004002          266 PKD  268 (780)
Q Consensus       266 pk~  268 (780)
                      ++.
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.56  E-value=1.9e-15  Score=133.69  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=70.0

Q ss_pred             cceeecCCCCCCChhHHHHHhcccC-CeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhC-CCccCCceEEEEecC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN-RSDIAGKRIKLEPSR  350 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG-~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~Ln-G~~i~Gr~L~V~~a~  350 (780)
                      .+|||+|||.++|+++|+++|++|| .|++|++     ++.++|||||+|.+.++|++||+.|+ +..+.|++|+|.+++
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 8999875     57789999999999999999999885 568999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8753

>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=99.56  E-value=1.8e-14  Score=129.66  Aligned_cols=82  Identities=20%  Similarity=0.340  Sum_probs=74.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccc---ccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRR---RKLDI  261 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g---r~I~V  261 (780)
                      ..+.++|||+|||.++++++|+++|++||.|..|+    .+++++|||||+|.+.++|++|++.|++..+.+   ++|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            34679999999999999999999999999999987    357789999999999999999999999999988   99999


Q ss_pred             ccCCCCCCC
Q 004002          262 HFSIPKDNP  270 (780)
Q Consensus       262 ~~a~pk~~~  270 (780)
                      .|+.++...
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.3e-14  Score=130.36  Aligned_cols=83  Identities=18%  Similarity=0.414  Sum_probs=75.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..+.++|||+|||+++|+++|+++|++||+|..|+.   +++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            446799999999999999999999999999999873   56899999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 004002          266 PKDNPS  271 (780)
Q Consensus       266 pk~~~s  271 (780)
                      ++....
T Consensus        92 ~~~~~~   97 (103)
T 2d9p_A           92 RKEERQ   97 (103)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876543

>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=99.56  E-value=5.5e-15  Score=128.25  Aligned_cols=77  Identities=18%  Similarity=0.415  Sum_probs=70.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      +.++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|++..+.|++|.|.|+.
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            5689999999999999999999999999999873     67789999999999999999999999999999999999987


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.56  E-value=1.8e-14  Score=130.83  Aligned_cols=83  Identities=17%  Similarity=0.335  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...+.++|||+|||.++|+++|+++|++||+|..|+  ..++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            345679999999999999999999999999999987  356689999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 004002          266 PKDNP  270 (780)
Q Consensus       266 pk~~~  270 (780)
                      ++...
T Consensus        98 ~~~~~  102 (109)
T 1x4a_A           98 SGRGT  102 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            76543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=1.8e-14  Score=130.05  Aligned_cols=83  Identities=25%  Similarity=0.490  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcceEEEEEEecHHHHHHHHHHc-cCccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLD  260 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~------tgkskG~aFV~F~~~e~A~~Al~~L-ng~~l~gr~I~  260 (780)
                      ...+.++|||+|||.++|+++|+++|++||+|..|+.      +++++|||||+|.+.++|++|++.| ++..|.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456799999999999999999999999999999983      5678999999999999999999999 99999999999


Q ss_pred             cccCCCCCCC
Q 004002          261 IHFSIPKDNP  270 (780)
Q Consensus       261 V~~a~pk~~~  270 (780)
                      |.|+.++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1e-14  Score=131.06  Aligned_cols=83  Identities=22%  Similarity=0.450  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
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            3456799999999999999999999999999999873     57889999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      |+.++...
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.4e-14  Score=130.05  Aligned_cols=83  Identities=22%  Similarity=0.328  Sum_probs=75.5

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .....++|||+|||.++++++|+++|++||.|+.|++   ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            3446689999999999999999999999999999876   3567899999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2d9p_A           91 QRKEER   96 (103)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            987643

>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=99.55  E-value=1.1e-14  Score=125.19  Aligned_cols=76  Identities=22%  Similarity=0.297  Sum_probs=71.1

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      .+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.+++++
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            47999999999999999999999999999875     4667899999999999999999999999999999999999886


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.4e-14  Score=130.46  Aligned_cols=81  Identities=25%  Similarity=0.303  Sum_probs=74.7

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      .....+|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.+
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            345679999999999999999999999999999986     566789999999999999999999999999999999999


Q ss_pred             cCCCch
Q 004002          349 SRPGGA  354 (780)
Q Consensus       349 a~~k~~  354 (780)
                      ++++..
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            988764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=8.4e-15  Score=132.12  Aligned_cols=80  Identities=18%  Similarity=0.458  Sum_probs=73.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.|
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            346689999999999999999999999999999873     478899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 004002          264 SIPKD  268 (780)
Q Consensus       264 a~pk~  268 (780)
                      +.++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98754

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=1.9e-14  Score=129.91  Aligned_cols=82  Identities=24%  Similarity=0.464  Sum_probs=74.7

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe------CCCcccEEEEEEcCHHHHHHHHHHh-CCCccCCceEE
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIK  345 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~L-nG~~i~Gr~L~  345 (780)
                      ......+|||+|||..+++++|+++|++||.|+.|++      ++.++|||||+|.+.++|++||+.| ||..+.|++|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3445689999999999999999999999999999987      4456899999999999999999999 99999999999


Q ss_pred             EEecCCCch
Q 004002          346 LEPSRPGGA  354 (780)
Q Consensus       346 V~~a~~k~~  354 (780)
                      |.+++++..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999998754

>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=99.55  E-value=1e-14  Score=126.59  Aligned_cols=77  Identities=18%  Similarity=0.390  Sum_probs=70.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++
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            4568999999999999999999999999999976     55678999999999999999999999999999999999998


Q ss_pred             CC
Q 004002          351 PG  352 (780)
Q Consensus       351 ~k  352 (780)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.55  E-value=7.8e-15  Score=132.42  Aligned_cols=79  Identities=13%  Similarity=0.276  Sum_probs=71.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcc--ccccccccccCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSIP  266 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~--l~gr~I~V~~a~p  266 (780)
                      ..++++|||+|||.++|+++|+++|++||.|.+++. .+.||||||+|.+.++|++|++.|++..  |.|++|.|.|+.+
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i-~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV-MPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEE-EcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            347899999999999999999999999999999975 3578999999999999999999999986  7899999999986


Q ss_pred             CC
Q 004002          267 KD  268 (780)
Q Consensus       267 k~  268 (780)
                      ++
T Consensus        97 k~   98 (100)
T 3r27_A           97 QK   98 (100)
T ss_dssp             SC
T ss_pred             cc
Confidence            54

>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=99.55  E-value=1.7e-14  Score=131.03  Aligned_cols=81  Identities=30%  Similarity=0.469  Sum_probs=73.6

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++  ++.+++||||+|.+.++|++||+.||+..+.|++|+|+++++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            345679999999999999999999999999999886  445689999999999999999999999999999999999988


Q ss_pred             Cch
Q 004002          352 GGA  354 (780)
Q Consensus       352 k~~  354 (780)
                      +..
T Consensus        99 ~~~  101 (109)
T 1x4a_A           99 GRG  101 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=1.2e-14  Score=129.12  Aligned_cols=81  Identities=25%  Similarity=0.452  Sum_probs=73.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe--------CCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~--------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      .+.++|||+|||+++|+++|+++|++||+|..|+.        +++++|||||+|.+.++|++|++.|++..|.|++|.|
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            46789999999999999999999999999998872        3378999999999999999999999999999999999


Q ss_pred             ccCCCCCCC
Q 004002          262 HFSIPKDNP  270 (780)
Q Consensus       262 ~~a~pk~~~  270 (780)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.55  E-value=2.1e-14  Score=131.56  Aligned_cols=83  Identities=17%  Similarity=0.394  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++|+++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456799999999999999999999999999999873     67889999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      |+.++...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99876544

>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=99.55  E-value=9.6e-15  Score=126.13  Aligned_cols=76  Identities=26%  Similarity=0.488  Sum_probs=71.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|..+.|++|.|.|+
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            4679999999999999999999999999999987     35778999999999999999999999999999999999987


Q ss_pred             C
Q 004002          265 I  265 (780)
Q Consensus       265 ~  265 (780)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.54  E-value=2e-14  Score=130.56  Aligned_cols=83  Identities=20%  Similarity=0.460  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHcc------Cccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQ------NKPLRR  256 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Ln------g~~l~g  256 (780)
                      ...+.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+      +..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            3456799999999999999999999999999999983     46789999999999999999999999      999999


Q ss_pred             cccccccCCCCCCC
Q 004002          257 RKLDIHFSIPKDNP  270 (780)
Q Consensus       257 r~I~V~~a~pk~~~  270 (780)
                      ++|.|.++.++...
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99999999887544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.54  E-value=8.2e-15  Score=128.74  Aligned_cols=73  Identities=18%  Similarity=0.192  Sum_probs=69.0

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..-|||+||+..+|+++|+++|.+||+|+++++. .+||||||+|.+.++|++|++.||+..+.|+.|+|++|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~-~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY-LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEc-CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4579999999999999999999999999999984 479999999999999999999999999999999999993

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.54  E-value=4.8e-15  Score=132.55  Aligned_cols=76  Identities=22%  Similarity=0.396  Sum_probs=68.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCC--eeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCC----ccCCceE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE--VKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS----DIAGKRI  344 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~--I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~----~i~Gr~L  344 (780)
                      .-.+|||+|||+++|+++|+++|++||.  |.+|++     ++.+||||||+|.+.++|++||+.|||.    .|+||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3458999999999999999999999995  567764     5778999999999999999999999997    4899999


Q ss_pred             EEEecCC
Q 004002          345 KLEPSRP  351 (780)
Q Consensus       345 ~V~~a~~  351 (780)
                      .|++|+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999975

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=2.3e-14  Score=126.35  Aligned_cols=78  Identities=26%  Similarity=0.448  Sum_probs=72.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++
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            345679999999999999999999999999999976     356789999999999999999999999999999999999


Q ss_pred             cCC
Q 004002          349 SRP  351 (780)
Q Consensus       349 a~~  351 (780)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            976

>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=99.54  E-value=2.9e-14  Score=128.04  Aligned_cols=83  Identities=22%  Similarity=0.384  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...+.++|||+|||+++|+++|+++|++||+|..|+.   ...++|||||+|.+.++|++|++.|++..|.|++|.|.++
T Consensus        11 ~~~~~~~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           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3456799999999999999999999999999999873   3447999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cq3_A           91 TARVMT   96 (103)
T ss_dssp             CSSCCC
T ss_pred             ccCCCC
Confidence            876644

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.9e-14  Score=129.21  Aligned_cols=82  Identities=21%  Similarity=0.321  Sum_probs=74.9

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            345689999999999999999999999999999976     456789999999999999999999999999999999999


Q ss_pred             cCCCchh
Q 004002          349 SRPGGAR  355 (780)
Q Consensus       349 a~~k~~r  355 (780)
                      ++++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9987643

>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=99.54  E-value=2.1e-14  Score=130.98  Aligned_cols=81  Identities=22%  Similarity=0.471  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.
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            3456799999999999999999999999999999872     57889999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 004002          263 FSIPKD  268 (780)
Q Consensus       263 ~a~pk~  268 (780)
                      ++.++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998764

>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=99.54  E-value=2e-14  Score=129.02  Aligned_cols=83  Identities=18%  Similarity=0.429  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...+.++|||+|||+++++++|+++|++||.|..|+.   ...++|||||+|.+.++|++|++.|++..|.|++|.|.|+
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 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            3456799999999999999999999999999999873   3447899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cqi_A           91 TTPSSQ   96 (103)
T ss_dssp             CCTTCC
T ss_pred             CCCccc
Confidence            876543

>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=99.54  E-value=1.4e-14  Score=132.85  Aligned_cols=81  Identities=25%  Similarity=0.417  Sum_probs=74.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..+.|++|+|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35579999999999999999999999999999875     5667899999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpz_A          103 RSKNDS  108 (115)
T ss_dssp             CCSCCC
T ss_pred             CCCCcC
Confidence            987643

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.54  E-value=9.4e-15  Score=134.46  Aligned_cols=89  Identities=20%  Similarity=0.145  Sum_probs=71.9

Q ss_pred             ccccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccC-CeeEEEe-CCCcccEEEEEEcCHHHHHHHHHHhC
Q 004002          258 KLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLN  335 (780)
Q Consensus       258 ~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG-~I~~v~~-~g~srG~aFV~F~~~e~A~~Ai~~Ln  335 (780)
                      ++.+.|..+..       ...+|||+|||.++++++|+++|++|| +|..+++ ...++|||||+|.+.++|++||+.||
T Consensus        16 ~~~~~~~~~p~-------~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~ln   88 (111)
T 2jvr_A           16 PRGSHMSKLPA-------KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLN   88 (111)
T ss_dssp             ---------CC-------CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTT
T ss_pred             ecchhcCCCCC-------CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcC
Confidence            45566654322       356899999999999999999999999 9999988 46789999999999999999999999


Q ss_pred             CCccCCceEEEEecCCCc
Q 004002          336 RSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       336 G~~i~Gr~L~V~~a~~k~  353 (780)
                      |..+.|++|+|++++...
T Consensus        89 g~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           89 NIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             TEEETTEEEEEEESCC--
T ss_pred             CCEECCeEEEEEECCCCC
Confidence            999999999999997653

>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=99.54  E-value=1.3e-14  Score=133.01  Aligned_cols=83  Identities=16%  Similarity=0.360  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3346689999999999999999999999999988872     68899999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      |+.++...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpz_A          101 LKRSKNDS  108 (115)
T ss_dssp             CCCCSCCC
T ss_pred             EcCCCCcC
Confidence            99876543

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.54  E-value=4.3e-15  Score=130.55  Aligned_cols=77  Identities=17%  Similarity=0.271  Sum_probs=66.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCC--CEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYG--DIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG--~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .+|||+|||+++|+++|+++|++||  +|.+++     .+++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5899999999999999999999999  888876     378899999999999999999999999999999999999998


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=2.3e-14  Score=126.47  Aligned_cols=79  Identities=27%  Similarity=0.388  Sum_probs=73.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++
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            3568999999999999999999999999999976     45678999999999999999999999999999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        84 ~~~~   87 (95)
T 2dnz_A           84 ERLD   87 (95)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            8754

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=3.4e-14  Score=127.68  Aligned_cols=82  Identities=22%  Similarity=0.398  Sum_probs=75.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhc-CCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCcc-ccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQ-YGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKP-LRRRKLDIH  262 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~-yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~-l~gr~I~V~  262 (780)
                      ..+.++|||+|||+++|+++|+++|++ ||.|..|+.    +++++|||||+|.+.++|++|++.|++.. |.|++|.|.
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            346799999999999999999999999 999999873    67899999999999999999999999999 999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99876543

>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=99.54  E-value=1.7e-14  Score=124.60  Aligned_cols=75  Identities=27%  Similarity=0.462  Sum_probs=70.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            4579999999999999999999999999999975     45578999999999999999999999999999999999985

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=7.7e-15  Score=129.84  Aligned_cols=81  Identities=20%  Similarity=0.439  Sum_probs=74.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE-E-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL-Y-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv-~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      .+.++|||+|||.++++++|+++|++||.|..+ +     .+++++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            467999999999999999999999999999877 5     3577899999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9877644

>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=99.54  E-value=2.8e-14  Score=126.59  Aligned_cols=79  Identities=18%  Similarity=0.275  Sum_probs=73.4

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.++++
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            468999999999999999999999999999986     366789999999999999999999999999999999999998


Q ss_pred             Cchh
Q 004002          352 GGAR  355 (780)
Q Consensus       352 k~~r  355 (780)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            7644

>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=99.54  E-value=2.7e-14  Score=128.49  Aligned_cols=81  Identities=20%  Similarity=0.273  Sum_probs=73.9

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC---ceEEEE
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG---KRIKLE  347 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G---r~L~V~  347 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++||+.|||..+.|   +.|+|.
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            34679999999999999999999999999999976    45568999999999999999999999999998   999999


Q ss_pred             ecCCCchh
Q 004002          348 PSRPGGAR  355 (780)
Q Consensus       348 ~a~~k~~r  355 (780)
                      +++++..+
T Consensus        93 ~a~~~~~~  100 (105)
T 2dnh_A           93 FADTDKES  100 (105)
T ss_dssp             ESCSSCCC
T ss_pred             ECccCccc
Confidence            99987654

>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=99.54  E-value=2.6e-14  Score=128.31  Aligned_cols=82  Identities=30%  Similarity=0.397  Sum_probs=74.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~---g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++.   ..++|||||+|.+.++|++|++.|||..+.|+.|+|.+++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            3456799999999999999999999999999999863   3367999999999999999999999999999999999999


Q ss_pred             CCchh
Q 004002          351 PGGAR  355 (780)
Q Consensus       351 ~k~~r  355 (780)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2cqi_A           92 TPSSQ   96 (103)
T ss_dssp             CTTCC
T ss_pred             CCccc
Confidence            86543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.4e-14  Score=129.80  Aligned_cols=81  Identities=22%  Similarity=0.464  Sum_probs=74.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            346799999999999999999999999999999883     567899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          264 SIPKDN  269 (780)
Q Consensus       264 a~pk~~  269 (780)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            987654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=8.1e-15  Score=133.53  Aligned_cols=79  Identities=15%  Similarity=0.212  Sum_probs=71.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC--CccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG--~~i~Gr~L~V~~a~~k~  353 (780)
                      ...+|||+|||.++|+++|+++|++||.|++|++.. .||||||+|++.++|++|++.|++  ..+.|++|+|.+++++.
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~-~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            457899999999999999999999999999999854 489999999999999999999874  78999999999998765


Q ss_pred             hh
Q 004002          354 AR  355 (780)
Q Consensus       354 ~r  355 (780)
                      ..
T Consensus        94 ~~   95 (105)
T 1sjq_A           94 LK   95 (105)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=2.9e-14  Score=127.12  Aligned_cols=80  Identities=23%  Similarity=0.449  Sum_probs=73.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+ |||..+.|+.|+|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            45679999999999999999999999999999986     35678999999999999999998 9999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++..+
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            987643

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.53  E-value=1.7e-14  Score=130.22  Aligned_cols=77  Identities=21%  Similarity=0.248  Sum_probs=70.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCc--cCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~--i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++|+++|+++|++||.|++|++. +.||+|||+|++.++|.+|++.|+|..  +.|++|+|.+++++.
T Consensus        20 ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            45789999999999999999999999999999985 468999999999999999999999985  789999999998753

>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=99.53  E-value=1.8e-14  Score=129.92  Aligned_cols=82  Identities=24%  Similarity=0.482  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccc---ccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPL---RRRKL  259 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l---~gr~I  259 (780)
                      .+.+.++|||+|||.++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+   .+++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            3456799999999999999999999999999999983     577899999999999999999999999987   89999


Q ss_pred             ccccCCCCCC
Q 004002          260 DIHFSIPKDN  269 (780)
Q Consensus       260 ~V~~a~pk~~  269 (780)
                      .|.++.++..
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999987654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.53  E-value=2.9e-14  Score=130.60  Aligned_cols=82  Identities=21%  Similarity=0.410  Sum_probs=74.8

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      .....+|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..+.|+.|+|.+
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            345679999999999999999999999999999976     456789999999999999999999999999999999999


Q ss_pred             cCCCchh
Q 004002          349 SRPGGAR  355 (780)
Q Consensus       349 a~~k~~r  355 (780)
                      ++++..+
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9987643

>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=99.53  E-value=2.1e-14  Score=138.79  Aligned_cols=82  Identities=28%  Similarity=0.478  Sum_probs=75.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ....++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999983     688999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++..+
T Consensus       147 a~~~~~~  153 (158)
T 2kn4_A          147 ARYGRPP  153 (158)
T ss_dssp             ECCSSCC
T ss_pred             CCCCCCC
Confidence            9876543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.8e-14  Score=129.94  Aligned_cols=80  Identities=26%  Similarity=0.417  Sum_probs=73.5

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.+
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            345678999999999999999999999999999976     366789999999999999999999999999999999999


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      ++++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98765

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.2e-14  Score=130.15  Aligned_cols=82  Identities=26%  Similarity=0.461  Sum_probs=75.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            346799999999999999999999999999999873     467899999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++...
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.7e-14  Score=127.24  Aligned_cols=78  Identities=21%  Similarity=0.381  Sum_probs=72.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.|
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            356799999999999999999999999999999873     478899999999999999999999999999999999999


Q ss_pred             CCC
Q 004002          264 SIP  266 (780)
Q Consensus       264 a~p  266 (780)
                      +.+
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=2.9e-14  Score=124.97  Aligned_cols=78  Identities=26%  Similarity=0.411  Sum_probs=72.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      .+.++|||+|||.++|+++|+++|++||+|..|+..   +|||||+|.+.++|++|++.|++..|.|++|.|.++.++..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            467999999999999999999999999999999864   79999999999999999999999999999999999987664


Q ss_pred             C
Q 004002          270 P  270 (780)
Q Consensus       270 ~  270 (780)
                      .
T Consensus        83 ~   83 (90)
T 2dnq_A           83 A   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.53  E-value=2e-14  Score=133.88  Aligned_cols=86  Identities=24%  Similarity=0.327  Sum_probs=74.7

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccC--cccccccccccc
Q 004002          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIHF  263 (780)
Q Consensus       186 ~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng--~~l~gr~I~V~~  263 (780)
                      .....++++|||+|||+++|+++|+++|++||+|.+|++. +.||||||+|.+.++|++|++.|++  ..|.|++|+|.|
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~-~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~  103 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF  103 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEE-GGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEE
Confidence            3344578999999999999999999999999999998843 3589999999999999999999875  689999999999


Q ss_pred             CCCCCCCCC
Q 004002          264 SIPKDNPSD  272 (780)
Q Consensus       264 a~pk~~~s~  272 (780)
                      +.++.....
T Consensus       104 a~~k~~~~~  112 (119)
T 2ad9_A          104 SNHKELKTD  112 (119)
T ss_dssp             CSSSSCCCC
T ss_pred             ccCCCCCcc
Confidence            987765443

>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=99.53  E-value=5.6e-15  Score=129.82  Aligned_cols=77  Identities=17%  Similarity=0.225  Sum_probs=66.1

Q ss_pred             cceeecCCCCCCChhHHHHHhcccC--CeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG--~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      .+|||+|||.++++++|+++|++||  .|.+|++     +++++|||||+|.+.++|++||+.|||..+.|++|+|.++.
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            3799999999999999999999999  8988875     66789999999999999999999999999999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7653

>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=99.53  E-value=4.9e-15  Score=166.94  Aligned_cols=145  Identities=25%  Similarity=0.354  Sum_probs=104.5

Q ss_pred             HHHHhhcCCCEEEEEe-------CCCcceEE-----EEEEecHHHHHHHHHHccCccccccc-------------ccccc
Q 004002          209 LRALFEQYGDIRTLYT-------ACKHRGFV-----MISYYDIRAARTAMRALQNKPLRRRK-------------LDIHF  263 (780)
Q Consensus       209 Lr~lF~~yG~I~sv~~-------tgkskG~a-----FV~F~~~e~A~~Al~~Lng~~l~gr~-------------I~V~~  263 (780)
                      |..+|.++|+|..|..       ..+..+|+     |+.|....+|..++..++......+.             ..+..
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            6789999999887631       11233444     77887766655555433332221110             01111


Q ss_pred             CCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       264 a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      ..+...+........+|||+|||..+|+++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||..|||..
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            2222222223344579999999999999999999999999999976     56679999999999999999999999999


Q ss_pred             cCCceEEEEecCCCc
Q 004002          339 IAGKRIKLEPSRPGG  353 (780)
Q Consensus       339 i~Gr~L~V~~a~~k~  353 (780)
                      |.|+.|.|.++.++.
T Consensus       169 i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          169 IDGRRVLVDVERGRT  183 (437)
T ss_pred             ECCEEEEEEEeCCCC
Confidence            999999999998754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=1.8e-14  Score=128.25  Aligned_cols=80  Identities=11%  Similarity=0.344  Sum_probs=73.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEE-EEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccc----c
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIR-TLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK----L  259 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~-sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~----I  259 (780)
                      .+.++|||+|||+++++++|+++|++||+|. .|+     .+++++|||||+|.+.++|++|++.|+|..|.|+.    |
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            4679999999999999999999999999998 876     25789999999999999999999999999999999    9


Q ss_pred             ccccCCCCCC
Q 004002          260 DIHFSIPKDN  269 (780)
Q Consensus       260 ~V~~a~pk~~  269 (780)
                      +|.|+.+...
T Consensus        87 ~v~~a~~~~~   96 (99)
T 2div_A           87 KLNYATYSGP   96 (99)
T ss_dssp             CEEETTCCSS
T ss_pred             EEeecCCCCC
Confidence            9999987653

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=3.9e-14  Score=124.77  Aligned_cols=76  Identities=30%  Similarity=0.444  Sum_probs=70.5

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            45679999999999999999999999999999986     3567899999999999999999999999999999999998


Q ss_pred             C
Q 004002          350 R  350 (780)
Q Consensus       350 ~  350 (780)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.52  E-value=2.2e-14  Score=130.35  Aligned_cols=82  Identities=23%  Similarity=0.388  Sum_probs=74.5

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||..+++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.+
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            345679999999999999999999999999999986     456789999999999999999999999999999999999


Q ss_pred             cCCCchh
Q 004002          349 SRPGGAR  355 (780)
Q Consensus       349 a~~k~~r  355 (780)
                      ++++..+
T Consensus       103 a~~~~~~  109 (110)
T 1oo0_B          103 CFVKGPK  109 (110)
T ss_dssp             SEESSCC
T ss_pred             cccCCCC
Confidence            9877643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.9e-14  Score=128.91  Aligned_cols=81  Identities=26%  Similarity=0.443  Sum_probs=74.2

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++
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            35679999999999999999999999999999986     3567899999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887643

>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=99.52  E-value=3.8e-14  Score=125.99  Aligned_cols=78  Identities=21%  Similarity=0.374  Sum_probs=72.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC--CceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA--GKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~--Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++... +|||||+|.+.++|++|++.|||..+.  |++|+|.+++++.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            4578999999999999999999999999999998543 899999999999999999999999999  9999999999875


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        95 ~   95 (97)
T 1why_A           95 S   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.52  E-value=5.2e-14  Score=126.37  Aligned_cols=82  Identities=21%  Similarity=0.375  Sum_probs=74.1

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~---g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .....++|||+|||.++++++|+++|++||.|+.|++.   ..++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus        11 ~~~~~~~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           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34456899999999999999999999999999999873   235899999999999999999999999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus        91 ~~~~~   95 (103)
T 2cq3_A           91 TARVM   95 (103)
T ss_dssp             CSSCC
T ss_pred             ccCCC
Confidence            88754

>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=99.52  E-value=2e-14  Score=130.91  Aligned_cols=95  Identities=21%  Similarity=0.313  Sum_probs=81.2

Q ss_pred             cccccccccCCCCCCCCCCCCCccceeecCCCCC-CChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHH
Q 004002          255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       255 ~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                      .|.+|.|..+.+.... ......++|||+|||.+ +++++|+++|++||.|+.|++   ++|||||+|.+.++|++|++.
T Consensus         6 ~g~~~~~~~s~~~~~~-~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~   81 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKN-DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLG   81 (110)
T ss_dssp             CSCCCCCCCCCSCCSC-CCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHH
T ss_pred             CCcccccccCCCCCCC-CCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHH
Confidence            4667777766544332 22334579999999999 999999999999999999998   689999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCCc
Q 004002          334 LNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       334 LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      |||..+.|++|+|+++++..
T Consensus        82 l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           82 ENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HTTCEETTEECCEEESCCCC
T ss_pred             cCCCEECCeEEEEEECCCCC
Confidence            99999999999999998654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=1.8e-14  Score=126.94  Aligned_cols=77  Identities=25%  Similarity=0.466  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.|
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            346789999999999999999999999999999883     477899999999999999999999999999999999998


Q ss_pred             CC
Q 004002          264 SI  265 (780)
Q Consensus       264 a~  265 (780)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.52  E-value=4.5e-14  Score=128.30  Aligned_cols=81  Identities=15%  Similarity=0.244  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCc--cccccccccccCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK--PLRRRKLDIHFSI  265 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~--~l~gr~I~V~~a~  265 (780)
                      ...++++|||+|||+++++++|+++|++||+|..|+.. +.||||||+|.+.++|++|++.|++.  .|.|++|.|.|+.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~   89 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcc
Confidence            34577999999999999999999999999999998853 35899999999999999999999765  4899999999998


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      ++..
T Consensus        90 ~~~~   93 (104)
T 1wex_A           90 SKRI   93 (104)
T ss_dssp             SSSC
T ss_pred             Cccc
Confidence            7553

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.3e-14  Score=128.63  Aligned_cols=80  Identities=29%  Similarity=0.442  Sum_probs=73.6

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..+.|+.|+|.++
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            34679999999999999999999999999999986     3667899999999999999999999999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            87653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.9e-14  Score=124.99  Aligned_cols=77  Identities=26%  Similarity=0.416  Sum_probs=72.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++.   ++||||+|.+.++|++|++.|||..+.|++|+|++++++..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            356799999999999999999999999999999986   79999999999999999999999999999999999988754

>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=99.52  E-value=1.8e-14  Score=130.97  Aligned_cols=81  Identities=20%  Similarity=0.415  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3446789999999999999999999999999999983     57789999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 004002          263 FSIPKD  268 (780)
Q Consensus       263 ~a~pk~  268 (780)
                      |+.++.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            998754

>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=99.52  E-value=2.6e-14  Score=134.70  Aligned_cols=81  Identities=25%  Similarity=0.463  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456799999999999999999999999999999883     47899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 004002          263 FSIPKD  268 (780)
Q Consensus       263 ~a~pk~  268 (780)
                      |+.++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            998754

>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=99.52  E-value=5.5e-14  Score=124.94  Aligned_cols=79  Identities=27%  Similarity=0.477  Sum_probs=72.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccc--ccccccccCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIP  266 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~--gr~I~V~~a~p  266 (780)
                      ..+.++|||+|||.++|+++|+++|++||+|..|+... .+|||||+|.+.++|++|++.|++..|.  |++|.|.|+.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~   92 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCC
Confidence            34679999999999999999999999999999998543 3899999999999999999999999999  99999999987


Q ss_pred             CC
Q 004002          267 KD  268 (780)
Q Consensus       267 k~  268 (780)
                      +.
T Consensus        93 ~~   94 (97)
T 1why_A           93 GP   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.52  E-value=2.1e-14  Score=124.59  Aligned_cols=79  Identities=25%  Similarity=0.435  Sum_probs=71.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeC-----CC-cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PH-KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~-----g~-srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ..++|||+|||.++++++|+++|++||.|..|++.     +. ++|||||+|.+.++|++|++.|||..+.|+.|+|+++
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            45689999999999999999999999999999862     12 7899999999999999999999999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      .+...
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=1.8e-14  Score=128.02  Aligned_cols=79  Identities=23%  Similarity=0.359  Sum_probs=72.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeC--------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~--------g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++.        +.++|||||+|.+.++|++|++.|||..+.|++|+|.
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            45689999999999999999999999999998762        2678999999999999999999999999999999999


Q ss_pred             ecCCCch
Q 004002          348 PSRPGGA  354 (780)
Q Consensus       348 ~a~~k~~  354 (780)
                      +++++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9988653

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.8e-14  Score=129.02  Aligned_cols=79  Identities=24%  Similarity=0.511  Sum_probs=73.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.+++
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 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   90 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4579999999999999999999999999999986     34578999999999999999999999999999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        91 ~~~~   94 (102)
T 1x5s_A           91 KSSD   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.52  E-value=7.4e-15  Score=131.34  Aligned_cols=77  Identities=17%  Similarity=0.361  Sum_probs=68.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCC--EEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcc----ccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGD--IRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKP----LRRRK  258 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~--I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~----l~gr~  258 (780)
                      ..-.||||+|||+++|+++|+++|++||.  |.+|+     .++++||||||+|.+.++|++|++.|++..    |.||+
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34579999999999999999999999995  44565     368899999999999999999999999974    88999


Q ss_pred             cccccCCC
Q 004002          259 LDIHFSIP  266 (780)
Q Consensus       259 I~V~~a~p  266 (780)
                      |.|.||+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999864

>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=99.52  E-value=5e-14  Score=127.90  Aligned_cols=81  Identities=21%  Similarity=0.373  Sum_probs=74.4

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhC------CCccCCce
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN------RSDIAGKR  343 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~Ln------G~~i~Gr~  343 (780)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++||+.||      |..+.|++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            35679999999999999999999999999999986     35689999999999999999999999      99999999


Q ss_pred             EEEEecCCCchh
Q 004002          344 IKLEPSRPGGAR  355 (780)
Q Consensus       344 L~V~~a~~k~~r  355 (780)
                      |+|.++.++..+
T Consensus        93 l~v~~a~~~~~~  104 (111)
T 1x4h_A           93 LKVDLAVTRDEA  104 (111)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEECCCCccC
Confidence            999999987643

>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=99.52  E-value=1.8e-14  Score=127.25  Aligned_cols=78  Identities=23%  Similarity=0.333  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      .+.+.++|||+|||+++++++|+++|++||+|..|+.    .++++|||||+|.+.++|++|++.|++..|.|++|.|.+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3456799999999999999999999999999999872    467899999999999999999999999999999999998


Q ss_pred             CC
Q 004002          264 SI  265 (780)
Q Consensus       264 a~  265 (780)
                      +.
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.52  E-value=2.9e-14  Score=128.53  Aligned_cols=82  Identities=18%  Similarity=0.376  Sum_probs=74.3

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCcc---CCceE
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI---AGKRI  344 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i---~Gr~L  344 (780)
                      ......+|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+   .|++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            3445689999999999999999999999999999986     356789999999999999999999999988   89999


Q ss_pred             EEEecCCCch
Q 004002          345 KLEPSRPGGA  354 (780)
Q Consensus       345 ~V~~a~~k~~  354 (780)
                      +|.+++++..
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999988754

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.52  E-value=2.5e-14  Score=134.69  Aligned_cols=80  Identities=28%  Similarity=0.411  Sum_probs=72.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HHhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr----~lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ..+.++|||+|||+++++++|+    ++|++||+|.+|..  +++++|||||+|.+.++|++|++.|+|..|.|++|.|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            3467899999999999999876    69999999999874  57899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 004002          263 FSIPKD  268 (780)
Q Consensus       263 ~a~pk~  268 (780)
                      |+.++.
T Consensus       106 ~a~~~~  111 (127)
T 2a3j_A          106 FSETPQ  111 (127)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            998654

>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=99.52  E-value=2.5e-14  Score=124.20  Aligned_cols=78  Identities=12%  Similarity=0.325  Sum_probs=71.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..++|||+|||.++|+++|+++|++||+|..++.      .++++|||||+|.+.++|++|++.|+|..+.|++|.|.++
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            4589999999999999999999999999999873      1238999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.52  E-value=1.3e-14  Score=128.58  Aligned_cols=81  Identities=22%  Similarity=0.385  Sum_probs=75.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      +.+.++|||+|||.++++++|+++|++||+|..+..+++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.++.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            34679999999999999999999999999998887788999999999999999999999999999999999999998765


Q ss_pred             C
Q 004002          269 N  269 (780)
Q Consensus       269 ~  269 (780)
                      .
T Consensus        93 ~   93 (96)
T 1fjc_A           93 G   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.52  E-value=4.4e-14  Score=127.78  Aligned_cols=81  Identities=23%  Similarity=0.331  Sum_probs=71.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHcc--CccccccccccccCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLDIHFSIP  266 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Ln--g~~l~gr~I~V~~a~p  266 (780)
                      ..++++|||+|||+++|+++|+++|++||+|..|+.. +.||||||+|.+.++|++|++.|+  +..|.|++|.|.|+.+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   90 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   90 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCc
Confidence            3577999999999999999999999999999998743 348999999999999999999875  5679999999999987


Q ss_pred             CCCC
Q 004002          267 KDNP  270 (780)
Q Consensus       267 k~~~  270 (780)
                      +...
T Consensus        91 ~~~~   94 (101)
T 2cq1_A           91 KELK   94 (101)
T ss_dssp             SSCC
T ss_pred             ccCc
Confidence            6543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.52  E-value=2.7e-14  Score=125.34  Aligned_cols=79  Identities=19%  Similarity=0.245  Sum_probs=73.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ...+|||+|||.++++++|+++|++||.|+.|++   ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            4579999999999999999999999999999876   4567899999999999999999999999999999999999886


Q ss_pred             ch
Q 004002          353 GA  354 (780)
Q Consensus       353 ~~  354 (780)
                      ..
T Consensus        87 ~~   88 (92)
T 2dgv_A           87 SG   88 (92)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.52  E-value=1.7e-14  Score=127.78  Aligned_cols=82  Identities=21%  Similarity=0.335  Sum_probs=75.7

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      .....+|||+|||..+++++|+++|++||.|..+..++.++|||||+|.+.++|++|++.|||..+.|++|+|.+++++.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            34567999999999999999999999999998887788889999999999999999999999999999999999998876


Q ss_pred             hh
Q 004002          354 AR  355 (780)
Q Consensus       354 ~r  355 (780)
                      .+
T Consensus        93 ~~   94 (96)
T 1fjc_A           93 GT   94 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.52  E-value=3.6e-14  Score=129.40  Aligned_cols=80  Identities=28%  Similarity=0.398  Sum_probs=73.5

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++
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            345679999999999999999999999999999875     456789999999999999999999999999999999999


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      ++++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98864

>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=99.51  E-value=5.5e-14  Score=127.14  Aligned_cols=79  Identities=15%  Similarity=0.167  Sum_probs=71.2

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~k  352 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++.. .||||||+|++.++|++|++.|  ++..+.|++|+|.+++++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            3557999999999999999999999999999998754 4899999999999999999987  467899999999999876


Q ss_pred             ch
Q 004002          353 GA  354 (780)
Q Consensus       353 ~~  354 (780)
                      ..
T Consensus        92 ~~   93 (101)
T 2cq1_A           92 EL   93 (101)
T ss_dssp             SC
T ss_pred             cC
Confidence            54

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.51  E-value=3.1e-14  Score=131.03  Aligned_cols=78  Identities=15%  Similarity=0.353  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+|..|.|++|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4456799999999999999999999999999999873     47889999999999999999999999999999999999


Q ss_pred             cCC
Q 004002          263 FSI  265 (780)
Q Consensus       263 ~a~  265 (780)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            873

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.51  E-value=4.5e-14  Score=133.64  Aligned_cols=83  Identities=28%  Similarity=0.425  Sum_probs=75.1

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      .....++|||+|||.++++++|+++|++||.|+.|++     +++++|||||+|.+.++|++||+.|||..+.|++|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3445679999999999999999999999999999976     35678999999999999999999999999999999999


Q ss_pred             ecCCCchh
Q 004002          348 PSRPGGAR  355 (780)
Q Consensus       348 ~a~~k~~r  355 (780)
                      +++++..+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99987643

>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=99.51  E-value=4.2e-14  Score=127.32  Aligned_cols=81  Identities=16%  Similarity=0.374  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----C-CCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----A-CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----t-gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      ...+.++|||+|||+++|+++|+++|++|| |..|++     + ++++|||||+|.+.++|++|+ .|++..|.|++|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345679999999999999999999999999 999883     2 788999999999999999999 89999999999999


Q ss_pred             ccCCCCCCC
Q 004002          262 HFSIPKDNP  270 (780)
Q Consensus       262 ~~a~pk~~~  270 (780)
                      .++.++...
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=99.51  E-value=3.5e-14  Score=126.33  Aligned_cols=79  Identities=24%  Similarity=0.389  Sum_probs=72.0

Q ss_pred             CccceeecCCCCCCChhHHH----HHhcccCCeeEEEeCC--CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRETP--HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~----~~Fs~yG~I~~v~~~g--~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...+|||+|||.++++++|+    ++|++||.|++|++..  ..+|||||+|.+.++|++||+.|||..+.|++|+|+++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            45789999999999999999    9999999999998742  22899999999999999999999999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus        88 ~~~~~   92 (96)
T 2dgx_A           88 TGASG   92 (96)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87653

>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=99.51  E-value=2.3e-14  Score=129.93  Aligned_cols=79  Identities=15%  Similarity=0.199  Sum_probs=71.1

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcc--ccccccccccCC
Q 004002          189 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~--l~gr~I~V~~a~  265 (780)
                      ..++++|||+|||+ ++|+++|+++|++||+|.+|++. +.+|||||+|.+.++|++|++.|++..  |.|++|.|.|+.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   90 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   90 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECC
Confidence            34789999999999 99999999999999999999853 467999999999999999999998754  899999999998


Q ss_pred             CCC
Q 004002          266 PKD  268 (780)
Q Consensus       266 pk~  268 (780)
                      ...
T Consensus        91 ~~~   93 (102)
T 1x4d_A           91 KYK   93 (102)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            644

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=2.8e-14  Score=126.95  Aligned_cols=79  Identities=19%  Similarity=0.221  Sum_probs=71.5

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ....+|||+|||.++++++|+++|++||.|....+++.++|||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            3457999999999999999999999999996333456789999999999999999999999999999999999998865

>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=99.51  E-value=2.9e-14  Score=131.62  Aligned_cols=81  Identities=21%  Similarity=0.414  Sum_probs=74.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .+.++|||+|||.++|+++|+++|++||.|..|+.    +++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.
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            45789999999999999999999999999998873    57889999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 004002          266 PKDNP  270 (780)
Q Consensus       266 pk~~~  270 (780)
                      ++...
T Consensus        85 ~~~~~   89 (116)
T 2fy1_A           85 KPSFQ   89 (116)
T ss_dssp             CSSCS
T ss_pred             CCCCC
Confidence            76543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.5e-14  Score=123.84  Aligned_cols=76  Identities=22%  Similarity=0.347  Sum_probs=70.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|..|.|+.|++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            3678999999999999999999999999999987     35788999999999999999999999999999999999876


Q ss_pred             C
Q 004002          265 I  265 (780)
Q Consensus       265 ~  265 (780)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.51  E-value=2.2e-14  Score=130.01  Aligned_cols=77  Identities=17%  Similarity=0.236  Sum_probs=70.1

Q ss_pred             CccceeecCCCC-CCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC--ccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~-~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~--~i~Gr~L~V~~a~~k  352 (780)
                      ..++|||+|||. ++|+++|+++|++||.|++|++. ..++||||+|++.++|++||+.||+.  .+.|++|+|.++++.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            457899999999 99999999999999999999985 45799999999999999999999865  599999999999865


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        93 ~   93 (102)
T 1x4d_A           93 K   93 (102)
T ss_dssp             T
T ss_pred             C
Confidence            3

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.1e-14  Score=126.97  Aligned_cols=80  Identities=21%  Similarity=0.387  Sum_probs=72.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEE-Ee-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v-~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ..++|||+|||.++++++|+++|++||.|..| ++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++
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            45789999999999999999999999999888 65     4557899999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            887643

>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=99.51  E-value=3.6e-14  Score=125.25  Aligned_cols=77  Identities=21%  Similarity=0.271  Sum_probs=71.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...++|||+|||..+++++|+++|++||.|+.|++    .+.++|||||+|.+.++|++|++.|||..+.|++|+|++++
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            35679999999999999999999999999999976    34568999999999999999999999999999999999987


Q ss_pred             C
Q 004002          351 P  351 (780)
Q Consensus       351 ~  351 (780)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3.7e-14  Score=124.84  Aligned_cols=80  Identities=24%  Similarity=0.422  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ...+.++|||+|||+++|+++|+++|++||+|..|+..   ++||||+|.+.++|++|++.|++..|.|++|.|.++.++
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   82 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR   82 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCC
Confidence            34567999999999999999999999999999999863   569999999999999999999999999999999999876


Q ss_pred             CCC
Q 004002          268 DNP  270 (780)
Q Consensus       268 ~~~  270 (780)
                      ...
T Consensus        83 ~~~   85 (92)
T 2dgt_A           83 LRT   85 (92)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=5.7e-14  Score=128.96  Aligned_cols=82  Identities=24%  Similarity=0.409  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      .+.+.++|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++ .|.|++|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            4456799999999999999999999999999999883     577899999999999999999999998 8999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      ++.++..+
T Consensus        92 ~a~~~~~~   99 (116)
T 2cqd_A           92 LAYLGAKP   99 (116)
T ss_dssp             ESTTTCCC
T ss_pred             EcccCCCc
Confidence            99775543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3.5e-14  Score=127.95  Aligned_cols=82  Identities=24%  Similarity=0.442  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++++++|+++|++||+|..|+     .+++++|||||+|.+.++|++|++. ++..|.|++|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            345679999999999999999999999999999987     2578899999999999999999998 9999999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99887644

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.51  E-value=9.8e-15  Score=131.10  Aligned_cols=77  Identities=17%  Similarity=0.276  Sum_probs=72.0

Q ss_pred             CCcEEEEeCCCC------CCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccc-cc
Q 004002          191 PSRTLFVRNINS------NVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR-RK  258 (780)
Q Consensus       191 ~s~tLfVgNLp~------~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g-r~  258 (780)
                      .+++|||+|||.      ++++++|+++|++||.|.+|+.     +++++|||||+|.+.++|++|++.|+|..|.| ++
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            468999999999      9999999999999999999983     48899999999999999999999999999999 99


Q ss_pred             cccccCCCC
Q 004002          259 LDIHFSIPK  267 (780)
Q Consensus       259 I~V~~a~pk  267 (780)
                      |.|.++.++
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999998754

>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=99.51  E-value=4.9e-14  Score=132.77  Aligned_cols=79  Identities=27%  Similarity=0.435  Sum_probs=73.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..|.|++|+|+++
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999986     3577899999999999999999999999999999999999


Q ss_pred             CCCc
Q 004002          350 RPGG  353 (780)
Q Consensus       350 ~~k~  353 (780)
                      +++.
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8865

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.8e-14  Score=130.08  Aligned_cols=81  Identities=21%  Similarity=0.411  Sum_probs=73.7

Q ss_pred             CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       272 ~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~---g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ......++|||+|||.++++++|+++|++||.|+.|++.   +.++|||||+|.+.++|++|++.|||..+.|++|+|++
T Consensus        24 ~~~~~~~~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           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344566899999999999999999999999999999873   34689999999999999999999999999999999999


Q ss_pred             cCCC
Q 004002          349 SRPG  352 (780)
Q Consensus       349 a~~k  352 (780)
                      ++++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9876

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=5.3e-14  Score=123.81  Aligned_cols=78  Identities=26%  Similarity=0.410  Sum_probs=72.4

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++.   ++||||+|.+.++|++|++.|||..+.|+.|+|++++++.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            3456799999999999999999999999999999986   5699999999999999999999999999999999998875


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        84 ~   84 (92)
T 2dgt_A           84 R   84 (92)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.50  E-value=3.3e-14  Score=126.84  Aligned_cols=77  Identities=23%  Similarity=0.397  Sum_probs=70.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE--------EE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s--------v~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                      ..+.++|||+|||.++|+++|+++|++||.|..        ++     .+++++|||||+|.+.++|++|++.|+|..|.
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            346799999999999999999999999999988        65     25788999999999999999999999999999


Q ss_pred             ccccccccCC
Q 004002          256 RRKLDIHFSI  265 (780)
Q Consensus       256 gr~I~V~~a~  265 (780)
                      |++|+|+++.
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            9999999873

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.50  E-value=5.1e-14  Score=125.60  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=70.0

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeE--------EEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~--------v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G  341 (780)
                      ....+|||+|||.++++++|+++|++||.|..        |++     ++.++|||||+|.+.++|++|++.|||..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            35679999999999999999999999999998        765     46678999999999999999999999999999


Q ss_pred             ceEEEEecC
Q 004002          342 KRIKLEPSR  350 (780)
Q Consensus       342 r~L~V~~a~  350 (780)
                      ++|+|++|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.50  E-value=5.5e-14  Score=126.34  Aligned_cols=80  Identities=20%  Similarity=0.420  Sum_probs=72.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||+++++++|+++|++|| |..|+.     +++++|||||+|.+.++|++|+ .|++..|.|++|.|.+
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            45679999999999999999999999997 988872     5788999999999999999999 8999999999999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9876543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.50  E-value=3.1e-14  Score=129.90  Aligned_cols=79  Identities=23%  Similarity=0.422  Sum_probs=72.9

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      .....++|||+|||.++++++|+++|++||.|+.|++.   +|||||+|.+.++|++|++.|||..+.|+.|+|.+++++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            34566899999999999999999999999999999986   899999999999999999999999999999999999987


Q ss_pred             ch
Q 004002          353 GA  354 (780)
Q Consensus       353 ~~  354 (780)
                      ..
T Consensus       104 ~~  105 (108)
T 2jvo_A          104 AK  105 (108)
T ss_dssp             C-
T ss_pred             CC
Confidence            54

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.50  E-value=2.8e-14  Score=134.29  Aligned_cols=83  Identities=18%  Similarity=0.348  Sum_probs=74.5

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE--EE-----eCCCcceEEEEEEecHHHHHHHHHHccCc----ccc
Q 004002          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--LY-----TACKHRGFVMISYYDIRAARTAMRALQNK----PLR  255 (780)
Q Consensus       187 ~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s--v~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~----~l~  255 (780)
                      ..+.+.++|||+|||+++|+++|+++|++||.|..  |+     .++++||||||+|.+. +|++|++.|+|.    .|.
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            34456789999999999999999999999999965  65     3788999999999999 999999999999    999


Q ss_pred             ccccccccCCCCCCC
Q 004002          256 RRKLDIHFSIPKDNP  270 (780)
Q Consensus       256 gr~I~V~~a~pk~~~  270 (780)
                      |++|.|.++.++...
T Consensus        97 gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           97 GKTINVEFAKGSKRD  111 (131)
T ss_dssp             GCCCCCEECCCSCCC
T ss_pred             CEEEEEEECCCCCCC
Confidence            999999999886543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=3.1e-14  Score=127.40  Aligned_cols=83  Identities=19%  Similarity=0.399  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      ...+.++|||+|||.++|+++|+++|++||.|.-++ .+++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   90 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP   90 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCC
Confidence            345679999999999999999999999999995444 3678999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 004002          267 KDNP  270 (780)
Q Consensus       267 k~~~  270 (780)
                      +...
T Consensus        91 ~~~~   94 (101)
T 2fc9_A           91 RGSP   94 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.50  E-value=2.6e-14  Score=127.83  Aligned_cols=76  Identities=24%  Similarity=0.379  Sum_probs=71.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ..++|||+|||.++++++|+++|++||.|.+++.. +++|||||+|.+.++|++|++.|+|..+.|++|.|.|+.++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            46899999999999999999999999999998853 78999999999999999999999999999999999998763

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=7.4e-14  Score=127.53  Aligned_cols=80  Identities=19%  Similarity=0.237  Sum_probs=73.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+.++|||+|||.++++++|+++|++||+|..|+    .+++++|||||+|.+.++|++|++.|++..|.|++|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            34679999999999999999999999999999887    25678999999999999999999999999999999999998


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .+..
T Consensus        92 ~~~~   95 (114)
T 2do0_A           92 ERAL   95 (114)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7543

>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=99.50  E-value=4.8e-14  Score=128.16  Aligned_cols=78  Identities=19%  Similarity=0.238  Sum_probs=70.6

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC--ccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~--~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++.. .||||||+|++.++|++|++.|++.  .+.|++|+|.+++++.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~   92 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcc
Confidence            457999999999999999999999999999998753 4899999999999999999999765  5999999999998765


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        93 ~   93 (104)
T 1wex_A           93 I   93 (104)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.50  E-value=4.1e-14  Score=133.22  Aligned_cols=81  Identities=16%  Similarity=0.309  Sum_probs=73.6

Q ss_pred             CccceeecCCCCCCChhHHH----HHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~----~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...+|||+|||..+++++|+    ++|++||.|.+|.+  +++++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a  107 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS  107 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEc
Confidence            45689999999999999876    69999999999876  4678999999999999999999999999999999999999


Q ss_pred             CCCchhh
Q 004002          350 RPGGARR  356 (780)
Q Consensus       350 ~~k~~r~  356 (780)
                      +++....
T Consensus       108 ~~~~~~~  114 (127)
T 2a3j_A          108 ETPQSQV  114 (127)
T ss_dssp             CCCCHHH
T ss_pred             cCcchhc
Confidence            9876543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=4.4e-14  Score=125.66  Aligned_cols=79  Identities=20%  Similarity=0.265  Sum_probs=71.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ...++|||+|||+++|+++|+++|++||.|.....+++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.++.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            4568999999999999999999999999986222467899999999999999999999999999999999999998764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=3.7e-14  Score=129.45  Aligned_cols=83  Identities=22%  Similarity=0.373  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEE--------EEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIR--------TLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~--------sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l  254 (780)
                      .+.+.++|||+|||.++|+++|+++|++||.|.        .|+     .+++++|||||+|.+.++|++|++.|++..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345679999999999999999999999999998        465     3578899999999999999999999999999


Q ss_pred             cccccccccCCCCCCC
Q 004002          255 RRRKLDIHFSIPKDNP  270 (780)
Q Consensus       255 ~gr~I~V~~a~pk~~~  270 (780)
                      .|++|.|.++.++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999876543

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.50  E-value=4.2e-14  Score=131.64  Aligned_cols=83  Identities=18%  Similarity=0.464  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++|+++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3345789999999999999999999999999999983     67889999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      |+.++...
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=5e-14  Score=123.46  Aligned_cols=78  Identities=28%  Similarity=0.409  Sum_probs=72.2

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++.   ++||||+|.+.++|++|++.|||..+.|++|+|.+++++.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            3456799999999999999999999999999999986   5699999999999999999999999999999999998765


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.50  E-value=1.3e-14  Score=130.21  Aligned_cols=77  Identities=19%  Similarity=0.221  Sum_probs=71.7

Q ss_pred             ccceeecCCCC------CCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC-ceE
Q 004002          277 QGTLVVFNLDP------SVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-KRI  344 (780)
Q Consensus       277 ~~~L~V~NLp~------~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G-r~L  344 (780)
                      .++|||+|||.      ++++++|+++|++||.|.+|++     +++++|||||+|.+.++|++||+.|||..+.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            46899999999      9999999999999999999986     47789999999999999999999999999999 999


Q ss_pred             EEEecCCCc
Q 004002          345 KLEPSRPGG  353 (780)
Q Consensus       345 ~V~~a~~k~  353 (780)
                      +|.++.++.
T Consensus        86 ~V~~a~~~~   94 (100)
T 3ns6_A           86 FLYTMKDVE   94 (100)
T ss_dssp             EEEESHHHH
T ss_pred             EEEECchhh
Confidence            999997643

>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=99.50  E-value=4.4e-14  Score=130.45  Aligned_cols=78  Identities=28%  Similarity=0.464  Sum_probs=72.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4578999999999999999999999999999976    456789999999999999999999999999999999999987


Q ss_pred             Cc
Q 004002          352 GG  353 (780)
Q Consensus       352 k~  353 (780)
                      +.
T Consensus        86 ~~   87 (116)
T 2fy1_A           86 PS   87 (116)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.50  E-value=4.1e-14  Score=121.66  Aligned_cols=71  Identities=15%  Similarity=0.371  Sum_probs=65.8

Q ss_pred             CcEEEEeCCCCCC------CHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCcccccc-cccc
Q 004002          192 SRTLFVRNINSNV------EDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-KLDI  261 (780)
Q Consensus       192 s~tLfVgNLp~~v------teeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr-~I~V  261 (780)
                      +++|||+|||.++      ++++|+++|++||+|.+++   .+++++|||||+|.+.++|++|++.|+|..|.|+ +|+|
T Consensus         1 ~~~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            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3799999999999      7799999999999999987   4678899999999999999999999999999999 8887


Q ss_pred             c
Q 004002          262 H  262 (780)
Q Consensus       262 ~  262 (780)
                      .
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.50  E-value=4.5e-14  Score=133.64  Aligned_cols=83  Identities=23%  Similarity=0.437  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++|+++|+++|++||+|.+|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456799999999999999999999999999999873     47789999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      ++.++...
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
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=99.50  E-value=5.1e-14  Score=121.66  Aligned_cols=77  Identities=22%  Similarity=0.436  Sum_probs=70.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHc-cCccccccccccccCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIHFSI  265 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~L-ng~~l~gr~I~V~~a~  265 (780)
                      .+.+.++|||+|||.++++++|+++|++||+|..|+.. +++|||||+|.+.++|++|++.| ++..+.|++|.|.|++
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            34567999999999999999999999999999999853 46899999999999999999999 9999999999999874

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.50  E-value=5.1e-14  Score=127.40  Aligned_cols=80  Identities=15%  Similarity=0.321  Sum_probs=72.9

Q ss_pred             CCCCcEEEEeCCCCCC------CHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCcccccc-c
Q 004002          189 EHPSRTLFVRNINSNV------EDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-K  258 (780)
Q Consensus       189 e~~s~tLfVgNLp~~v------teeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr-~  258 (780)
                      ....++|||+|||+.+      |+++|+++|++||.|..|+   .+++++|||||+|.+.++|++|++.|+|..|.|+ +
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            3457899999999999      7899999999999999988   3678899999999999999999999999999999 9


Q ss_pred             cccccCCCCC
Q 004002          259 LDIHFSIPKD  268 (780)
Q Consensus       259 I~V~~a~pk~  268 (780)
                      |.|.++...+
T Consensus        92 l~V~~a~~~~  101 (105)
T 2nlw_A           92 FRVNLFTDFD  101 (105)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEEcchHh
Confidence            9999987543

>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=99.50  E-value=2.2e-14  Score=127.06  Aligned_cols=80  Identities=24%  Similarity=0.597  Sum_probs=73.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HHhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr----~lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ..++++|||+|||.++++++|+    ++|++||.|..|+.  +++++|||||+|.+.++|++|++.|+|..+.|++|.|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3467999999999999999999    99999999999974  45789999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 004002          263 FSIPKD  268 (780)
Q Consensus       263 ~a~pk~  268 (780)
                      |+.++.
T Consensus        85 ~a~~~~   90 (97)
T 1nu4_A           85 YAKTDS   90 (97)
T ss_dssp             ECSSCC
T ss_pred             EccCCC
Confidence            998754

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.50  E-value=3e-14  Score=127.51  Aligned_cols=76  Identities=14%  Similarity=0.242  Sum_probs=71.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++. .++|||||+|.+.++|++|+..|||..+.|++|+|.+++++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            35789999999999999999999999999999986 67899999999999999999999999999999999999864

>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=99.50  E-value=4.3e-14  Score=126.11  Aligned_cols=79  Identities=30%  Similarity=0.544  Sum_probs=72.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      .+.++|||+|||+++|+++|+++|++||+|..|+. .+.+|||||+|.+.++|++|++.|++..|.|++|.|.|+.++..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~-~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE-ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEE-ecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            46789999999999999999999999999999875 35689999999999999999999999999999999999987553

>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=99.50  E-value=3.6e-14  Score=132.13  Aligned_cols=79  Identities=15%  Similarity=0.212  Sum_probs=71.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC--CccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG--~~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++|+++|+++|++||.|++|++.. .||||||+|++.++|++|++.|++  ..+.|++|+|.+++++.
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~-~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG-GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCC
Confidence            457899999999999999999999999999998753 489999999999999999999984  68999999999998765


Q ss_pred             hh
Q 004002          354 AR  355 (780)
Q Consensus       354 ~r  355 (780)
                      .+
T Consensus       109 ~~  110 (119)
T 2ad9_A          109 LK  110 (119)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.49  E-value=6.1e-14  Score=126.24  Aligned_cols=79  Identities=23%  Similarity=0.357  Sum_probs=72.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeC------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~------g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....+|||+|||.++++++|+++|++|| |+.|++.      +.++|||||+|.+.++|++|| .|||..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            3557999999999999999999999999 9999863      677899999999999999999 9999999999999999


Q ss_pred             cCCCchh
Q 004002          349 SRPGGAR  355 (780)
Q Consensus       349 a~~k~~r  355 (780)
                      ++++..+
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9987643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.49  E-value=4.9e-14  Score=129.66  Aligned_cols=77  Identities=22%  Similarity=0.418  Sum_probs=70.4

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++     +++++|||||+|.+.++|++|++.|||..+.|++|+|++
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            345679999999999999999999999999999986     356789999999999999999999999999999999998


Q ss_pred             cC
Q 004002          349 SR  350 (780)
Q Consensus       349 a~  350 (780)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            75

>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=99.49  E-value=6.1e-14  Score=127.08  Aligned_cols=82  Identities=21%  Similarity=0.321  Sum_probs=74.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCC-EEEEEe------CCCcceEEEEEEecHHHHHHHHHHcc--Cccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLYT------ACKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLD  260 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~-I~sv~~------tgkskG~aFV~F~~~e~A~~Al~~Ln--g~~l~gr~I~  260 (780)
                      .+.++|||+|||+++|+++|+++|++||. |..|+.      +++++|||||+|.+.++|++|++.|+  +..+.|++|.
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            35789999999999999999999999998 999884      35789999999999999999999996  5899999999


Q ss_pred             cccCCCCCCCC
Q 004002          261 IHFSIPKDNPS  271 (780)
Q Consensus       261 V~~a~pk~~~s  271 (780)
                      |.|+.++..+.
T Consensus        86 V~~a~~~~~~~   96 (109)
T 2dis_A           86 VDWAEPEIDVD   96 (109)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCcC
Confidence            99998876543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.49  E-value=2.4e-14  Score=125.82  Aligned_cols=73  Identities=22%  Similarity=0.289  Sum_probs=68.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.-|||+||++.+||++|+++|.+||+|.+++. ..+||||||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l-~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-YLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEE-cCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4678999999999999999999999999999985 458999999999999999999999999999999999987

>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=99.49  E-value=1.3e-14  Score=130.17  Aligned_cols=79  Identities=24%  Similarity=0.445  Sum_probs=72.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.++
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            35689999999999999999999999999988872     5788999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .++.
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            8754

>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=99.49  E-value=4.1e-14  Score=126.95  Aligned_cols=81  Identities=22%  Similarity=0.393  Sum_probs=74.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.+++
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            4579999999999999999999999999999875     45668999999999999999999999999999999999999


Q ss_pred             CCchhh
Q 004002          351 PGGARR  356 (780)
Q Consensus       351 ~k~~r~  356 (780)
                      ++..+.
T Consensus        87 ~~~~~~   92 (104)
T 1p1t_A           87 SEKNKE   92 (104)
T ss_dssp             CTTHHH
T ss_pred             Cccchh
Confidence            876543

>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=99.49  E-value=6.5e-14  Score=124.94  Aligned_cols=78  Identities=24%  Similarity=0.412  Sum_probs=72.7

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++. +.+|||||+|.+.++|++|++.|||..+.|++|+|.+++++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            355799999999999999999999999999999985 458999999999999999999999999999999999998865

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=2.9e-14  Score=130.07  Aligned_cols=80  Identities=23%  Similarity=0.418  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .....++|||+|||.++|+++|+++|++||+|..|+.   .++++|||||+|.+.++|++|++.|+|..|.|++|.|.++
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3456799999999999999999999999999998873   3557999999999999999999999999999999999999


Q ss_pred             CCC
Q 004002          265 IPK  267 (780)
Q Consensus       265 ~pk  267 (780)
                      .++
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            765

>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=99.49  E-value=8.2e-14  Score=124.44  Aligned_cols=76  Identities=29%  Similarity=0.410  Sum_probs=71.1

Q ss_pred             CCccceeecCCCC-CCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          275 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       275 ~~~~~L~V~NLp~-~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ...++|||+|||. ++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            3567999999998 99999999999999999999983   8999999999999999999999999999999999998754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=5.7e-14  Score=125.75  Aligned_cols=83  Identities=20%  Similarity=0.436  Sum_probs=75.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...+.++|||+|||.++|+++|+++|++|+.|..+.  .+++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK   90 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            345679999999999999999999999998887776  467899999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 004002          266 PKDNP  270 (780)
Q Consensus       266 pk~~~  270 (780)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87643

>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=99.49  E-value=7e-14  Score=120.80  Aligned_cols=76  Identities=30%  Similarity=0.470  Sum_probs=70.3

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHh-CCCccCCceEEEEecC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSR  350 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~L-nG~~i~Gr~L~V~~a~  350 (780)
                      +...++|||+|||.++++++|+++|++||.|..|++. .++|||||+|.+.++|++|++.| +|..+.|++|+|++++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            3456799999999999999999999999999999985 35899999999999999999999 9999999999999985

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=5.5e-14  Score=128.31  Aligned_cols=82  Identities=26%  Similarity=0.365  Sum_probs=73.9

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCee--------EEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK--------EIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~--------~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~  340 (780)
                      ....++|||+|||.++++++|+++|++||.|+        .|++     ++.++|||||+|.+.++|++||+.|||..+.
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            34567999999999999999999999999998        4764     4567899999999999999999999999999


Q ss_pred             CceEEEEecCCCchh
Q 004002          341 GKRIKLEPSRPGGAR  355 (780)
Q Consensus       341 Gr~L~V~~a~~k~~r  355 (780)
                      |++|+|.+++++..+
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999987643

>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=99.49  E-value=2e-14  Score=131.63  Aligned_cols=79  Identities=20%  Similarity=0.415  Sum_probs=72.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~-----g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++.     +.++|||||+|.+.++|++|| .|||..|.|+.|+|.++
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            345799999999999999999999999999999873     677899999999999999999 99999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus       102 ~~~~~  106 (114)
T 2cq4_A          102 QAEKN  106 (114)
T ss_dssp             HHHHH
T ss_pred             CCCcc
Confidence            77543

>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=99.49  E-value=5.7e-14  Score=126.82  Aligned_cols=77  Identities=21%  Similarity=0.405  Sum_probs=71.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+.++|||+|||+++|+++|+++|++||.|..|+    .+++++|||||+|.+.++|++|++.|++..|.|++|.|.++
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            35679999999999999999999999999999887    35788999999999999999999999999999999999987


Q ss_pred             C
Q 004002          265 I  265 (780)
Q Consensus       265 ~  265 (780)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.49  E-value=5e-14  Score=122.65  Aligned_cols=76  Identities=24%  Similarity=0.445  Sum_probs=70.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|+ .|++..+.|++|.|.++.
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            358999999999999999999999999999987     26788999999999999999999 899999999999999987


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=4.8e-14  Score=126.65  Aligned_cols=80  Identities=23%  Similarity=0.306  Sum_probs=73.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcc-cCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCc-cCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGA-YGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSD-IAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~-yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~-i~Gr~L~V~~a  349 (780)
                      ...+|||+|||.++++++|+++|++ ||.|+.|++    ++.++|||||+|.+.++|++||+.|||.. +.|++|+|.++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a   87 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVA   87 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEc
Confidence            4578999999999999999999999 999999976    56689999999999999999999999999 99999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      .++..+
T Consensus        88 ~~~~~~   93 (104)
T 2dhg_A           88 IPKASR   93 (104)
T ss_dssp             CCCCSC
T ss_pred             cCCCcC
Confidence            887644

>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=99.49  E-value=5.8e-14  Score=127.57  Aligned_cols=79  Identities=23%  Similarity=0.363  Sum_probs=73.2

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      ...++|||+|||.++++++|+++|++||.|..|++... +|||||+|.+.++|++|++.|||..+.|++|+|.+++++..
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            34579999999999999999999999999999998644 89999999999999999999999999999999999998764

>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=99.48  E-value=4.6e-14  Score=129.10  Aligned_cols=82  Identities=21%  Similarity=0.395  Sum_probs=74.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCE----EEEE-eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDI----RTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I----~sv~-~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||.++|+++|+++|++||.|    ..++ .+++++|||||+|.+.++|++|++.|++..|.|++|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3467999999999999999999999999998    4444 5789999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876543

>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=99.48  E-value=6.9e-14  Score=127.84  Aligned_cols=81  Identities=12%  Similarity=0.310  Sum_probs=72.9

Q ss_pred             CCCCccceeecCCCCCCChhHHH---HHhcccCCeeEEEeCC--------CcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLR---QIFGAYGEVKEIRETP--------HKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~---~~Fs~yG~I~~v~~~g--------~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G  341 (780)
                      +.....+|||+|||.++++++|+   ++|++||.|+.|++..        .++|||||+|.+.++|++||+.|||..+.|
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            34456799999999999999999   9999999999998632        345899999999999999999999999999


Q ss_pred             ceEEEEecCCCc
Q 004002          342 KRIKLEPSRPGG  353 (780)
Q Consensus       342 r~L~V~~a~~k~  353 (780)
                      ++|+|.+++++.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999998875

>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=99.48  E-value=5.9e-14  Score=130.60  Aligned_cols=81  Identities=26%  Similarity=0.407  Sum_probs=74.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++|+++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..|.|+.|+|+++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            34679999999999999999999999999999986     5667999999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      .++..+
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876543

>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=99.48  E-value=6.6e-14  Score=125.92  Aligned_cols=77  Identities=25%  Similarity=0.478  Sum_probs=72.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCchh
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r  355 (780)
                      +.++|||+|||.++|+++|+++|++||.|+.|++.   ++||||+|.+.++|++||+.|||..+.|+.|+|.+++++..+
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            45799999999999999999999999999999985   679999999999999999999999999999999999987654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.3e-13  Score=122.94  Aligned_cols=77  Identities=27%  Similarity=0.376  Sum_probs=71.6

Q ss_pred             CCccceeecCCCCCCChhHHHHHhccc--CCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~y--G~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ...++|||+|||..+++++|+++|++|  |.|..|++.   +|||||+|.+.++|++|++.|||..+.|++|+|.+++++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            356799999999999999999999999  999999874   789999999999999999999999999999999999886


Q ss_pred             ch
Q 004002          353 GA  354 (780)
Q Consensus       353 ~~  354 (780)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpd_A           90 DK   91 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.48  E-value=8.4e-14  Score=125.24  Aligned_cols=78  Identities=26%  Similarity=0.502  Sum_probs=72.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      .+.++|||+|||+++|+++|+++|++||+|..|+..   +|||||+|.+.++|++|++.|++..|.|++|.|.|+.++..
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            467999999999999999999999999999999853   68999999999999999999999999999999999987654


Q ss_pred             C
Q 004002          270 P  270 (780)
Q Consensus       270 ~  270 (780)
                      .
T Consensus        86 ~   86 (103)
T 2dgu_A           86 K   86 (103)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.48  E-value=6.5e-14  Score=121.95  Aligned_cols=76  Identities=28%  Similarity=0.473  Sum_probs=70.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|+ .|||..+.|++|+|.+++
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            3568999999999999999999999999999875     5667999999999999999999 999999999999999998


Q ss_pred             CC
Q 004002          351 PG  352 (780)
Q Consensus       351 ~k  352 (780)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            74

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=5.1e-14  Score=125.93  Aligned_cols=81  Identities=32%  Similarity=0.448  Sum_probs=72.6

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ....++|||+|||.++++++|+++|++||.|..++. +++++|||||+|.+.++|++||+.|||..+.|+.|+|++++++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   91 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPR   91 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCC
Confidence            345689999999999999999999999999854443 6678999999999999999999999999999999999999887


Q ss_pred             ch
Q 004002          353 GA  354 (780)
Q Consensus       353 ~~  354 (780)
                      ..
T Consensus        92 ~~   93 (101)
T 2fc9_A           92 GS   93 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.48  E-value=4.9e-14  Score=125.35  Aligned_cols=80  Identities=15%  Similarity=0.269  Sum_probs=71.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHH----HHhhcCCCEEEEEeC--CCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr----~lF~~yG~I~sv~~t--gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..++|||+|||+++++++|+    ++|++||+|.+|+..  ...+|||||+|.+.++|++|++.|+|..|.|++|+|.++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            45899999999999999999    999999999999842  222899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      .+...+
T Consensus        88 ~~~~~~   93 (96)
T 2dgx_A           88 TGASGP   93 (96)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=1.2e-13  Score=126.24  Aligned_cols=79  Identities=19%  Similarity=0.167  Sum_probs=72.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++||+.|||..+.|+.|+|++++
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            34579999999999999999999999999999875    34568999999999999999999999999999999999998


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      ...
T Consensus        93 ~~~   95 (114)
T 2do0_A           93 RAL   95 (114)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.48  E-value=2.4e-14  Score=135.85  Aligned_cols=84  Identities=27%  Similarity=0.469  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999873     57899999999999999999999999999999999999


Q ss_pred             cCCCCCCCC
Q 004002          263 FSIPKDNPS  271 (780)
Q Consensus       263 ~a~pk~~~s  271 (780)
                      |+.++..+.
T Consensus       123 ~a~~~~~~~  131 (135)
T 2lea_A          123 MARYGRPPD  131 (135)
T ss_dssp             ECCCCCCCT
T ss_pred             ECCCCCCCc
Confidence            998765443

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.48  E-value=1.1e-13  Score=124.38  Aligned_cols=78  Identities=18%  Similarity=0.254  Sum_probs=71.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++++++|+++|++|| |+.|++     ++.++|||||+|.+.++|++|| .|||..+.|++|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            3567999999999999999999999997 999876     4667899999999999999999 89999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus        91 ~~~~~   95 (103)
T 2dng_A           91 EGRKQ   95 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            88754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.48  E-value=5.3e-14  Score=125.03  Aligned_cols=78  Identities=24%  Similarity=0.411  Sum_probs=71.5

Q ss_pred             CCCcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          190 HPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       190 ~~s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      .+.++|||+|||+ ++|+++|+++|++||+|..|+.   ++|||||+|.+.++|++|++.|++..+.|++|.|.++.++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            4679999999998 9999999999999999999986   48999999999999999999999999999999999998765


Q ss_pred             CC
Q 004002          269 NP  270 (780)
Q Consensus       269 ~~  270 (780)
                      .+
T Consensus        85 ~~   86 (96)
T 2kvi_A           85 RP   86 (96)
T ss_dssp             C-
T ss_pred             CC
Confidence            43

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=9.1e-14  Score=127.58  Aligned_cols=80  Identities=28%  Similarity=0.358  Sum_probs=72.9

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ++...++|||+|||.++++++|+++|++||.|+.|++     +++++|||||+|.+.++|++||+.|++ .+.|++|+|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            4456689999999999999999999999999999986     456789999999999999999999998 8999999999


Q ss_pred             ecCCCc
Q 004002          348 PSRPGG  353 (780)
Q Consensus       348 ~a~~k~  353 (780)
                      ++.++.
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            998754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=8.5e-14  Score=121.98  Aligned_cols=78  Identities=19%  Similarity=0.406  Sum_probs=71.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ..+.++|||+|||+++|+++|+++|++||+|..|+..   ++||||+|.+.++|++|++.|++..+.|++|.|.++.++.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            3467899999999999999999999999999999864   5699999999999999999999999999999999998765


Q ss_pred             C
Q 004002          269 N  269 (780)
Q Consensus       269 ~  269 (780)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.48  E-value=4.3e-14  Score=126.68  Aligned_cols=78  Identities=18%  Similarity=0.399  Sum_probs=69.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ....++|||+|||.++++++|+++|++|| |.+|+.      +++++|||||+|.+.++|++|+ .|+|..|.|++|.|.
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            34669999999999999999999999999 999983      5778999999999999999999 899999999999999


Q ss_pred             cCCCCC
Q 004002          263 FSIPKD  268 (780)
Q Consensus       263 ~a~pk~  268 (780)
                      ++.++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=5.2e-14  Score=125.31  Aligned_cols=78  Identities=24%  Similarity=0.370  Sum_probs=72.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCee-EEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce----EE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR----IK  345 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~-~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~----L~  345 (780)
                      ..++|||+|||.++++++|+++|++||.|. .|++     ++.++|||||+|.+.++|++|++.|||..+.|+.    |+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~   87 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK   87 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEE
Confidence            467999999999999999999999999999 8875     4667899999999999999999999999999999    99


Q ss_pred             EEecCCCc
Q 004002          346 LEPSRPGG  353 (780)
Q Consensus       346 V~~a~~k~  353 (780)
                      |.++++..
T Consensus        88 v~~a~~~~   95 (99)
T 2div_A           88 LNYATYSG   95 (99)
T ss_dssp             EEETTCCS
T ss_pred             EeecCCCC
Confidence            99998764

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1e-13  Score=124.03  Aligned_cols=84  Identities=23%  Similarity=0.401  Sum_probs=74.5

Q ss_pred             CCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEE--eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       272 ~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~--~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ......++|||+|||.++++++|+++|+.|+.|..++  .++.++|||||+|.+.++|++||+.|||..|.|++|+|.++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            3445668999999999999999999999998777665  36678899999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2fc8_A           90 KPKGEG   95 (102)
T ss_dssp             CCCCSS
T ss_pred             cCCCCC
Confidence            987643

>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=99.48  E-value=1.2e-13  Score=125.42  Aligned_cols=80  Identities=14%  Similarity=0.215  Sum_probs=72.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccc-----ccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR-----RKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g-----r~I~V~~  263 (780)
                      ....++|||+|||+++|+++|+++|++||+|..|++...  |||||+|.+.++|++||+.|++..|.|     ++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~   89 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   89 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEe
Confidence            346789999999999999999999999999999985333  999999999999999999999999999     9999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++...
T Consensus        90 a~~~~~~   96 (108)
T 1x4c_A           90 DGPRSPS   96 (108)
T ss_dssp             SSCCSCC
T ss_pred             CCCCCCC
Confidence            9886543

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.4e-13  Score=125.79  Aligned_cols=79  Identities=16%  Similarity=0.322  Sum_probs=71.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccc--------cc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPL--------RR  256 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l--------~g  256 (780)
                      +.+.++|||+|||+++|+++|+++|++||+|..|+.    +++++|||||+|.+.++|++|++.|+|..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            446799999999999999999999999999999873    578899999999999999999999999999        56


Q ss_pred             cccccccCCCC
Q 004002          257 RKLDIHFSIPK  267 (780)
Q Consensus       257 r~I~V~~a~pk  267 (780)
                      ++|.|.|+.|+
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            77888888754

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.48  E-value=7.2e-14  Score=126.46  Aligned_cols=78  Identities=14%  Similarity=0.148  Sum_probs=71.2

Q ss_pred             CCccceeecCCCCCC------ChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc-eE
Q 004002          275 LNQGTLVVFNLDPSV------SNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RI  344 (780)
Q Consensus       275 ~~~~~L~V~NLp~~v------teedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr-~L  344 (780)
                      ...++|||+|||..+      ++++|+++|++||.|+.|++   ++.++|||||+|.+.++|++||+.|||..+.|+ +|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            345789999999999      78999999999999999986   456789999999999999999999999999998 99


Q ss_pred             EEEecCCC
Q 004002          345 KLEPSRPG  352 (780)
Q Consensus       345 ~V~~a~~k  352 (780)
                      +|.++...
T Consensus        93 ~V~~a~~~  100 (105)
T 2nlw_A           93 RVNLFTDF  100 (105)
T ss_dssp             EEECSCCC
T ss_pred             EEEEcchH
Confidence            99999754

>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=99.48  E-value=9.6e-14  Score=123.99  Aligned_cols=76  Identities=24%  Similarity=0.372  Sum_probs=71.0

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          189 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       189 e~~s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ..+.++|||+|||. ++++++|+++|++||.|..++.   .+|||||+|.+.++|++|++.|+|..+.|++|.|.++.++
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE---CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            34679999999998 9999999999999999999986   4899999999999999999999999999999999998764

>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=99.48  E-value=6.3e-14  Score=124.52  Aligned_cols=78  Identities=21%  Similarity=0.223  Sum_probs=70.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++++++|+++|++||.|+.++     .++.++|||||+|.+.++|++||+.|||..+.|++|+|+++
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            3457899999999999999999999999986543     25677899999999999999999999999999999999999


Q ss_pred             CCC
Q 004002          350 RPG  352 (780)
Q Consensus       350 ~~k  352 (780)
                      ...
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            764

>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=99.48  E-value=8.7e-14  Score=126.43  Aligned_cols=77  Identities=21%  Similarity=0.275  Sum_probs=71.4

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC-----ceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-----KRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G-----r~L~V~~a~  350 (780)
                      ...+|||+|||.++++++|+++|++||.|+.|++...  |||||+|.+.++|++||+.|||..+.|     +.|+|++++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~   91 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   91 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCC
Confidence            4578999999999999999999999999999998544  999999999999999999999999999     999999999


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        92 ~~~~   95 (108)
T 1x4c_A           92 PRSP   95 (108)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8653

>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=99.47  E-value=3.6e-14  Score=130.78  Aligned_cols=80  Identities=16%  Similarity=0.209  Sum_probs=71.8

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccC--ccccccccccccCC
Q 004002          189 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~-vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng--~~l~gr~I~V~~a~  265 (780)
                      ..++++|||+|||++ +|+++|+++|++||+|.+|++ .++||||||+|.+.++|++|++.|++  ..|.|++|.|.|+.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  100 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE  100 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEE-ecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECc
Confidence            457899999999998 999999999999999999985 46799999999999999999999875  45999999999997


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      .+..
T Consensus       101 ~~~~  104 (112)
T 1x4f_A          101 KYKK  104 (112)
T ss_dssp             SCSS
T ss_pred             cccc
Confidence            6553

>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=99.47  E-value=1e-13  Score=126.02  Aligned_cols=80  Identities=14%  Similarity=0.291  Sum_probs=73.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      ...++|||+|||.++++++|+.+|++||.|..|+... .+|||||+|.+.++|++|++.|++..|.|++|.|.|+.++..
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            4568999999999999999999999999999998533 389999999999999999999999999999999999987654


Q ss_pred             C
Q 004002          270 P  270 (780)
Q Consensus       270 ~  270 (780)
                      .
T Consensus       102 ~  102 (109)
T 1x4g_A          102 M  102 (109)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.47  E-value=6.4e-14  Score=128.32  Aligned_cols=76  Identities=17%  Similarity=0.267  Sum_probs=71.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++. .+++||||+|.+.++|++||+.|||..+.|++|+|++++..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            45799999999999999999999999999999985 57899999999999999999999999999999999999764

>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=99.47  E-value=5.4e-14  Score=124.61  Aligned_cols=80  Identities=21%  Similarity=0.416  Sum_probs=73.5

Q ss_pred             CccceeecCCCCCCChhHHH----HHhcccCCeeEEEeC--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~----~~Fs~yG~I~~v~~~--g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ..++|||+|||.++++++|+    ++|++||.|..|++.  +.++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   86 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999    999999999999873  456899999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++...
T Consensus        87 ~~~~~~   92 (97)
T 1nu4_A           87 KTDSDI   92 (97)
T ss_dssp             SSCCTH
T ss_pred             cCCCcc
Confidence            987644

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.47  E-value=5.7e-14  Score=124.81  Aligned_cols=77  Identities=29%  Similarity=0.404  Sum_probs=71.2

Q ss_pred             CCccceeecCCCC-CCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          275 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       275 ~~~~~L~V~NLp~-~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ...++|||+|||. .+++++|+++|++||.|+.|++.   +|||||+|.+.++|++|++.|||..+.|++|+|.+++++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            3567999999998 99999999999999999999983   8999999999999999999999999999999999998765


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.47  E-value=7.4e-14  Score=127.72  Aligned_cols=81  Identities=28%  Similarity=0.357  Sum_probs=73.0

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCe----eEEE-eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV----KEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I----~~v~-~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++|+++|+++|++||.|    ..++ .++.++|||||+|.+.++|++||+.|||..+.|+.|+|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            345799999999999999999999999998    4554 37888999999999999999999999999999999999999


Q ss_pred             CCCchh
Q 004002          350 RPGGAR  355 (780)
Q Consensus       350 ~~k~~r  355 (780)
                      +++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            987643

>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=99.47  E-value=1.1e-13  Score=133.80  Aligned_cols=80  Identities=23%  Similarity=0.298  Sum_probs=74.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++|+++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.|||..|.|++|+|++++
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  117 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA  117 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            5579999999999999999999999999999987     46678999999999999999999999999999999999998


Q ss_pred             CCchh
Q 004002          351 PGGAR  355 (780)
Q Consensus       351 ~k~~r  355 (780)
                      +...+
T Consensus       118 ~~~~~  122 (156)
T 1h2v_Z          118 GFKEG  122 (156)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            86543

>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=99.47  E-value=4.9e-14  Score=128.81  Aligned_cols=79  Identities=18%  Similarity=0.301  Sum_probs=72.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHH---HHhhcCCCEEEEEe--------CCCcceEEEEEEecHHHHHHHHHHccCccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELR---ALFEQYGDIRTLYT--------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr---~lF~~yG~I~sv~~--------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~  258 (780)
                      ...++|||+|||+++++++|+   ++|++||+|..|+.        .++++|||||+|.+.++|++|++.|++..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            456899999999999999999   99999999999873        2256799999999999999999999999999999


Q ss_pred             cccccCCCCC
Q 004002          259 LDIHFSIPKD  268 (780)
Q Consensus       259 I~V~~a~pk~  268 (780)
                      |.|.|+.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998765

>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=99.47  E-value=3.6e-14  Score=126.12  Aligned_cols=79  Identities=19%  Similarity=0.240  Sum_probs=70.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ....++|||+|||+++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.|++..|.|++|.|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34568999999999999999999999999985432     4678999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          264 SIPK  267 (780)
Q Consensus       264 a~pk  267 (780)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.47  E-value=2.5e-13  Score=126.25  Aligned_cols=79  Identities=20%  Similarity=0.288  Sum_probs=72.7

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...++|||+|||..+++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++.
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            45579999999999999999999999999999976    45578999999999999999999999999999999999998


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      +..
T Consensus       113 ~~~  115 (124)
T 2kt5_A          113 SQI  115 (124)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            754

>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=99.47  E-value=5.1e-14  Score=126.21  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=69.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ...++|||+|||.++++++|+++|++|| |++|++      +++++|||||+|.+.++|++|| .|||..+.|+.|+|++
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            3567999999999999999999999999 999986      4557899999999999999999 8999999999999999


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      ++++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            98764

>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=99.47  E-value=4.4e-14  Score=129.43  Aligned_cols=77  Identities=13%  Similarity=0.268  Sum_probs=71.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ...++|||+|||+++|+++|+++|++||.|..|+. .+++|||||+|.+.++|++|++.|+|..|.|++|.|.|+...
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            34689999999999999999999999999999985 358999999999999999999999999999999999998653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=2e-13  Score=121.76  Aligned_cols=77  Identities=21%  Similarity=0.420  Sum_probs=71.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcC--CCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQY--GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~y--G~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      .+.++|||+|||+++|+++|+++|++|  |.|..|+.   .+|||||+|.+.++|++|++.|++..|.|++|.|.|+.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE---CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE---eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            467899999999999999999999999  99999874   4799999999999999999999999999999999999876


Q ss_pred             CC
Q 004002          268 DN  269 (780)
Q Consensus       268 ~~  269 (780)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpd_A           90 DK   91 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=3.6e-14  Score=126.96  Aligned_cols=76  Identities=28%  Similarity=0.408  Sum_probs=71.5

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ++|||+|||.++|+++|+++|++||.|+.|++...++|||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            3799999999999999999999999999998755578999999999999999999999999999999999998865

>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=99.47  E-value=4e-14  Score=124.73  Aligned_cols=77  Identities=26%  Similarity=0.354  Sum_probs=70.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCC-eeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC-CccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR-SDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~-I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG-~~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++||. |..+.+  .++|||||+|.+.++|++|++.||| ..+.|++|+|++++++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            4578999999999999999999999999 666665  3689999999999999999999999 99999999999998875


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        85 ~   85 (93)
T 2cqh_A           85 L   85 (93)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.47  E-value=1.3e-13  Score=124.56  Aligned_cols=75  Identities=24%  Similarity=0.383  Sum_probs=70.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||..+++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++.
T Consensus        28 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            4579999999999999999999999999999875    45678999999999999999999999999999999999985

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.47  E-value=6.2e-14  Score=127.88  Aligned_cols=79  Identities=24%  Similarity=0.509  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      .+.+.++|||+|||.++|+++|+++|++||+|..|+..   +|||||+|.+.++|++|++.|+|..+.|++|.|.|+.++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            44567999999999999999999999999999998864   899999999999999999999999999999999999876


Q ss_pred             CC
Q 004002          268 DN  269 (780)
Q Consensus       268 ~~  269 (780)
                      ..
T Consensus       104 ~~  105 (108)
T 2jvo_A          104 AK  105 (108)
T ss_dssp             C-
T ss_pred             CC
Confidence            43

>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=99.47  E-value=6.1e-14  Score=129.20  Aligned_cols=78  Identities=19%  Similarity=0.197  Sum_probs=70.7

Q ss_pred             CccceeecCCCCC-CChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC--CccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG--~~i~Gr~L~V~~a~~k  352 (780)
                      ..++|||+|||.+ +++++|+++|++||.|++|++. ++||||||+|++.++|++|++.|++  ..+.|++|+|.+++++
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY  102 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccc
Confidence            4579999999998 9999999999999999999985 5689999999999999999999864  5699999999999876


Q ss_pred             ch
Q 004002          353 GA  354 (780)
Q Consensus       353 ~~  354 (780)
                      ..
T Consensus       103 ~~  104 (112)
T 1x4f_A          103 KK  104 (112)
T ss_dssp             SS
T ss_pred             cc
Confidence            53

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.47  E-value=1.6e-14  Score=134.15  Aligned_cols=77  Identities=25%  Similarity=0.446  Sum_probs=71.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|| .|||..+.|+.|+|.+++
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            3579999999999999999999999999999875     5677999999999999999999 899999999999999998


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.47  E-value=4.3e-14  Score=130.02  Aligned_cols=77  Identities=10%  Similarity=0.098  Sum_probs=71.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCC-CEEEEEe-CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG-~I~sv~~-tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ..++|||+|||+++|+++|+++|++|| +|..+++ ..+++|||||+|.+.++|++|++.|+|..|.|++|.|.++...
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            458999999999999999999999999 8999885 4678999999999999999999999999999999999998643

>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=99.47  E-value=8.1e-14  Score=121.07  Aligned_cols=75  Identities=19%  Similarity=0.393  Sum_probs=68.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      +.+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++ +++..|.|++|.|++
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            456799999999999999999999999999999872     58889999999999999999997 588889999999987


Q ss_pred             C
Q 004002          264 S  264 (780)
Q Consensus       264 a  264 (780)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.47  E-value=6.8e-14  Score=136.21  Aligned_cols=78  Identities=13%  Similarity=0.209  Sum_probs=71.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccC--CeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG--~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ...+|||+|||.++|+++|+++|++||  .|.+|++     ++.++|||||+|.+.++|++||+.|||..|.|+.|+|.+
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            346999999999999999999999999  8999876     677899999999999999999999999999999999999


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            98754

>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=99.46  E-value=4.7e-14  Score=124.26  Aligned_cols=79  Identities=20%  Similarity=0.353  Sum_probs=70.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCC-EEEEEeCCCcceEEEEEEecHHHHHHHHHHccC-ccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLYTACKHRGFVMISYYDIRAARTAMRALQN-KPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~-I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng-~~l~gr~I~V~~a~pk  267 (780)
                      .+.++|||+|||.++|+++|+++|++||+ |..+..  .++|||||+|.+.++|++|++.|++ ..|.|++|.|.|+.++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            45689999999999999999999999999 555543  4789999999999999999999999 9999999999999876


Q ss_pred             CCC
Q 004002          268 DNP  270 (780)
Q Consensus       268 ~~~  270 (780)
                      ...
T Consensus        84 ~~~   86 (93)
T 2cqh_A           84 KLR   86 (93)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=9e-14  Score=125.21  Aligned_cols=80  Identities=33%  Similarity=0.473  Sum_probs=73.2

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+. ++..|.|+.|+|.+
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            445679999999999999999999999999999875     456789999999999999999998 99999999999999


Q ss_pred             cCCCch
Q 004002          349 SRPGGA  354 (780)
Q Consensus       349 a~~k~~  354 (780)
                      ++++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            998764

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1e-13  Score=125.58  Aligned_cols=78  Identities=10%  Similarity=0.166  Sum_probs=71.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      +...++|||+|||.++|+++|+++|++||.|..|++    .+.++|||||+|.+.++|++||. ++|..+.|+.|.|.++
T Consensus         8 ~~~~~~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            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            345689999999999999999999999999999976    26689999999999999999999 9999999999999988


Q ss_pred             CCC
Q 004002          350 RPG  352 (780)
Q Consensus       350 ~~k  352 (780)
                      ..-
T Consensus        87 ~~~   89 (103)
T 1s79_A           87 DDY   89 (103)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            653

>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=99.46  E-value=1.4e-13  Score=133.01  Aligned_cols=80  Identities=25%  Similarity=0.426  Sum_probs=74.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++||+.|++..|.|++|.|.|+
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            46799999999999999999999999999999884     5789999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 004002          265 IPKDN  269 (780)
Q Consensus       265 ~pk~~  269 (780)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=6.9e-14  Score=126.75  Aligned_cols=76  Identities=12%  Similarity=0.306  Sum_probs=69.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...++|||+|||+++|+++|+++|++||+|.+|+.    .++++|||||+|.+.++|++|++ +++..|.|+.|.|.++.
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            35689999999999999999999999999999872    37899999999999999999999 89999999999998864


Q ss_pred             C
Q 004002          266 P  266 (780)
Q Consensus       266 p  266 (780)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=2e-13  Score=121.44  Aligned_cols=77  Identities=19%  Similarity=0.377  Sum_probs=71.0

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      ...++|||+||  ++++++|+++|++||.|..|++ +.++|||||+|.+.++|++||+.|||..+.|++|+|.+++++..
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            35579999996  8999999999999999999998 47789999999999999999999999999999999999988653

>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=99.46  E-value=2.9e-14  Score=125.89  Aligned_cols=76  Identities=20%  Similarity=0.232  Sum_probs=68.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||+++|+++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.|++..|.|++|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            3568999999999999999999999999986433     35789999999999999999999999999999999999987


Q ss_pred             C
Q 004002          265 I  265 (780)
Q Consensus       265 ~  265 (780)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.46  E-value=6.6e-14  Score=118.21  Aligned_cols=70  Identities=20%  Similarity=0.340  Sum_probs=65.6

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      +|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++ |||..+.|++|+|++|
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            5899999999999999999999999999975     56678999999999999999998 9999999999999875

>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=99.46  E-value=1.4e-13  Score=119.55  Aligned_cols=75  Identities=27%  Similarity=0.401  Sum_probs=68.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++ +++..+.|++|+|++
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            345679999999999999999999999999999976     46778999999999999999996 588899999999987


Q ss_pred             c
Q 004002          349 S  349 (780)
Q Consensus       349 a  349 (780)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.46  E-value=6.9e-14  Score=136.17  Aligned_cols=77  Identities=16%  Similarity=0.252  Sum_probs=71.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCC--CEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG--~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..++|||+|||+++|+++|+++|++||  +|.+|++     +++++|||||+|.+.++|++||+.|+|..|.|++|.|.+
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            468999999999999999999999999  9999873     688999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          264 SIPK  267 (780)
Q Consensus       264 a~pk  267 (780)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8653

>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=99.46  E-value=1.6e-13  Score=131.70  Aligned_cols=80  Identities=25%  Similarity=0.438  Sum_probs=74.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|+....++|||||+|.+.++|++|++.|+|..|.|++|.|.|+.++.
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            45679999999999999999999999999999999766689999999999999999999999999999999999998754

>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=99.46  E-value=2.4e-14  Score=125.24  Aligned_cols=76  Identities=21%  Similarity=0.414  Sum_probs=67.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.+ |++|++.|+|..+.|++|.|.++.+.
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            68999999999999999999999999999873     4788999999999999 99999999999999999999999875


Q ss_pred             CC
Q 004002          268 DN  269 (780)
Q Consensus       268 ~~  269 (780)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>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=99.46  E-value=2.3e-13  Score=124.40  Aligned_cols=78  Identities=21%  Similarity=0.284  Sum_probs=71.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCcc--------CCc
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI--------AGK  342 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i--------~Gr  342 (780)
                      ....+|||+|||.++++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++|++.|||..+        .++
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            45579999999999999999999999999999976    456789999999999999999999999999        578


Q ss_pred             eEEEEecCCC
Q 004002          343 RIKLEPSRPG  352 (780)
Q Consensus       343 ~L~V~~a~~k  352 (780)
                      .|.|.+++++
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            8999999875

>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=99.46  E-value=2.2e-13  Score=122.18  Aligned_cols=81  Identities=15%  Similarity=0.318  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++  ++..|.|++|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            3456789999999999999999999999999999872     58899999999999999999999  4778999999999


Q ss_pred             cCCCCCCC
Q 004002          263 FSIPKDNP  270 (780)
Q Consensus       263 ~a~pk~~~  270 (780)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99887654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.46  E-value=1.1e-13  Score=130.62  Aligned_cols=76  Identities=24%  Similarity=0.301  Sum_probs=70.8

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccE-EEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCc
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-KFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  353 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~-aFV~F~~~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~k~  353 (780)
                      -.|||+||+..+|+++|+++|++||.|.+|++..+++|+ |||+|.+.++|++|++.|||..|.|  ++|+|.+++++.
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            468899999999999999999999999999886666788 9999999999999999999999988  899999999864

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.46  E-value=1.2e-13  Score=126.09  Aligned_cols=81  Identities=27%  Similarity=0.401  Sum_probs=70.9

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+.+ +..+.|+.|+|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345679999999999999999999999999999986     3667899999999999999999986 5999999999999


Q ss_pred             cCCCchh
Q 004002          349 SRPGGAR  355 (780)
Q Consensus       349 a~~k~~r  355 (780)
                      +.++..+
T Consensus       101 a~~~~~~  107 (109)
T 2rs2_A          101 AFPRRAQ  107 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9987643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.1e-13  Score=121.45  Aligned_cols=78  Identities=9%  Similarity=0.220  Sum_probs=71.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ....++|||+|||+++|+++|+++|++| .|..|+    .+++++|||||+|.+.++|++|++ |++..|.|++|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            3466899999999999999999999999 888876    367889999999999999999999 9999999999999998


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7754

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.46  E-value=5.2e-14  Score=132.45  Aligned_cols=79  Identities=23%  Similarity=0.381  Sum_probs=72.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeE--EEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCC----ccCCc
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS----DIAGK  342 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~--v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~----~i~Gr  342 (780)
                      ....++|||+|||.++|+++|+++|++||.|..  |++     +++++|||||+|.+. +|++||+.|||.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345679999999999999999999999999966  764     677899999999999 999999999999    99999


Q ss_pred             eEEEEecCCCc
Q 004002          343 RIKLEPSRPGG  353 (780)
Q Consensus       343 ~L~V~~a~~k~  353 (780)
                      +|+|++++++.
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2.9e-13  Score=120.39  Aligned_cols=79  Identities=19%  Similarity=0.323  Sum_probs=72.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ..+.++|||+||  ++|+++|+++|++||+|..|++ ++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.++.
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            346789999996  9999999999999999999986 5789999999999999999999999999999999999998765


Q ss_pred             CC
Q 004002          269 NP  270 (780)
Q Consensus       269 ~~  270 (780)
                      ..
T Consensus        89 ~~   90 (97)
T 1x5p_A           89 ML   90 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.45  E-value=5.5e-14  Score=124.05  Aligned_cols=76  Identities=20%  Similarity=0.241  Sum_probs=68.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||.++++++|+++|++||.|+.+++     ++.++|||||+|.+.++|++||+.|||..+.|++|+|+++.
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            3479999999999999999999999999876542     45778999999999999999999999999999999999986


Q ss_pred             C
Q 004002          351 P  351 (780)
Q Consensus       351 ~  351 (780)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.45  E-value=5.4e-14  Score=118.78  Aligned_cols=70  Identities=16%  Similarity=0.401  Sum_probs=65.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +|||+|||+++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++ |++..+.|++|.|++|
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            5899999999999999999999999999872     67889999999999999999998 9999999999999875

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.45  E-value=9.5e-14  Score=126.68  Aligned_cols=80  Identities=16%  Similarity=0.420  Sum_probs=70.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||.++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.+ +..|.|+.|.|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            346799999999999999999999999999999983     4788999999999999999999976 5899999999999


Q ss_pred             CCCCCC
Q 004002          264 SIPKDN  269 (780)
Q Consensus       264 a~pk~~  269 (780)
                      +.++..
T Consensus       101 a~~~~~  106 (109)
T 2rs2_A          101 AFPRRA  106 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.45  E-value=1.3e-13  Score=125.55  Aligned_cols=76  Identities=25%  Similarity=0.510  Sum_probs=71.1

Q ss_pred             CCCcEEEEeCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          190 HPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       190 ~~s~tLfVgNLp~~-vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ...++|||+|||++ +|+++|+++|++||+|..|+.   ++|||||+|.+.++|++|++.|++..|.|++|.|.++.+..
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            35589999999999 999999999999999999987   78999999999999999999999999999999999997544

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=4e-14  Score=122.49  Aligned_cols=76  Identities=21%  Similarity=0.371  Sum_probs=69.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|++.+++
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            3568999999999999999999999999999975     45678999999999999999999999999999999988765


Q ss_pred             C
Q 004002          351 P  351 (780)
Q Consensus       351 ~  351 (780)
                      .
T Consensus        84 s   84 (85)
T 1x4e_A           84 S   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=7.5e-14  Score=128.14  Aligned_cols=79  Identities=16%  Similarity=0.299  Sum_probs=72.2

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+. ++..|.|++|+|.++
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            34579999999999999999999999999999976     356789999999999999999998 999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      +++..
T Consensus       104 ~~~~~  108 (116)
T 1x4b_A          104 VAREE  108 (116)
T ss_dssp             SSCCC
T ss_pred             CCCcc
Confidence            98764

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.45  E-value=5.9e-14  Score=120.70  Aligned_cols=69  Identities=16%  Similarity=0.247  Sum_probs=64.0

Q ss_pred             cceeecCCCCCC------ChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc-eEEE
Q 004002          278 GTLVVFNLDPSV------SNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RIKL  346 (780)
Q Consensus       278 ~~L~V~NLp~~v------teedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr-~L~V  346 (780)
                      ++|||+|||..+      ++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|||..+.|+ +|+|
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 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            579999999999      67999999999999999976   456789999999999999999999999999999 8876

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.45  E-value=1.3e-13  Score=128.07  Aligned_cols=81  Identities=21%  Similarity=0.400  Sum_probs=74.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+.++|||+|||.++++++|+++|++||+|..|+.    +++++|||||+|.+.++|++|++.|+|..|.|++|.|.++
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            456789999999999999999999999999998873    5778999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 004002          265 IPKDN  269 (780)
Q Consensus       265 ~pk~~  269 (780)
                      .+...
T Consensus       112 ~~~~~  116 (124)
T 2kt5_A          112 ASQID  116 (124)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87543

>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=99.45  E-value=1.5e-13  Score=124.41  Aligned_cols=79  Identities=20%  Similarity=0.245  Sum_probs=72.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCC-eeEEEeC------CCcccEEEEEEcCHHHHHHHHHHhC--CCccCCceEEE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRET------PHKRHHKFIEFYDVRAAEAALKSLN--RSDIAGKRIKL  346 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~-I~~v~~~------g~srG~aFV~F~~~e~A~~Ai~~Ln--G~~i~Gr~L~V  346 (780)
                      ..++|||+|||.++++++|+++|++||. |+.|++.      +.++|||||+|.+.++|++|++.|+  +..+.|++|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4578999999999999999999999998 9999864      4678999999999999999999996  58999999999


Q ss_pred             EecCCCch
Q 004002          347 EPSRPGGA  354 (780)
Q Consensus       347 ~~a~~k~~  354 (780)
                      .+++++..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99998764

>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=99.44  E-value=2.5e-13  Score=122.62  Aligned_cols=78  Identities=12%  Similarity=0.195  Sum_probs=71.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE-EE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRT-LY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s-v~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||+++|+++|+++|++||.|.. |+    .+++++|||||+|.+.++|++||+. ++..|.|+.|.|.++
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            45689999999999999999999999999987 65    3688999999999999999999997 999999999999988


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .+++
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.44  E-value=1.7e-13  Score=129.31  Aligned_cols=77  Identities=26%  Similarity=0.490  Sum_probs=70.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||.++|+++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456799999999999999999999999999999983     47789999999999999999999999999999999998


Q ss_pred             cC
Q 004002          263 FS  264 (780)
Q Consensus       263 ~a  264 (780)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.44  E-value=6.3e-14  Score=125.37  Aligned_cols=79  Identities=16%  Similarity=0.236  Sum_probs=70.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE----EeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv----~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .+.++|||+|||.++|+++|+++|++||.|..+    ..+++++|||||+|.+.++|++|++ |++..|.|++|.|.++.
T Consensus        15 ~~~~~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           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            456899999999999999999999999977551    1457899999999999999999999 99999999999999998


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      ++..
T Consensus        94 ~~~~   97 (101)
T 1fj7_A           94 GRDG   97 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.44  E-value=1.2e-13  Score=120.69  Aligned_cols=76  Identities=13%  Similarity=0.302  Sum_probs=70.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++| .|+.|++. +++|||||+|.+.++|++|++.|||..+.|++|+|+++..+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            35689999999999999999999999 99999885 789999999999999999999999999999999999997653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=2.4e-13  Score=119.21  Aligned_cols=77  Identities=19%  Similarity=0.270  Sum_probs=70.7

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ....+|||+|||.++++++|+++|++| .|..|++    +++++|||||+|.+.++|++||+ |||..+.|+.|+|.+++
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            345789999999999999999999999 9999875    46678999999999999999999 99999999999999998


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      ++.
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            764

>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=99.43  E-value=4.6e-14  Score=123.46  Aligned_cols=75  Identities=23%  Similarity=0.453  Sum_probs=67.4

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.+ |++|++.|||..+.|++|+|++|.+.
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            47999999999999999999999999999986     3677999999999999 99999999999999999999999876


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.43  E-value=5.1e-14  Score=119.23  Aligned_cols=71  Identities=17%  Similarity=0.424  Sum_probs=66.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.++ ..+.|++|.|+++
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            5899999999999999999999999998877     257889999999999999999999999 9999999999886

>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=99.43  E-value=2.2e-13  Score=133.32  Aligned_cols=77  Identities=23%  Similarity=0.295  Sum_probs=70.4

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeC-CCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~-g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~k~  353 (780)
                      ..+|||+||+..+|+++|+++|++||+|++|++. ..++|||||+|.+.++|++|++.|||..|.|  ++|+|++++++.
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~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            4579999999999999999999999999999874 4457899999999999999999999999965  999999999864

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.43  E-value=3.8e-13  Score=126.82  Aligned_cols=76  Identities=26%  Similarity=0.437  Sum_probs=69.7

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||..+++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345679999999999999999999999999999986     356789999999999999999999999999999999987


Q ss_pred             c
Q 004002          349 S  349 (780)
Q Consensus       349 a  349 (780)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=3.7e-13  Score=119.10  Aligned_cols=78  Identities=19%  Similarity=0.185  Sum_probs=70.4

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEE-e-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-E-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-~-~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ...+|||+|||.++++++|+++|++||.|+.|+ + .....+.|||+|.+.++|++|++.|||..+.|++|+|.++.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            457899999999999999999999999999995 4 33345669999999999999999999999999999999999874

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.43  E-value=7.4e-14  Score=124.92  Aligned_cols=80  Identities=23%  Similarity=0.318  Sum_probs=71.2

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEE----EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v----~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ....+|||+|||.++++++|+++|++||.|..+    +.++.++|||||+|.+.++|++||+ |||..+.|+.|+|.+++
T Consensus        15 ~~~~~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           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            346799999999999999999999999988662    2356789999999999999999998 99999999999999999


Q ss_pred             CCchh
Q 004002          351 PGGAR  355 (780)
Q Consensus       351 ~k~~r  355 (780)
                      ++..+
T Consensus        94 ~~~~~   98 (101)
T 1fj7_A           94 GRDGT   98 (101)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87654

>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=99.42  E-value=9.7e-14  Score=121.34  Aligned_cols=76  Identities=16%  Similarity=0.371  Sum_probs=70.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ...++|||+|||+++++++|+++|++| +|..++.. +++|||||+|.+.++|++|++.|+|..+.|++|+|.++...
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            356899999999999999999999999 99988763 89999999999999999999999999999999999998643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.42  E-value=2.6e-13  Score=125.84  Aligned_cols=77  Identities=18%  Similarity=0.371  Sum_probs=71.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||.++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|+ .|+|..|.|+.|.|.++.
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            3589999999999999999999999999998873     6888999999999999999999 799999999999999987


Q ss_pred             CCC
Q 004002          266 PKD  268 (780)
Q Consensus       266 pk~  268 (780)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.42  E-value=3.5e-13  Score=127.22  Aligned_cols=78  Identities=23%  Similarity=0.325  Sum_probs=71.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceE-EEEEEecHHHHHHHHHHccCccccc--cccccccCCCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF-VMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKDN  269 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~-aFV~F~~~e~A~~Al~~Lng~~l~g--r~I~V~~a~pk~~  269 (780)
                      -.|||+||++.+|+++|+++|++||+|.+|++..+.+|| |||+|.+.++|++|++.|+|..|.+  ++|+|.|++++..
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            578899999999999999999999999999865567888 9999999999999999999999988  8999999988654


Q ss_pred             C
Q 004002          270 P  270 (780)
Q Consensus       270 ~  270 (780)
                      .
T Consensus       109 ~  109 (130)
T 3zzy_A          109 N  109 (130)
T ss_dssp             C
T ss_pred             e
Confidence            3

>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=99.42  E-value=5.6e-13  Score=119.57  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=71.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ....++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|++||+  ++..+.|++|+|.+
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            345678999999999999999999999999999976     46778999999999999999999  57899999999999


Q ss_pred             cCCCch
Q 004002          349 SRPGGA  354 (780)
Q Consensus       349 a~~k~~  354 (780)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            988754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.42  E-value=1.3e-13  Score=116.78  Aligned_cols=71  Identities=27%  Similarity=0.417  Sum_probs=66.2

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ++|||+|||.++++++|+++|++||.|..|++     ++.++|+|||+|.+.++|++|++.++ ..+.|++|+|++|
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            37999999999999999999999999999875     45678999999999999999999999 9999999999987

>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=99.42  E-value=2.5e-13  Score=132.77  Aligned_cols=82  Identities=20%  Similarity=0.406  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...+.++|||+|||+++|+++|+.+|++||.|..|.+     +++++|||||+|.+.++|++||+.|+|..|.|++|.|.
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            3456789999999999999999999999999999873     67789999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 004002          263 FSIPKDN  269 (780)
Q Consensus       263 ~a~pk~~  269 (780)
                      |+.++..
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9987654

>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=99.42  E-value=1.4e-13  Score=131.05  Aligned_cols=77  Identities=17%  Similarity=0.146  Sum_probs=69.6

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCC---eeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~---I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ...+|||+|||.++|+++|+++|++||.   |+.|++    .++++|||||+|.+.++|++||+ |||..+.|+.|+|.+
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~  121 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFK  121 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            4578999999999999999999999999   777764    46788999999999999999999 999999999999999


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      +.++.
T Consensus       122 a~~~e  126 (136)
T 2hgl_A          122 SHRTE  126 (136)
T ss_dssp             CCHHH
T ss_pred             CChHH
Confidence            86543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.42  E-value=4e-13  Score=125.99  Aligned_cols=75  Identities=25%  Similarity=0.257  Sum_probs=68.3

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccE-EEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCc
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-KFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  353 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~-aFV~F~~~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~k~  353 (780)
                      -.|||+||+..+++++|+++|++||.|++|++..+ .|+ |||+|.+.++|++|+++|||..|.|  +.|+|.+|+++.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            35789999999999999999999999999987544 586 9999999999999999999999987  699999999875

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=5.2e-13  Score=118.13  Aligned_cols=79  Identities=23%  Similarity=0.296  Sum_probs=71.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ...++|||+|||+++|+++|+++|++||+|..|+  ...+..|.|||+|.+.++|++|++.|+|..|.|++|.|.++.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            3468999999999999999999999999999994  34445667999999999999999999999999999999999876


Q ss_pred             C
Q 004002          268 D  268 (780)
Q Consensus       268 ~  268 (780)
                      +
T Consensus        93 ~   93 (96)
T 2e44_A           93 M   93 (96)
T ss_dssp             C
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=99.42  E-value=4.5e-13  Score=131.18  Aligned_cols=80  Identities=21%  Similarity=0.273  Sum_probs=71.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeC-CCcceEEEEEEecHHHHHHHHHHccCccccc--cccccccCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-CKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPK  267 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~t-gkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~I~V~~a~pk  267 (780)
                      ...+|||+||++.+|+++|+++|++||+|.+|++. .+.+|||||+|.+.++|++|++.|+|..|.+  ++|+|.|++++
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            34679999999999999999999999999999853 4468999999999999999999999999965  99999999987


Q ss_pred             CCC
Q 004002          268 DNP  270 (780)
Q Consensus       268 ~~~  270 (780)
                      ...
T Consensus       125 ~l~  127 (164)
T 1sjr_A          125 SLN  127 (164)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            543

>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=99.41  E-value=2.2e-13  Score=129.77  Aligned_cols=80  Identities=19%  Similarity=0.386  Sum_probs=72.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE----------EeCCCcceEEEEEEecHHHHHHHHHHccCcccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----------YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv----------~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I  259 (780)
                      .+.++|||+|||+++|+++|+.+|++||.|..+          ..+++++|||||+|.+.++|++|++.|+|..|.|++|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            467899999999999999999999999987542          2578999999999999999999999999999999999


Q ss_pred             ccccCCCCCC
Q 004002          260 DIHFSIPKDN  269 (780)
Q Consensus       260 ~V~~a~pk~~  269 (780)
                      .|.|+.+...
T Consensus       123 ~V~~a~~~~~  132 (143)
T 3egn_A          123 VVQFARSARP  132 (143)
T ss_dssp             EEEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9999977543

>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=99.41  E-value=1.2e-13  Score=126.45  Aligned_cols=77  Identities=17%  Similarity=0.389  Sum_probs=71.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|+ .|++..|.|++|.|.++
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            34589999999999999999999999999999984     3789999999999999999999 89999999999999998


Q ss_pred             CCC
Q 004002          265 IPK  267 (780)
Q Consensus       265 ~pk  267 (780)
                      .++
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=1.8e-13  Score=125.61  Aligned_cols=79  Identities=19%  Similarity=0.441  Sum_probs=72.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      +.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++||+. ++..|.|++|.|.++.
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            4589999999999999999999999999988872     478899999999999999999997 9999999999999998


Q ss_pred             CCCCC
Q 004002          266 PKDNP  270 (780)
Q Consensus       266 pk~~~  270 (780)
                      ++...
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            87643

>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=99.41  E-value=6.4e-13  Score=119.96  Aligned_cols=78  Identities=23%  Similarity=0.293  Sum_probs=70.7

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeE-EEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~-v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++|+++|+++|++||.|.. |++    +++++|||||+|.+.++|++||+. ++..+.|+.|+|.++
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            34579999999999999999999999999987 765    677899999999999999999997 999999999999998


Q ss_pred             CCCc
Q 004002          350 RPGG  353 (780)
Q Consensus       350 ~~k~  353 (780)
                      .++.
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=5.8e-13  Score=118.21  Aligned_cols=75  Identities=17%  Similarity=0.335  Sum_probs=67.1

Q ss_pred             CCcE-EEEeCCCCCCCHHH----HHHHhhcC-CCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          191 PSRT-LFVRNINSNVEDSE----LRALFEQY-GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       191 ~s~t-LfVgNLp~~vteee----Lr~lF~~y-G~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ++.| |||+|||.++++++    |+++|++| |+|.+|  ++   |+|||.|.+.++|++|++.|+|..+.||+|+|.|+
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A   81 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFT   81 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESS
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEec
Confidence            4555 99999999999988    55899999 599998  34   99999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      ..+.+.
T Consensus        82 ~~~sd~   87 (96)
T 2diu_A           82 PKNREL   87 (96)
T ss_dssp             CCSCCC
T ss_pred             CCCcce
Confidence            876543

>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=99.40  E-value=5.6e-13  Score=117.25  Aligned_cols=76  Identities=24%  Similarity=0.389  Sum_probs=63.8

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc--CCceEEEEecCCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI--AGKRIKLEPSRPG  352 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i--~Gr~L~V~~a~~k  352 (780)
                      ....+|||+|||.++|+++|+++|++||.|++|++...+||||||+|++.++|++    |+|..+  .|++|.|.++.++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            3457999999999999999999999999999999877789999999999999983    566654  5999999999987


Q ss_pred             ch
Q 004002          353 GA  354 (780)
Q Consensus       353 ~~  354 (780)
                      ..
T Consensus        85 ~~   86 (89)
T 3d2w_A           85 HN   86 (89)
T ss_dssp             --
T ss_pred             Cc
Confidence            64

>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=99.40  E-value=3.8e-13  Score=124.25  Aligned_cols=78  Identities=17%  Similarity=0.320  Sum_probs=69.7

Q ss_pred             CCCCcEEEE--eCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccc-----ccccccc
Q 004002          189 EHPSRTLFV--RNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL-----RRRKLDI  261 (780)
Q Consensus       189 e~~s~tLfV--gNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l-----~gr~I~V  261 (780)
                      ..++++|||  +||++++|+++|+++|++||+|..|+.. ..||||||+|.+.++|++|+++|+|+.|     .+++|.|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v  100 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL  100 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEE
Confidence            356789999  6699999999999999999999998853 4689999999999999999999999988     6899999


Q ss_pred             ccCCCC
Q 004002          262 HFSIPK  267 (780)
Q Consensus       262 ~~a~pk  267 (780)
                      .|+...
T Consensus       101 ~~a~~~  106 (114)
T 2cq2_A          101 NFVEKV  106 (114)
T ss_dssp             EEESCC
T ss_pred             EecccC
Confidence            988643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=1.4e-12  Score=115.30  Aligned_cols=80  Identities=16%  Similarity=0.296  Sum_probs=69.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      ...++|||+|||+++|+++|+++|++||+|..|........||||+|.+.++|++|++ |++..|.|++|.|.++.++..
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            3568999999999999999999999999999985322211199999999999999999 999999999999999876554


Q ss_pred             C
Q 004002          270 P  270 (780)
Q Consensus       270 ~  270 (780)
                      .
T Consensus        85 ~   85 (94)
T 2e5g_A           85 Q   85 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.40  E-value=1.2e-13  Score=132.00  Aligned_cols=121  Identities=12%  Similarity=0.062  Sum_probs=69.5

Q ss_pred             ceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCCCCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEE
Q 004002          229 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR  308 (780)
Q Consensus       229 kG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~  308 (780)
                      +|+||..|...+.+..++..+... ..+....-.....  ..........+|||+|||.++|+++|+++|++|| |+.|+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~--~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~   76 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDS--EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVH   76 (139)
T ss_dssp             -----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEE
T ss_pred             CCcccccccCccccchhcccchhc-cCCCCCCCCCCCc--ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEE
Confidence            367888888888888887765433 2332221111111  1112223456899999999999999999999999 66887


Q ss_pred             e----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          309 E----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       309 ~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      +    .++++|||||+|.+.++|++|| .+|+..+.|+.|+|..+.+...
T Consensus        77 i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           77 IEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             EEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            5    4677999999999999999999 7999999999999999887653

>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=99.40  E-value=2.4e-13  Score=124.77  Aligned_cols=79  Identities=10%  Similarity=0.107  Sum_probs=71.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCe-eEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-KEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I-~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++|+++|+++|++||.| ..|++    +++++|||||+|.+.++|++||+. ||..|.|+.|+|.++
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            355789999999999999999999999999 67765    467899999999999999999987 999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      .++..
T Consensus        92 ~~~~~   96 (114)
T 2cpy_A           92 TLEDM   96 (114)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            86543

>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=99.40  E-value=3.5e-13  Score=121.66  Aligned_cols=78  Identities=9%  Similarity=0.215  Sum_probs=69.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ....++|||+|||+++|+++|+++|++||.+ .|+    .+++++|||||+|.+.++|++||+ +++..|.++.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3456899999999999999999999999955 665    368899999999999999999995 7999999999999988


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .+..
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.39  E-value=3.5e-13  Score=124.44  Aligned_cols=77  Identities=18%  Similarity=0.208  Sum_probs=69.5

Q ss_pred             Cccceee--cCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc-----CCceEEEEe
Q 004002          276 NQGTLVV--FNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI-----AGKRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V--~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i-----~Gr~L~V~~  348 (780)
                      ...+|||  +||+.++++++|+++|++||.|..|.+. ..||||||+|.+.++|++|++.|||+++     .|+.|.|.+
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            4568999  7799999999999999999999999875 3589999999999999999999999988     689999999


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      ++...
T Consensus       103 a~~~p  107 (114)
T 2cq2_A          103 VEKVQ  107 (114)
T ss_dssp             ESCCC
T ss_pred             cccCc
Confidence            87543

>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=99.39  E-value=5.3e-13  Score=122.89  Aligned_cols=75  Identities=21%  Similarity=0.294  Sum_probs=66.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce-----EEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-----IKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~-----L~V~~a~  350 (780)
                      ...+|||+|||.++++++|+++|++||+|+.|++...  |||||+|.+.++|++||+.|||..|.|++     |+|..+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            3468999999999999999999999999999998544  99999999999999999999999999998     7777766


Q ss_pred             CC
Q 004002          351 PG  352 (780)
Q Consensus       351 ~k  352 (780)
                      ++
T Consensus        93 ~~   94 (115)
T 3beg_B           93 PR   94 (115)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.39  E-value=6.7e-13  Score=117.31  Aligned_cols=77  Identities=23%  Similarity=0.372  Sum_probs=67.6

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++||.|..|........||||+|.+.++|++||+ |||..+.|+.|+|.++.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            456899999999999999999999999999985432222299999999999999999 99999999999999887654

>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=99.38  E-value=6.5e-13  Score=116.88  Aligned_cols=75  Identities=23%  Similarity=0.474  Sum_probs=63.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcc--ccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~--l~gr~I~V~~a~pk  267 (780)
                      .+..+|||+|||+++|+++|+++|++||+|.+|+...++||||||+|.+.++|++    +++..  +.|++|.|.++.++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            4678999999999999999999999999999999766799999999999999984    45554  45899999999876


Q ss_pred             C
Q 004002          268 D  268 (780)
Q Consensus       268 ~  268 (780)
                      .
T Consensus        85 ~   85 (89)
T 3d2w_A           85 H   85 (89)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=8e-13  Score=117.31  Aligned_cols=73  Identities=26%  Similarity=0.383  Sum_probs=65.8

Q ss_pred             ccceeecCCCCCCChhH----HHHHhccc-CCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNED----LRQIFGAY-GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteed----L~~~Fs~y-G~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .+.|||+|||.++++++    |+++|++| |+|.+|  ++   |+|||+|.+.++|++|++.|||..+.||+|+|.+|+.
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            34499999999999988    55899999 599998  33   9999999999999999999999999999999999998


Q ss_pred             Cch
Q 004002          352 GGA  354 (780)
Q Consensus       352 k~~  354 (780)
                      +..
T Consensus        84 ~sd   86 (96)
T 2diu_A           84 NRE   86 (96)
T ss_dssp             SCC
T ss_pred             Ccc
Confidence            753

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.08  E-value=3.5e-14  Score=130.49  Aligned_cols=82  Identities=22%  Similarity=0.374  Sum_probs=74.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE--------EE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s--------v~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                      ..+.++|||+|||.++++++|+++|++||.|..        |+     .+++++|||||+|.+.++|++|++.|++..|.
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            346789999999999999999999999999987        54     35788999999999999999999999999999


Q ss_pred             ccccccccCCCCCCC
Q 004002          256 RRKLDIHFSIPKDNP  270 (780)
Q Consensus       256 gr~I~V~~a~pk~~~  270 (780)
                      |++|.|.++.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.38  E-value=3.8e-13  Score=124.49  Aligned_cols=76  Identities=18%  Similarity=0.172  Sum_probs=69.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCC---eeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~---I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ...+|||+|||.++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++||+ |||..|.|+.|+|.+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~   94 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFK   94 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEE
Confidence            4578999999999999999999999999   777765    46778999999999999999999 999999999999999


Q ss_pred             cCCC
Q 004002          349 SRPG  352 (780)
Q Consensus       349 a~~k  352 (780)
                      +.++
T Consensus        95 a~~~   98 (118)
T 2db1_A           95 SHRT   98 (118)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

>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=99.38  E-value=4.9e-13  Score=120.74  Aligned_cols=76  Identities=13%  Similarity=0.195  Sum_probs=68.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ...+|||+|||.++|+++|+++|++||.| .|++    +++++|||||+|.+.++|++||+ +|+..|.|+.|+|..+.+
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~   91 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCC
Confidence            45789999999999999999999999954 7765    56788999999999999999995 899999999999998876


Q ss_pred             Cc
Q 004002          352 GG  353 (780)
Q Consensus       352 k~  353 (780)
                      ..
T Consensus        92 ~~   93 (102)
T 1wez_A           92 AG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.37  E-value=2.3e-13  Score=126.70  Aligned_cols=77  Identities=17%  Similarity=0.200  Sum_probs=69.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEE-E----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-R----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v-~----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||.++|+++|+++|++||.|..+ .    .+++++|||||+|.+.++|++||+ |||..|.|+.|+|.++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            45799999999999999999999999998652 2    367789999999999999999999 99999999999999997


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      ++.
T Consensus       103 ~~~  105 (124)
T 1wel_A          103 KKG  105 (124)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=99.37  E-value=1.3e-13  Score=128.47  Aligned_cols=76  Identities=9%  Similarity=0.198  Sum_probs=68.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE---EE--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s---v~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||+++|+++|+++|++||.|..   +.  .+++++|||||+|.+.++|++||+ |++..|.|+.|.|.++
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            45689999999999999999999999999754   22  468899999999999999999999 9999999999999988


Q ss_pred             CC
Q 004002          265 IP  266 (780)
Q Consensus       265 ~p  266 (780)
                      .+
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            64

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.37  E-value=1.7e-13  Score=122.74  Aligned_cols=78  Identities=22%  Similarity=0.483  Sum_probs=70.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...++|||+|||.++++++|+++|++||.|..|+.    +++++|||||+|.+.++|++|++  ++..+.|++|.|.++.
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            45689999999999999999999999999999873    57799999999999999999999  8999999999999987


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      ++..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            6543

>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=99.37  E-value=1.9e-13  Score=115.19  Aligned_cols=70  Identities=19%  Similarity=0.477  Sum_probs=64.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +|||+|||+++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++. ++..+.|++|.|+++
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            6899999999999999999999999998872     478899999999999999999994 899999999999864

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.37  E-value=1.3e-12  Score=122.52  Aligned_cols=75  Identities=17%  Similarity=0.261  Sum_probs=67.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceE-EEEEEecHHHHHHHHHHccCccccc--cccccccCCCCCC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF-VMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKDN  269 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~-aFV~F~~~e~A~~Al~~Lng~~l~g--r~I~V~~a~pk~~  269 (780)
                      .|||+||++.+|+++|+++|++||+|.+|++..+ .|| |||+|.+.++|++|+++|+|..|.|  ++|+|.|++++..
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            4689999999999999999999999999985434 496 9999999999999999999999987  6899999988754

>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=99.37  E-value=1.4e-13  Score=126.32  Aligned_cols=78  Identities=14%  Similarity=0.171  Sum_probs=70.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCE-EEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I-~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..+.++|||+|||+++|+++|+++|++||.| ..|+    .+++++|||||+|.+.++|++||+. ++..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            3467899999999999999999999999999 5555    2578999999999999999999997 99999999999999


Q ss_pred             CCCC
Q 004002          264 SIPK  267 (780)
Q Consensus       264 a~pk  267 (780)
                      +.++
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

>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=99.37  E-value=7.8e-13  Score=125.92  Aligned_cols=80  Identities=28%  Similarity=0.380  Sum_probs=71.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeE--------E--EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------I--RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~--------v--~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      ...+|||+|||.++|+++|+++|++||.|..        +  ..++.++|||||+|.+.++|.+||..|||..+.|+.|+
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~  123 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV  123 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            4578999999999999999999999999865        3  24688899999999999999999999999999999999


Q ss_pred             EEecCCCchh
Q 004002          346 LEPSRPGGAR  355 (780)
Q Consensus       346 V~~a~~k~~r  355 (780)
                      |.++++...+
T Consensus       124 V~~a~~~~~~  133 (143)
T 3egn_A          124 VQFARSARPK  133 (143)
T ss_dssp             EEECCCSCC-
T ss_pred             EEECCCCCCc
Confidence            9999876543

>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=99.37  E-value=4.5e-13  Score=138.40  Aligned_cols=79  Identities=15%  Similarity=0.210  Sum_probs=72.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccC--CeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG--~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ...+|||+||+.++|+++|+++|++||  .|++|++     ++++||||||+|.+.++|++||+.|||+.|.|++|+|.+
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            356899999999999999999999999  9999975     677899999999999999999999999999999999999


Q ss_pred             cCCCch
Q 004002          349 SRPGGA  354 (780)
Q Consensus       349 a~~k~~  354 (780)
                      +++...
T Consensus       147 a~~~~~  152 (229)
T 3q2s_C          147 VNKQFL  152 (229)
T ss_dssp             CCHHHH
T ss_pred             CCCCcc
Confidence            986543

>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=99.37  E-value=4.3e-13  Score=121.75  Aligned_cols=78  Identities=15%  Similarity=0.107  Sum_probs=70.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCC---eeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~---I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ....+|||+|||.++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++||+ |||..+.|+.|+|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            34578999999999999999999999988   888875    36678999999999999999999 99999999999999


Q ss_pred             ecCCCc
Q 004002          348 PSRPGG  353 (780)
Q Consensus       348 ~a~~k~  353 (780)
                      ++.++.
T Consensus        88 ~a~~~~   93 (107)
T 2lmi_A           88 EINNED   93 (107)
T ss_dssp             ECCHHH
T ss_pred             ECCHHH
Confidence            987644

>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=99.36  E-value=3e-13  Score=114.00  Aligned_cols=70  Identities=23%  Similarity=0.453  Sum_probs=64.7

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      +|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++ +++..+.|++|+|++|
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            5899999999999999999999999999976     35678999999999999999998 4999999999999875

>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=99.36  E-value=4.7e-13  Score=138.25  Aligned_cols=76  Identities=16%  Similarity=0.249  Sum_probs=70.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCC--CEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG--~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..++|||+|||+++|+++|+++|++||  +|.+|+     .++++||||||+|.+.++|++||+.|++..|.|++|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            467999999999999999999999999  999987     2788999999999999999999999999999999999999


Q ss_pred             CCC
Q 004002          264 SIP  266 (780)
Q Consensus       264 a~p  266 (780)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.05  E-value=6e-14  Score=128.92  Aligned_cols=80  Identities=23%  Similarity=0.307  Sum_probs=72.5

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeE--------EEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~--------v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G  341 (780)
                      ...++|||+|||.++++++|+++|++||.|..        |++     ++.++|||||+|.+.++|++|++.|||..+.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34578999999999999999999999999988        654     45678999999999999999999999999999


Q ss_pred             ceEEEEecCCCch
Q 004002          342 KRIKLEPSRPGGA  354 (780)
Q Consensus       342 r~L~V~~a~~k~~  354 (780)
                      ++|+|.+++++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=1e-12  Score=120.44  Aligned_cols=73  Identities=16%  Similarity=0.260  Sum_probs=67.1

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ..+|||+|||.++|+++|+++|++| .|..|++    .++++|||||+|.+.++|++|| .|||..+.|+.|+|..+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 8988876    4678999999999999999999 6999999999999988854

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.35  E-value=5.5e-13  Score=123.40  Aligned_cols=76  Identities=7%  Similarity=0.124  Sum_probs=68.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCC---EEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~---I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...++|||+|||+++|+++|+++|++||.   |..|+    ..++++|||||+|.+.++|++||+ |++..|.|+.|.|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            35689999999999999999999999998   66655    248899999999999999999999 99999999999998


Q ss_pred             cCCC
Q 004002          263 FSIP  266 (780)
Q Consensus       263 ~a~p  266 (780)
                      ++.+
T Consensus        94 ~a~~   97 (118)
T 2db1_A           94 KSHR   97 (118)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>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=99.35  E-value=4.8e-13  Score=121.38  Aligned_cols=76  Identities=9%  Similarity=0.054  Sum_probs=69.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCC---EEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~---I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...++|||+|||+++|+++|+++|+.||.   |..|+    ..++++|||||+|.+.++|++||+ +++..|.|+.|.|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            45689999999999999999999999988   77776    247899999999999999999999 99999999999999


Q ss_pred             cCCC
Q 004002          263 FSIP  266 (780)
Q Consensus       263 ~a~p  266 (780)
                      ++.+
T Consensus        88 ~a~~   91 (107)
T 2lmi_A           88 EINN   91 (107)
T ss_dssp             ECCH
T ss_pred             ECCH
Confidence            8765

>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=99.35  E-value=4.4e-13  Score=116.91  Aligned_cols=79  Identities=24%  Similarity=0.452  Sum_probs=67.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      .++++|||+|||+++|+++|+++|++||+|..|+....++|||||+|.+.++|++|+..  ...+.+++|.|.++.++..
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCC
Confidence            35699999999999999999999999999999997667899999999999999865432  3455899999999987654


Q ss_pred             C
Q 004002          270 P  270 (780)
Q Consensus       270 ~  270 (780)
                      .
T Consensus        81 ~   81 (88)
T 1wf0_A           81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.34  E-value=1.4e-12  Score=120.07  Aligned_cols=72  Identities=14%  Similarity=0.209  Sum_probs=63.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ...++|||+|||+++|+++|+++|++||+|..|++...  |||||+|.+.++|++||+.|++..|.|++|+|.+
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~   85 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   85 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEE
Confidence            34689999999999999999999999999999986433  9999999999999999999999999999944443

>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=99.34  E-value=4.4e-13  Score=127.69  Aligned_cols=76  Identities=7%  Similarity=0.102  Sum_probs=68.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCC---EEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~---I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ...++|||+|||+++|+++|+++|++||.   |..|+    ..++++|||||+|.+.++|++|++ |++..|.|++|.|.
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            45689999999999999999999999998   65554    248899999999999999999999 99999999999999


Q ss_pred             cCCC
Q 004002          263 FSIP  266 (780)
Q Consensus       263 ~a~p  266 (780)
                      ++.+
T Consensus       121 ~a~~  124 (136)
T 2hgl_A          121 KSHR  124 (136)
T ss_dssp             ECCH
T ss_pred             ECCh
Confidence            8754

>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=99.34  E-value=2.1e-12  Score=129.89  Aligned_cols=115  Identities=13%  Similarity=0.147  Sum_probs=88.6

Q ss_pred             cHHHHHHHHHHc--cCccccccccccccCCCCCCCCC-----CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-
Q 004002          238 DIRAARTAMRAL--QNKPLRRRKLDIHFSIPKDNPSD-----KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-  309 (780)
Q Consensus       238 ~~e~A~~Al~~L--ng~~l~gr~I~V~~a~pk~~~s~-----~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-  309 (780)
                      +.+.+..|++..  ....+.+....|........+..     +....++|||+|||.++|+++|+++|++||.|..|++ 
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            567788888876  44455565556655422222211     2234579999999999999999999999999999976 


Q ss_pred             ---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          310 ---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       310 ---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                         ++.++|||||+|.+.++|++|+..++ ..+.|+.|.|.+++.-.
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDYF  188 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC-
T ss_pred             ECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHHH
Confidence               36678999999999999999998665 59999999999887643

>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=99.34  E-value=1.3e-12  Score=113.21  Aligned_cols=72  Identities=18%  Similarity=0.380  Sum_probs=66.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcC----C-------CEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~y----G-------~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~  258 (780)
                      .+.++|||+|||+++++++|+++|++|    |       +|.+++. .+.+|||||+|.+.++|++|+ .|++..+.|++
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~-~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~   81 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-CSSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEe-cCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            356899999999999999999999999    8       9999875 456999999999999999999 99999999999


Q ss_pred             ccccc
Q 004002          259 LDIHF  263 (780)
Q Consensus       259 I~V~~  263 (780)
                      |+|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99864

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.33  E-value=2.4e-12  Score=133.68  Aligned_cols=104  Identities=15%  Similarity=0.183  Sum_probs=77.5

Q ss_pred             CccccccccccccCCCCCCCCCCCCCccceeecCCCCCC---------ChhHHHHHhcccCCeeEEEeCCCcccEEEEEE
Q 004002          251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV---------SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEF  321 (780)
Q Consensus       251 g~~l~gr~I~V~~a~pk~~~s~~~~~~~~L~V~NLp~~v---------teedL~~~Fs~yG~I~~v~~~g~srG~aFV~F  321 (780)
                      ...+.|+.....+..............++|||+||+..+         ++++|+++|++||+|++|++. .++|||||+|
T Consensus       108 ~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~-~~kG~AFV~F  186 (240)
T 3u1l_A          108 VLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKF  186 (240)
T ss_dssp             SBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEE
T ss_pred             CcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEE-CCCCEEEEEe
Confidence            344456654444433222112223456799999999998         799999999999999999985 4689999999


Q ss_pred             cCHHHHHHHHHHhCCCcc------------CCceEEEEecCCCchh
Q 004002          322 YDVRAAEAALKSLNRSDI------------AGKRIKLEPSRPGGAR  355 (780)
Q Consensus       322 ~~~e~A~~Ai~~LnG~~i------------~Gr~L~V~~a~~k~~r  355 (780)
                      .+.++|++|+++|+|..+            .|+.|.|.||+.....
T Consensus       187 ~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          187 KYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             SSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             CCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence            999999999999999999            8999999999876543

>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=99.33  E-value=7.4e-13  Score=115.48  Aligned_cols=75  Identities=20%  Similarity=0.348  Sum_probs=66.4

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC--ccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~--~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++...++|||||+|.+.++|++|    ++.  .+.|++|+|.+++++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSL----CGEDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEECCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEEecCCCC
Confidence            3578999999999999999999999999999998777899999999999999764    444  5589999999998875


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        80 ~   80 (88)
T 1wf0_A           80 N   80 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.33  E-value=1.5e-12  Score=129.20  Aligned_cols=78  Identities=22%  Similarity=0.431  Sum_probs=72.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .+.++|||+|||+++++++|+++|++||+|..|++    +++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.
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            45689999999999999999999999999999874    47789999999999999999999999999999999999987


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      +.
T Consensus       166 ~~  167 (177)
T 2f3j_A          166 SQ  167 (177)
T ss_dssp             SG
T ss_pred             CC
Confidence            54

>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=99.33  E-value=2.2e-12  Score=111.65  Aligned_cols=71  Identities=21%  Similarity=0.383  Sum_probs=65.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhccc----C-------CeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAY----G-------EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~y----G-------~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L  344 (780)
                      ..++|||+|||.++++++|+++|++|    |       .|..+++. ..+|||||+|.+.++|++|+ .|||..+.|++|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~-~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l   82 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC-SSSSEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec-CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            45789999999999999999999999    8       89999885 45899999999999999999 999999999999


Q ss_pred             EEEe
Q 004002          345 KLEP  348 (780)
Q Consensus       345 ~V~~  348 (780)
                      +|+.
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9973

>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=99.32  E-value=7.6e-13  Score=126.50  Aligned_cols=78  Identities=9%  Similarity=0.203  Sum_probs=68.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ....++|||+|||+++|+++|+++|++|| |..|+    ..++++|||||+|.+.++|++|| .+++..|.++.|.|.++
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999 55776    24789999999999999999999 68999999999999988


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .+++
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.32  E-value=7.9e-13  Score=118.37  Aligned_cols=78  Identities=24%  Similarity=0.466  Sum_probs=70.4

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++  +|..+.|+.|.|.++.
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            34579999999999999999999999999999976    45678999999999999999999  9999999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            7653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.32  E-value=3.3e-12  Score=126.76  Aligned_cols=78  Identities=21%  Similarity=0.303  Sum_probs=72.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ...+|||+|||..+++++|+++|++||.|+.|++    ++.++|||||+|.+.++|++||+.|||..+.|+.|+|+++.+
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~  166 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS  166 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4579999999999999999999999999999987    356789999999999999999999999999999999999987


Q ss_pred             Cc
Q 004002          352 GG  353 (780)
Q Consensus       352 k~  353 (780)
                      ..
T Consensus       167 ~~  168 (177)
T 2f3j_A          167 QI  168 (177)
T ss_dssp             GG
T ss_pred             CC
Confidence            54

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=9.5e-13  Score=120.62  Aligned_cols=74  Identities=8%  Similarity=0.170  Sum_probs=66.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      ..++|||+|||+++|+++|+++|++| .|..|++    .++++|||||+|.+.++|++|| .+++..|.||.|.|..+.+
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            34799999999999999999999999 8888773    4789999999999999999999 5999999999999987643

>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=99.30  E-value=2.3e-12  Score=121.09  Aligned_cols=75  Identities=13%  Similarity=0.201  Sum_probs=66.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEE--EEE----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIR--TLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~--sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ...++|||+|||+++|+++|+++|++| .|.  .|+    ..++++|||||+|.+.++|++||+. ++..|.||.|.|.+
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-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEE
Confidence            456899999999999999999999999 666  776    2488999999999999999999995 78999999999988


Q ss_pred             CCC
Q 004002          264 SIP  266 (780)
Q Consensus       264 a~p  266 (780)
                      +.+
T Consensus       118 a~~  120 (126)
T 2hgm_A          118 SSQ  120 (126)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.30  E-value=1.2e-12  Score=122.42  Aligned_cols=77  Identities=19%  Similarity=0.198  Sum_probs=67.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCe----eEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV----KEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I----~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ...+|||+|||.++|+++|+++|++||.|    ..|++    +++++|||||+|.+.++|++||+. |+..+.|+.|+|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEE
Confidence            34689999999999999999999999975    45553    577899999999999999999996 9999999999999


Q ss_pred             ecCCCc
Q 004002          348 PSRPGG  353 (780)
Q Consensus       348 ~a~~k~  353 (780)
                      .+.++.
T Consensus       101 ~a~~~e  106 (123)
T 2dha_A          101 RSTAAE  106 (123)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            886543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.28  E-value=4.4e-12  Score=116.36  Aligned_cols=71  Identities=14%  Similarity=0.296  Sum_probs=60.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----C---CCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----A---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----t---gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      ...++|||+|||+++|+++|+++|++||+|. ++.     +   ++++|||||+|.+.++|++|++.|++  +.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEEe
Confidence            3568999999999999999999999999998 551     2   68899999999999999999999832  55555555


Q ss_pred             cc
Q 004002          262 HF  263 (780)
Q Consensus       262 ~~  263 (780)
                      ..
T Consensus        83 ~~   84 (114)
T 2dnl_A           83 VS   84 (114)
T ss_dssp             EC
T ss_pred             cc
Confidence            43

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=1.4e-12  Score=122.16  Aligned_cols=76  Identities=17%  Similarity=0.214  Sum_probs=66.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCE----EEEE----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDI----RTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I----~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      ...++|||+|||+++|+++|+++|++||.|    ..|+    .+++++|||||+|.+.++|++||+. ++..|.++.|.|
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            356899999999999999999999999975    3343    4688999999999999999999996 999999999999


Q ss_pred             ccCCC
Q 004002          262 HFSIP  266 (780)
Q Consensus       262 ~~a~p  266 (780)
                      ..+.+
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.27  E-value=4.1e-12  Score=131.88  Aligned_cols=82  Identities=21%  Similarity=0.374  Sum_probs=70.7

Q ss_pred             CCCCcEEEEeCCCCCC---------CHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccc-----
Q 004002          189 EHPSRTLFVRNINSNV---------EDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL-----  254 (780)
Q Consensus       189 e~~s~tLfVgNLp~~v---------teeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l-----  254 (780)
                      ....++|||+||+.++         ++++|+.+|++||+|.+|++ ..+||||||+|.+.++|+.|+++|+|..|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v-~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY-VESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEE-EGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEE-ECCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            3467999999999998         79999999999999999985 35799999999999999999999999999     


Q ss_pred             -------cccccccccCCCCCCCC
Q 004002          255 -------RRRKLDIHFSIPKDNPS  271 (780)
Q Consensus       255 -------~gr~I~V~~a~pk~~~s  271 (780)
                             .|+.|.|.|+.+..++.
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~pnp~  233 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDPDPA  233 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC------
T ss_pred             ccccccCCCCEEEEEEccCCCCHH
Confidence                   89999999998765543

>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=99.26  E-value=3.9e-12  Score=119.60  Aligned_cols=75  Identities=23%  Similarity=0.286  Sum_probs=66.5

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCee--EEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVK--EIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~--~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...+|||+|||+++|+++|+++|++| .|+  .|++    .++++|||||+|.+.++|++||+ +++..|.|+.|+|..+
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            45789999999999999999999999 666  7765    46789999999999999999998 4789999999999988


Q ss_pred             CCC
Q 004002          350 RPG  352 (780)
Q Consensus       350 ~~k  352 (780)
                      .++
T Consensus       119 ~~~  121 (126)
T 2hgm_A          119 SQE  121 (126)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=1.4e-11  Score=113.05  Aligned_cols=76  Identities=14%  Similarity=0.203  Sum_probs=65.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----C---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----T---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~---g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ..++|||+|||.++++++|+++|++||.|. +++     +   ++++|||||+|.+.++|++||+.|+  .++|+.|.+.
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 654     2   5779999999999999999999995  4788888887


Q ss_pred             ecCCCch
Q 004002          348 PSRPGGA  354 (780)
Q Consensus       348 ~a~~k~~  354 (780)
                      .+.+...
T Consensus        84 ~~~~~~~   90 (114)
T 2dnl_A           84 SSPTIKD   90 (114)
T ss_dssp             CCSSSCS
T ss_pred             cCCCcCC
Confidence            6665443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.24  E-value=7.1e-12  Score=117.39  Aligned_cols=77  Identities=16%  Similarity=0.292  Sum_probs=68.8

Q ss_pred             cceeecCC----CCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcC----HHH----HHHHHH--HhCCCc
Q 004002          278 GTLVVFNL----DPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYD----VRA----AEAALK--SLNRSD  338 (780)
Q Consensus       278 ~~L~V~NL----p~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~----~e~----A~~Ai~--~LnG~~  338 (780)
                      .+|||+||    |+.+++++|+++|+.||+|.+|++     ++.++|||||+|.+    .++    |.+|+.  .|||..
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            47999999    999999999999999999999974     78899999999996    333    899999  899999


Q ss_pred             cCCceEEEEecCCCch
Q 004002          339 IAGKRIKLEPSRPGGA  354 (780)
Q Consensus       339 i~Gr~L~V~~a~~k~~  354 (780)
                      |+|++|+|.+.+.+..
T Consensus        83 I~Gr~irV~ln~~g~~   98 (136)
T 2j8a_A           83 IMGFKFEVILNKHSIL   98 (136)
T ss_dssp             ETTEEEEEEECCTTHH
T ss_pred             ecCcEEEEEECcccHH
Confidence            9999999999988765

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.24  E-value=1.9e-11  Score=111.10  Aligned_cols=76  Identities=18%  Similarity=0.165  Sum_probs=66.6

Q ss_pred             CccceeecCCCC-----CCChhHHHHHhcccCCeeEEEeC------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 004002          276 NQGTLVVFNLDP-----SVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (780)
Q Consensus       276 ~~~~L~V~NLp~-----~vteedL~~~Fs~yG~I~~v~~~------g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L  344 (780)
                      ..++|+|.||-.     +-++++|+++|++||.|++|++.      ++++|+|||+|.+.++|++|++.|||+.+.|+.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            456899999953     23689999999999999999762      4678999999999999999999999999999999


Q ss_pred             EEEecCC
Q 004002          345 KLEPSRP  351 (780)
Q Consensus       345 ~V~~a~~  351 (780)
                      +|.++..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999975

>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=99.23  E-value=2.6e-11  Score=110.87  Aligned_cols=79  Identities=16%  Similarity=0.283  Sum_probs=69.1

Q ss_pred             CCccceeecCCCCCCC-----------hhHHHHHhcccCCeeEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 004002          275 LNQGTLVVFNLDPSVS-----------NEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vt-----------eedL~~~Fs~yG~I~~v~~-~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr  342 (780)
                      ...++|+|.||-...+           +++|+++|++||.|+.|.+ ...++|||||+|.+.++|++|++.|||..+.|+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   92 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   92 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            3567999999944332           5899999999999999976 345789999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 004002          343 RIKLEPSRPGG  353 (780)
Q Consensus       343 ~L~V~~a~~k~  353 (780)
                      +|+|.++.++.
T Consensus        93 ~l~v~~a~~~~  103 (112)
T 2dit_A           93 QITAQAWDGTT  103 (112)
T ss_dssp             ECEEEECCSCC
T ss_pred             EEEEEEeCCCC
Confidence            99999998764

>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=99.23  E-value=1.3e-11  Score=139.13  Aligned_cols=79  Identities=28%  Similarity=0.478  Sum_probs=73.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||++||+++|+.+|++||.|..|.+     +++++|||||+|.+.++|++||+.|+|..|.|++|.|.|+
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            45689999999999999999999999999999873     6788999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .++.
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            8654

>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=99.23  E-value=2.8e-11  Score=110.66  Aligned_cols=82  Identities=17%  Similarity=0.295  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEeCCCCCCC-----------HHHHHHHhhcCCCEEEEEe-CCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          188 GEHPSRTLFVRNINSNVE-----------DSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vt-----------eeeLr~lF~~yG~I~sv~~-tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                      ...++++|+|+||....+           +++|+++|++||+|..|.+ ...++|||||+|.+.++|++|++.|+|..|.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            445789999999954433           6899999999999999874 4458999999999999999999999999999


Q ss_pred             ccccccccCCCCCC
Q 004002          256 RRKLDIHFSIPKDN  269 (780)
Q Consensus       256 gr~I~V~~a~pk~~  269 (780)
                      |++|.|.++.++..
T Consensus        91 gr~l~v~~a~~~~~  104 (112)
T 2dit_A           91 GRQITAQAWDGTTD  104 (112)
T ss_dssp             TEECEEEECCSCCC
T ss_pred             CcEEEEEEeCCCCC
Confidence            99999999987653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.20  E-value=3.2e-11  Score=109.61  Aligned_cols=77  Identities=16%  Similarity=0.251  Sum_probs=67.7

Q ss_pred             CCCcEEEEeCCCC-----CCCHHHHHHHhhcCCCEEEEEe------CCCcceEEEEEEecHHHHHHHHHHccCccccccc
Q 004002          190 HPSRTLFVRNINS-----NVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (780)
Q Consensus       190 ~~s~tLfVgNLp~-----~vteeeLr~lF~~yG~I~sv~~------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~  258 (780)
                      .++++|+|+|+..     +-++++|+++|++||+|.+|++      +++++|||||+|.+.++|++|++.|+|..+.||+
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            4679999999963     2378999999999999999873      2578999999999999999999999999999999


Q ss_pred             cccccCCC
Q 004002          259 LDIHFSIP  266 (780)
Q Consensus       259 I~V~~a~p  266 (780)
                      |.|.++.+
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.16  E-value=1.4e-11  Score=115.36  Aligned_cols=73  Identities=19%  Similarity=0.312  Sum_probs=65.0

Q ss_pred             cEEEEeCC----CCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEec----HHH----HHHHHH--HccCcc
Q 004002          193 RTLFVRNI----NSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYD----IRA----ARTAMR--ALQNKP  253 (780)
Q Consensus       193 ~tLfVgNL----p~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~----~e~----A~~Al~--~Lng~~  253 (780)
                      ++|||+||    |+.+++++|+.+|++||+|.+|.     .+++++|||||+|.+    +++    |.+|++  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    99999999999999999999987     589999999999996    433    889988  789999


Q ss_pred             ccccccccccCC
Q 004002          254 LRRRKLDIHFSI  265 (780)
Q Consensus       254 l~gr~I~V~~a~  265 (780)
                      |.|++|+|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999998754

>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=99.15  E-value=4.5e-11  Score=120.14  Aligned_cols=75  Identities=12%  Similarity=0.318  Sum_probs=67.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      ..++|||+|||+++|+++|+++|++||+|..|+.    +++++|||||+|.+.++|++|++.+ +..+.|++|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            3589999999999999999999999999999873    4789999999999999999999865 5689999999998654

>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=99.12  E-value=1.2e-10  Score=105.81  Aligned_cols=77  Identities=23%  Similarity=0.323  Sum_probs=65.8

Q ss_pred             CccceeecCC--CCCCC--------hhHHHHHhcccCCeeEEEeC-------CCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          276 NQGTLVVFNL--DPSVS--------NEDLRQIFGAYGEVKEIRET-------PHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       276 ~~~~L~V~NL--p~~vt--------eedL~~~Fs~yG~I~~v~~~-------g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      +.+.|.+.|+  +.++.        +++|++.|++||.|++|++.       +.++|+|||+|.+.++|++|++.|||+.
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            4568899998  44443        37899999999999999873       2468999999999999999999999999


Q ss_pred             cCCceEEEEecCCC
Q 004002          339 IAGKRIKLEPSRPG  352 (780)
Q Consensus       339 i~Gr~L~V~~a~~k  352 (780)
                      ++||+|+|.++...
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999998653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=1e-10  Score=105.54  Aligned_cols=67  Identities=22%  Similarity=0.275  Sum_probs=60.5

Q ss_pred             CCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          286 DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       286 p~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      +..+++++|+++|++||.|+.|++.++++|||||+|.+.++|++||+.+++  +.|+.|+|.+++++..
T Consensus        26 ~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           26 KGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            357899999999999999999999888999999999999999999998554  6799999999987653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=3.9e-10  Score=101.68  Aligned_cols=75  Identities=19%  Similarity=0.282  Sum_probs=64.3

Q ss_pred             CcEEEEeCCC-------CCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          192 SRTLFVRNIN-------SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       192 s~tLfVgNLp-------~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+|.|.-..       .++++++|+++|++||+|..|++.++++|||||+|.+.++|++|++.+++  +.+++|.|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEc
Confidence            4566666544       46899999999999999999997789999999999999999999998554  67999999999


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .++.
T Consensus        88 ~~~~   91 (100)
T 2d9o_A           88 EGQP   91 (100)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            8664

>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=99.06  E-value=4.7e-11  Score=108.26  Aligned_cols=68  Identities=28%  Similarity=0.401  Sum_probs=58.5

Q ss_pred             ecCCCCCCChhHHHHHh------------cccCCeeEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          282 VFNLDPSVSNEDLRQIF------------GAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       282 V~NLp~~vteedL~~~F------------s~yG~I~~v~~~----g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      +.||+..+++++|+++|            ++||.|++|++.    ++++|||||+|.+.++|++|++.|||+.+.|++|+
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            45667777777776666            999999999873    45689999999999999999999999999999999


Q ss_pred             EEec
Q 004002          346 LEPS  349 (780)
Q Consensus       346 V~~a  349 (780)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9886

>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=99.05  E-value=2.5e-10  Score=103.69  Aligned_cols=77  Identities=17%  Similarity=0.375  Sum_probs=66.7

Q ss_pred             CCCcEEEEeCC--CCCCC--------HHHHHHHhhcCCCEEEEEeC-------CCcceEEEEEEecHHHHHHHHHHccCc
Q 004002          190 HPSRTLFVRNI--NSNVE--------DSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMRALQNK  252 (780)
Q Consensus       190 ~~s~tLfVgNL--p~~vt--------eeeLr~lF~~yG~I~sv~~t-------gkskG~aFV~F~~~e~A~~Al~~Lng~  252 (780)
                      .+++.|.++|+  |.++.        +++|++.|++||+|.+|++.       ++++|+|||+|.+.++|++|+++|||+
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            47899999998  44443        36899999999999999831       357899999999999999999999999


Q ss_pred             cccccccccccCCC
Q 004002          253 PLRRRKLDIHFSIP  266 (780)
Q Consensus       253 ~l~gr~I~V~~a~p  266 (780)
                      .+.||+|.|.|+.+
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            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=99.03  E-value=2.9e-10  Score=123.87  Aligned_cols=74  Identities=23%  Similarity=0.358  Sum_probs=65.3

Q ss_pred             CccceeecC--CCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC---Cc--eEEEEe
Q 004002          276 NQGTLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA---GK--RIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~N--Lp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~---Gr--~L~V~~  348 (780)
                      ...+|||+|  |+..+|+++|+++|++||+|++|++.. +||||||+|.+.++|++||++|||+++.   |+  .|.|.+
T Consensus        17 ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~   95 (345)
T 3tht_A           17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF   95 (345)
T ss_dssp             CCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEE
Confidence            457999999  578999999999999999999998854 7899999999999999999999999883   44  578888


Q ss_pred             cC
Q 004002          349 SR  350 (780)
Q Consensus       349 a~  350 (780)
                      +.
T Consensus        96 ~~   97 (345)
T 3tht_A           96 VE   97 (345)
T ss_dssp             CS
T ss_pred             ee
Confidence            75

>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=99.02  E-value=7.9e-11  Score=106.76  Aligned_cols=68  Identities=21%  Similarity=0.366  Sum_probs=60.1

Q ss_pred             EeCCCCCCCHHHHHHHh------------hcCCCEEEEEe----CCCcceEEEEEEecHHHHHHHHHHccCccccccccc
Q 004002          197 VRNINSNVEDSELRALF------------EQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (780)
Q Consensus       197 VgNLp~~vteeeLr~lF------------~~yG~I~sv~~----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~  260 (780)
                      +.+|++++++++|++.|            ++||+|.+|++    .++++|||||+|.+.++|++|++.|+|+.+.||+|.
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            56788888888877766            99999999984    356899999999999999999999999999999999


Q ss_pred             cccC
Q 004002          261 IHFS  264 (780)
Q Consensus       261 V~~a  264 (780)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9886

>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=99.01  E-value=3.6e-10  Score=123.21  Aligned_cols=75  Identities=19%  Similarity=0.342  Sum_probs=65.2

Q ss_pred             CCCCcEEEEeC--CCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccc---cc--cccc
Q 004002          189 EHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR---RR--KLDI  261 (780)
Q Consensus       189 e~~s~tLfVgN--Lp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~---gr--~I~V  261 (780)
                      ..++++|||+|  |+..+||++|+++|++||+|.+|+. ..+||||||+|.+.++|++|+++|||+.+.   |+  .|.|
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~-~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~   93 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEEC-CTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEE-eCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEE
Confidence            45789999999  5789999999999999999999875 347899999999999999999999999873   34  5666


Q ss_pred             ccC
Q 004002          262 HFS  264 (780)
Q Consensus       262 ~~a  264 (780)
                      .|+
T Consensus        94 ~~~   96 (345)
T 3tht_A           94 NFV   96 (345)
T ss_dssp             EEC
T ss_pred             EEe
Confidence            665

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.97  E-value=1.2e-09  Score=100.89  Aligned_cols=76  Identities=18%  Similarity=0.140  Sum_probs=64.0

Q ss_pred             CccceeecCCCC--CC--------ChhHHHHHhcccCCeeEEEeCC-CcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 004002          276 NQGTLVVFNLDP--SV--------SNEDLRQIFGAYGEVKEIRETP-HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (780)
Q Consensus       276 ~~~~L~V~NLp~--~v--------teedL~~~Fs~yG~I~~v~~~g-~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L  344 (780)
                      ..++|.+.|+=.  +.        -++||++.|++||.|++|.+.. ..+|++||+|.+.++|++|++.|||+.++|+.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            456788888722  21        2468999999999999998743 348999999999999999999999999999999


Q ss_pred             EEEecCC
Q 004002          345 KLEPSRP  351 (780)
Q Consensus       345 ~V~~a~~  351 (780)
                      +|.++..
T Consensus        86 ~v~~~~~   92 (114)
T 3s6e_A           86 TAAYVPL   92 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEEEcH
Confidence            9999864

>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=98.95  E-value=1e-09  Score=101.84  Aligned_cols=76  Identities=18%  Similarity=0.278  Sum_probs=64.2

Q ss_pred             CccceeecCCC--CCC---ChhHHHHHhcccCCeeEEEeC---------CCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 004002          276 NQGTLVVFNLD--PSV---SNEDLRQIFGAYGEVKEIRET---------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (780)
Q Consensus       276 ~~~~L~V~NLp--~~v---teedL~~~Fs~yG~I~~v~~~---------g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G  341 (780)
                      ..++|+|.|+-  .++   -++||++.|++||.|++|++.         ++++|++||+|.+.++|.+|++.|||+.++|
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            35688999983  222   368999999999999998752         2356999999999999999999999999999


Q ss_pred             ceEEEEecCC
Q 004002          342 KRIKLEPSRP  351 (780)
Q Consensus       342 r~L~V~~a~~  351 (780)
                      +.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>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=98.94  E-value=1.4e-09  Score=100.95  Aligned_cols=75  Identities=13%  Similarity=0.219  Sum_probs=65.2

Q ss_pred             CCcEEEEeCCC--CCC---CHHHHHHHhhcCCCEEEEEe---------CCCcceEEEEEEecHHHHHHHHHHccCccccc
Q 004002          191 PSRTLFVRNIN--SNV---EDSELRALFEQYGDIRTLYT---------ACKHRGFVMISYYDIRAARTAMRALQNKPLRR  256 (780)
Q Consensus       191 ~s~tLfVgNLp--~~v---teeeLr~lF~~yG~I~sv~~---------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g  256 (780)
                      ++++|+++|+-  .++   .+++|++.|++||+|.+|++         +++++|+|||+|.+.++|++|+++|+|+.+.|
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            67999999983  222   36899999999999999872         24578999999999999999999999999999


Q ss_pred             cccccccCC
Q 004002          257 RKLDIHFSI  265 (780)
Q Consensus       257 r~I~V~~a~  265 (780)
                      |.|.|.|+.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999875

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.79  E-value=7.8e-09  Score=95.33  Aligned_cols=76  Identities=14%  Similarity=0.209  Sum_probs=64.3

Q ss_pred             CCCcEEEEeCCCCCCC----------HHHHHHHhhcCCCEEEEEeC-CCcceEEEEEEecHHHHHHHHHHccCccccccc
Q 004002          190 HPSRTLFVRNINSNVE----------DSELRALFEQYGDIRTLYTA-CKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vt----------eeeLr~lF~~yG~I~sv~~t-gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~  258 (780)
                      .+++.|.++|+=..-+          +++|++.|++||.|.+|++. ...+|+|||+|.+.++|++|++.|||..+.||.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~   84 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM   84 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4678899999733221          35889999999999999853 335899999999999999999999999999999


Q ss_pred             cccccCC
Q 004002          259 LDIHFSI  265 (780)
Q Consensus       259 I~V~~a~  265 (780)
                      |.|.|+.
T Consensus        85 i~v~~~~   91 (114)
T 3s6e_A           85 ITAAYVP   91 (114)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEEc
Confidence            9999874

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.72  E-value=2.3e-08  Score=87.94  Aligned_cols=73  Identities=25%  Similarity=0.397  Sum_probs=62.1

Q ss_pred             CccceeecCCC----CCCCh----hHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          276 NQGTLVVFNLD----PSVSN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       276 ~~~~L~V~NLp----~~vte----edL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ...||+|.-.+    ..+-+    .+|.+.|++||+|..+|+..   +.+||+|.+.++|.+||+ |||.++.||.|+|.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            45688888776    23434    67999999999999999864   339999999999999998 99999999999999


Q ss_pred             ecCCC
Q 004002          348 PSRPG  352 (780)
Q Consensus       348 ~a~~k  352 (780)
                      ++.+.
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            99875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.64  E-value=1.2e-07  Score=88.28  Aligned_cols=86  Identities=19%  Similarity=0.147  Sum_probs=71.2

Q ss_pred             CccceeecCCCCC-CChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcC-HHHHHHHHHHhC--CCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYD-VRAAEAALKSLN--RSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~-~e~A~~Ai~~Ln--G~~i~Gr~L~V~~a~~  351 (780)
                      ....|+|+||+.+ +++++|+++|++||.|..|.+... ...|||+|.+ .++|++|+++||  |..|.|..++++...-
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g-~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~G   95 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   95 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecC-CCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCC
Confidence            4568999999999 999999999999999999998543 3479999999 899999999995  7799999999987764


Q ss_pred             CchhhhHhhhhc
Q 004002          352 GGARRNLMLQLN  363 (780)
Q Consensus       352 k~~r~~~l~ql~  363 (780)
                      .. -+.+++...
T Consensus        96 ee-E~~yw~Ki~  106 (121)
T 1owx_A           96 EV-EKEALKKII  106 (121)
T ss_dssp             HH-HHHHHHHHH
T ss_pred             HH-HHHHHHHHH
Confidence            33 344555543

>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=98.48  E-value=1.4e-07  Score=83.41  Aligned_cols=73  Identities=22%  Similarity=0.364  Sum_probs=61.6

Q ss_pred             CCccceeecCCCCC-----CCh----hHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          275 LNQGTLVVFNLDPS-----VSN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       275 ~~~~~L~V~NLp~~-----vte----edL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      ....||+|.-++.+     +-+    .+|.+.|+.||+|..+|+....   +||+|.+.++|.+||+ |||.++.||.|+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~   88 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            35679999988743     323    5689999999999999986433   9999999999999998 999999999999


Q ss_pred             EEecCC
Q 004002          346 LEPSRP  351 (780)
Q Consensus       346 V~~a~~  351 (780)
                      |.+..+
T Consensus        89 V~~k~~   94 (95)
T 1ufw_A           89 ISGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EeccCC
Confidence            998765

>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=98.42  E-value=5e-07  Score=79.80  Aligned_cols=66  Identities=18%  Similarity=0.235  Sum_probs=56.7

Q ss_pred             eeEEEecCCCCCCHHHHHHHHhhcCCCcceeEEe-eccccCC-cceeeEEeccCCccchHHHHHHhcCce
Q 004002          695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYL-PIDFKNK-CNVGYAFINMLSPLHIIPFYEVLFSCA  762 (780)
Q Consensus       695 tt~mirniPn~~~~~~l~~~i~~~~~~~ydf~yl-p~d~~~~-~n~gyafin~~~~~~~~~f~~~f~~~~  762 (780)
                      |.|+||++|..+|++.++++|....  ++||+|. |=+...+ +--+-|||||.+++++..|.+.|+|+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~--~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~   69 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMP--EHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV   69 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCC--CEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcc--cceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Confidence            7899999999999999999999764  6888875 6665544 334679999999999999999999996

>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=98.37  E-value=5.1e-07  Score=91.81  Aligned_cols=63  Identities=19%  Similarity=0.269  Sum_probs=56.8

Q ss_pred             CChhHHHHHhcccCCeeEEEe---------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          289 VSNEDLRQIFGAYGEVKEIRE---------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       289 vteedL~~~Fs~yG~I~~v~~---------~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      -.+++|++.|++||.|.++++         +++++|++||+|.+.++|++|++.|||+.++||.|.+.+...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            357899999999999999976         226789999999999999999999999999999999999863

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.35  E-value=1.2e-06  Score=81.51  Aligned_cols=72  Identities=15%  Similarity=0.159  Sum_probs=60.7

Q ss_pred             CCcEEEEeCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEec-HHHHHHHHHHcc--Ccccccccccccc
Q 004002          191 PSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD-IRAARTAMRALQ--NKPLRRRKLDIHF  263 (780)
Q Consensus       191 ~s~tLfVgNLp~~-vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~-~e~A~~Al~~Ln--g~~l~gr~I~V~~  263 (780)
                      +.+.|+|+||+.+ +++++|+++|++||+|..|... +..-.|||.|.+ .++|++|+++|+  +..|.+..+.++.
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~-~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            5689999999999 9999999999999999999832 223369999999 899999999994  6778887666653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.33  E-value=6.2e-07  Score=78.89  Aligned_cols=73  Identities=21%  Similarity=0.322  Sum_probs=60.8

Q ss_pred             CCcEEEEeCCC----CCCCH----HHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          191 PSRTLFVRNIN----SNVED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       191 ~s~tLfVgNLp----~~vte----eeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      +..||+|.-.+    .++-+    .+|.+.|.+||+|..++...   +.+||+|.+.++|.+|++ |+|..+.||.|+|+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            56788888776    23434    67899999999999998533   238999999999999999 99999999999999


Q ss_pred             cCCCC
Q 004002          263 FSIPK  267 (780)
Q Consensus       263 ~a~pk  267 (780)
                      ++.|.
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            88753

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=98.32  E-value=2.1e-07  Score=82.76  Aligned_cols=75  Identities=19%  Similarity=0.303  Sum_probs=59.8

Q ss_pred             eeEEEecCCCCCCHHHHHHHHhhcCCCcceeEE-eeccccCCcce-eeEEeccCCccchHHHHHHhcCceeEEEEeeCCC
Q 004002          695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLY-LPIDFKNKCNV-GYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNN  772 (780)
Q Consensus       695 tt~mirniPn~~~~~~l~~~i~~~~~~~ydf~y-lp~d~~~~~n~-gyafin~~~~~~~~~f~~~f~~~~~~~~~~~~~~  772 (780)
                      -.|+||++|+.+|++.+++.|+....  .||+| .|=|...+-++ ..|||||+++++|..|.+.|+|+.     |-|+.
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~--~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~-----F~D~k   82 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYI-----FLDSK   82 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSS--EEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEE-----EECTT
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCc--cceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcE-----EEeCC
Confidence            57999999999999999999997654  46665 56666554333 569999999999999999999997     66665


Q ss_pred             ceee
Q 004002          773 NYYY  776 (780)
Q Consensus       773 ~~~~  776 (780)
                      +..|
T Consensus        83 g~~~   86 (97)
T 2l08_A           83 GLEY   86 (97)
T ss_dssp             CCEE
T ss_pred             CCEe
Confidence            5444

>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=98.19  E-value=1.8e-06  Score=87.72  Aligned_cols=62  Identities=11%  Similarity=0.139  Sum_probs=56.2

Q ss_pred             CCHHHHHHHhhcCCCEEEEEe---------CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          204 VEDSELRALFEQYGDIRTLYT---------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       204 vteeeLr~lF~~yG~I~sv~~---------tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      -.+++|++.|++||+|.++++         +++++|++||+|.+.++|++|++.|+|+.+.||.|.+.|..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            457899999999999999873         23789999999999999999999999999999999999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.15  E-value=3.8e-06  Score=75.87  Aligned_cols=73  Identities=23%  Similarity=0.241  Sum_probs=66.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhccc-----CCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAY-----GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~y-----G~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ..++|-+-|||..+++..|+.+.++|     |.|+.|.+.+... -|+|+|.|...|.+|.-+|+|.+|.|++|+|.-.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~-GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN-GAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT-EEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC-ceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            35689999999999999999999999     9999998866654 4999999999999999999999999999999643

>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=98.00  E-value=4.1e-06  Score=74.09  Aligned_cols=71  Identities=15%  Similarity=0.211  Sum_probs=58.7

Q ss_pred             CCcEEEEeCCCCC-----CCH----HHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          191 PSRTLFVRNINSN-----VED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       191 ~s~tLfVgNLp~~-----vte----eeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      +..||+|.-++.+     +-+    .+|.+.|.+||+|..++.....   +||+|.+.++|.+||+ |+|..+.||.|+|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V   89 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKGRAVKI   89 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETTEEEEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCCeEEEE
Confidence            6789999988743     322    5688999999999988842221   9999999999999999 9999999999999


Q ss_pred             ccCC
Q 004002          262 HFSI  265 (780)
Q Consensus       262 ~~a~  265 (780)
                      ++..
T Consensus        90 ~~k~   93 (95)
T 1ufw_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            8643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.55  E-value=0.00011  Score=66.51  Aligned_cols=71  Identities=13%  Similarity=0.184  Sum_probs=63.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcC-----CCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~y-----G~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      ..++|-+-|||.+|++..|+.+.+++     |+|..+.....+. =|+|+|.+...|-+|.-+|+|..|.|++|+|.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~-GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN-GAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT-EEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC-ceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            46899999999999999999999999     9999988545444 49999999999999999999999999999885

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.55  E-value=0.0005  Score=61.60  Aligned_cols=88  Identities=18%  Similarity=0.244  Sum_probs=72.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhc-----CCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQ-----YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~-----yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|.|.|||+++.++.|.-+|+.     =|+|..+...+   +-|+|+|.+.+.|++.++. ....|.+.+|.|....
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAP   82 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCC
Confidence            4589999999999999999999986     26888887544   7799999999999999983 4778889888886544


Q ss_pred             CCCCCCCCCCCccceeecCCCCCCC
Q 004002          266 PKDNPSDKDLNQGTLVVFNLDPSVS  290 (780)
Q Consensus       266 pk~~~s~~~~~~~~L~V~NLp~~vt  290 (780)
                      +.        ....|++.||++.++
T Consensus        83 ~~--------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           83 PR--------APARLLLQGLPPGTS   99 (104)
T ss_dssp             CC--------CCCCCCCCSCCCCCC
T ss_pred             CC--------CcceEeeecCCCCCC
Confidence            43        245799999998875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.30  E-value=0.00057  Score=61.26  Aligned_cols=83  Identities=24%  Similarity=0.317  Sum_probs=71.2

Q ss_pred             ccceeecCCCCCCChhHHHHHhcc-----cCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGA-----YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~-----yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ..+|.|.|||.+++++.|+-.|+.     =|+|..+...+   +-|+|+|.+.+.|++.|+. ..+.+.+..|.|....+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            468999999999999999999986     27899998766   6699999999999999973 36789999999999988


Q ss_pred             CchhhhHhhhhc
Q 004002          352 GGARRNLMLQLN  363 (780)
Q Consensus       352 k~~r~~~l~ql~  363 (780)
                      +..++.+++.+.
T Consensus        84 ~~~~r~ll~gl~   95 (104)
T 2dhx_A           84 RAPARLLLQGLP   95 (104)
T ss_dssp             CCCCCCCCCSCC
T ss_pred             CCcceEeeecCC
Confidence            888887776654

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.97  E-value=0.00056  Score=61.48  Aligned_cols=75  Identities=19%  Similarity=0.237  Sum_probs=62.1

Q ss_pred             cceeecCCCCCC-Ch----hHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          278 GTLVVFNLDPSV-SN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       278 ~~L~V~NLp~~v-te----edL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      .+|+|.||+.++ +.    +.++++|..|+++.....-+.-| -..|.|.+.++|.+|...|++..+.|++|+|-++++.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-EEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            579999998876 32    56789999999988865433322 3799999999999999999999999999999999854


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        85 ~   85 (104)
T 1wey_A           85 H   85 (104)
T ss_dssp             S
T ss_pred             C
Confidence            3

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.51  E-value=0.0033  Score=56.53  Aligned_cols=77  Identities=19%  Similarity=0.216  Sum_probs=62.6

Q ss_pred             CCcEEEEeCCCCCC-C----HHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNV-E----DSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~v-t----eeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      -.++|+|.||+.+| +    .++++++|..|+++.+...- ++-.=..|.|.+.++|.+|...|++..+.|++++|.|+.
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~l-kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeec-CcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            34789999998876 3    25778999999998876532 232346899999999999999999999999999999988


Q ss_pred             CCC
Q 004002          266 PKD  268 (780)
Q Consensus       266 pk~  268 (780)
                      +..
T Consensus        83 ~~~   85 (104)
T 1wey_A           83 TLH   85 (104)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>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=96.44  E-value=0.0073  Score=55.63  Aligned_cols=76  Identities=16%  Similarity=0.193  Sum_probs=62.1

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC-ceEEEEecCCC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-KRIKLEPSRPG  352 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G-r~L~V~~a~~k  352 (780)
                      .....-|.|.+.|... -..+.+.|++||+|.+... .....+-.|+|.++.+|++||. .||..+.| -.|-|.+...+
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~d~   97 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   97 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECCCH
Confidence            3456789999999885 5667788999999999887 3456899999999999999998 59999985 66777776544

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=95.67  E-value=0.027  Score=49.52  Aligned_cols=65  Identities=5%  Similarity=0.051  Sum_probs=53.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-eCCC------cceEEEEEEecHHHHHHHHHHccCcccccc
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK------HRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-~tgk------skG~aFV~F~~~e~A~~Al~~Lng~~l~gr  257 (780)
                      ++|.||+||+.+||+++.+.++.+.++.-.+ ..|+      .-.-|+|.|.+.+++..-.+.++|..+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            5799999999999999999999988776544 2222      234699999999999999999999988643

>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=95.62  E-value=0.021  Score=50.66  Aligned_cols=54  Identities=19%  Similarity=0.303  Sum_probs=44.5

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~Ln  335 (780)
                      ..++| ++|+.+...||.++|++||.|.--.++   ...|||.|.+++.|..|+..++
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999966444443   3469999999999999999763

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=94.94  E-value=0.018  Score=51.20  Aligned_cols=54  Identities=19%  Similarity=0.300  Sum_probs=44.3

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~Ln  335 (780)
                      ..++| ++|+.+...||.++|++||.|.--.+.   ...|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEE---TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            35666 999999999999999999955433343   3469999999999999999875

>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=93.58  E-value=0.16  Score=46.70  Aligned_cols=71  Identities=17%  Similarity=0.192  Sum_probs=56.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccc-cccccccC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR-RKLDIHFS  264 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g-r~I~V~~a  264 (780)
                      ..+-|.|=+.|+.. ...+...|++||+|.+... .....+-.|.|.+..+|++||.+ ||..|.+ ..|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEEC
Confidence            35788898999885 6677889999999998875 33557899999999999999994 9999874 45555543

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=92.92  E-value=0.078  Score=49.53  Aligned_cols=73  Identities=18%  Similarity=0.246  Sum_probs=56.3

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEE-EeC----------------C--CcccEEEEEEcCHHHHHHHHHHhCCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RET----------------P--HKRHHKFIEFYDVRAAEAALKSLNRS  337 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v-~~~----------------g--~srG~aFV~F~~~e~A~~Ai~~LnG~  337 (780)
                      ..-|.|.+.|.+.+ ..+.+.|++||.|.+- ...                +  ...++.-|+|++..+|.+||. -||+
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            34688899987765 4566789999999772 111                1  135688999999999999998 5999


Q ss_pred             ccCCceEEEEecCC
Q 004002          338 DIAGKRIKLEPSRP  351 (780)
Q Consensus       338 ~i~Gr~L~V~~a~~  351 (780)
                      .|.|.-|=|.+..+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999888888853

>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=92.53  E-value=0.19  Score=44.59  Aligned_cols=55  Identities=18%  Similarity=0.315  Sum_probs=43.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHcc
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ  250 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Ln  250 (780)
                      .+.++| +.|+++...||..+|+.||.|.---+   .-..|||.|.+++.|..|++.+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            356777 99999999999999999996532112   12469999999999999999764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.14  E-value=0.16  Score=45.03  Aligned_cols=67  Identities=7%  Similarity=0.034  Sum_probs=50.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-eCCC------cceEEEEEEecHHHHHHHHHHccCcccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK------HRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-~tgk------skG~aFV~F~~~e~A~~Al~~Lng~~l~gr  257 (780)
                      .+-+|.||.||+.+||+++.+.++..=++...+ ..|+      .-.-|||.|.+.++...-.+..+|..+.+.
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            457899999999999999888887665543222 1111      123589999999999999999999888543

>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=91.57  E-value=0.17  Score=45.03  Aligned_cols=53  Identities=19%  Similarity=0.324  Sum_probs=43.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-eCCCcceEEEEEEecHHHHHHHHHHcc
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQ  250 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-~tgkskG~aFV~F~~~e~A~~Al~~Ln  250 (780)
                      +.++| +.|+++...||..+|+.||.|. |+ +.   -..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~-I~Wid---DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWID---DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEE-EEEEE---TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEE-EEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            45666 9999999999999999999554 32 22   2469999999999999999764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.55  E-value=0.076  Score=59.77  Aligned_cols=56  Identities=11%  Similarity=0.156  Sum_probs=43.4

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHH
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  333 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~  333 (780)
                      .+.|+|. .+..+++.+|.+.|++||.|..+........|+.|+|.+.+++.+++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            4689997 7999999999999999999999987766667999999999999977653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=90.14  E-value=0.11  Score=58.34  Aligned_cols=57  Identities=9%  Similarity=0.271  Sum_probs=42.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHH
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA  248 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~  248 (780)
                      ..|.|+|. .|..+++.+|.++|++||+|.++.......-||.|+|.+.+++..++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            34899997 7999999999999999999999874444446999999999999977663

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=88.13  E-value=0.23  Score=46.42  Aligned_cols=71  Identities=14%  Similarity=0.196  Sum_probs=52.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-eC-------------C-----CcceEEEEEEecHHHHHHHHHHccCc
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TA-------------C-----KHRGFVMISYYDIRAARTAMRALQNK  252 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-~t-------------g-----kskG~aFV~F~~~e~A~~Al~~Lng~  252 (780)
                      ..-|.|=+.|++.+ ..+.+.|++||.|.+-. ..             .     ....+..|+|.+..+|++||.. ||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCe
Confidence            45677777866655 45668899999997622 00             0     1356789999999999999995 999


Q ss_pred             cccccccccccC
Q 004002          253 PLRRRKLDIHFS  264 (780)
Q Consensus       253 ~l~gr~I~V~~a  264 (780)
                      .|.|..|-|...
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            999887777654

---

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	780
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-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	7e-16
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-15
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-14
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-14
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-13
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-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	8e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	6e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-10
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	9e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	5e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 9e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	8e-07
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	8e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.001
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	3e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	8e-04
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	7e-04

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.6 bits (213), Expect = 4e-20
 Identities = 34/171 (19%), Positives = 59/171 (34%), Gaps = 12/171 (7%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAM 246
            R LF+  ++    D  LR+ FEQ+G +            + RGF  ++Y  +     AM
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 247 RALQNKPLRRRKLDIHFSI-PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
            A  +K   R                   L    + V  +        LR  F  YG+++
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125

Query: 306 EI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            I     R +  KR   F+ F D  + +  +       + G   ++  +  
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS 175

>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 = 23/111 (20%), Positives = 55/111 (49%), Gaps = 8/111 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
            L + NL   ++ E++  IFG YG +++I    TP  R   ++ + D+  A+ A   L+ 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 337 SDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPP 387
            ++  + + +       A +    +++ + ++++ ++L+ + G  I   PP
Sbjct: 69  FNVCNRYLVVLYYNANRAFQ----KMDTKKKEEQLKLLKEKYG--INTDPP 113

>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 = 72.0 bits (176), Expect = 7e-16
 Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--HRGFVMISYYDIRAARTAMRA 248
            +R L++RN+   +   E+  +F +YG IR +        RG   + Y DI  A+ A   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
           L    +  R L + +          D  +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKK 94

>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 = 69.6 bits (170), Expect = 2e-15
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V +L P V+   L + F   G +  IR      T     + ++ F     AE AL +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 334 LNRSDIAGKRIKLEPSR 350
           +N   I GK +++  S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.3 bits (146), Expect = 4e-12
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRA 248
           +L+V +++ +V ++ L   F   G I            +  G+  +++     A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 249 LQNKPLRRRKLDIHFS 264
           +    ++ + + I +S
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>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 = 70.0 bits (171), Expect = 2e-15
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL V NL    + E + ++F   G++K+I     K         F+E+Y    AE A++ 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           +N + +  + I+ +        R
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEGR 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 = 63.8 bits (155), Expect = 3e-13
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTA 245
            S TL+V N++    + ++  LF + GDI+ +            GF  + YY    A  A
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
           MR +    L  R +   +    
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGF 87

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 68.5 bits (167), Expect = 5e-15
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
            L+V  L   +++ +L  +F A G +   R     +T +   + F++F     ++ A+K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 334 LNRSDIAGKRIKLEPSRPG 352
           LN   +  KR+K+  +RPG
Sbjct: 64  LNGITVRNKRLKVSYARPG 82

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.3 bits (138), Expect = 5e-11
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTAM 246
           +  L V  +  ++ D EL ALF   G I T      ++      +  + +     ++ A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 247 RALQNKPLRRRKLDIHFSIP 266
           + L    +R ++L + ++ P
Sbjct: 62  KVLNGITVRNKRLKVSYARP 81

>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 = 68.5 bits (167), Expect = 7e-15
 Identities = 20/87 (22%), Positives = 41/87 (47%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA 329
            S K     TL+  NL  +++ ++L+++F    E++ + +    +   +IEF     AE 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARR 356
            L+    ++I G+ + L  +   G  R
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGEKGGTR 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 = 64.7 bits (157), Expect = 2e-13
 Identities = 18/81 (22%), Positives = 37/81 (45%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            +RTL  +N++ N+ + EL+ +FE   +IR +    K +G   I +     A   +   Q
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
              +  R + ++++  K    
Sbjct: 75  GAEIDGRSVSLYYTGEKGGTR 95

>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 = 68.0 bits (166), Expect = 7e-15
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKS 333
           G L+V NLD  VS+ D++++F  +G +K+       +        + F     A  A+K 
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 334 LNRSDIAGKRIKLE 347
            N   + G+ + ++
Sbjct: 61  YNGVPLDGRPMNIQ 74

>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 = 53.8 bits (129), Expect = 7e-10
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRT----LYTACKHRGFVMISYYDIRAARTAMRALQ 250
           L V N++  V D++++ LF ++G ++        + +  G   + +     A  AM+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 251 NKPLRRRKLDIHFS 264
             PL  R ++I   
Sbjct: 63  GVPLDGRPMNIQLV 76

>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 = 68.1 bits (166), Expect = 1e-14
 Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 9/97 (9%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIE 320
           P DN S ++ +  T+    L   +   DL   F A G+V+++R      +   +   ++E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           F ++++   A+  L    + G  I ++ S+     +N
Sbjct: 67  FCEIQSVPLAIG-LTGQRLLGVPIIVQASQA---EKN 99

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 4e-10
 Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAAR 243
           E  +RT+F   + + +   +L   F   G +R +         + +G   + + +I++  
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDN 269
                L  + L    + +  S  + N
Sbjct: 75  -LAIGLTGQRLLGVPIIVQASQAEKN 99

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.7 bits (165), Expect = 1e-14
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDV 324
           P  +     T+ V  LD  VS   L ++F   G V          T   + + F+EF   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
             A+ A+K ++   + GK I++  +      +NL
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAH--NKNL 93

>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 = 58.9 bits (142), Expect = 2e-11
 Identities = 13/84 (15%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 245
              T++V  ++  V +  L  LF Q G      +       +H+G+  + +     A  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           ++ +    L  + + ++ +   + 
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 67.4 bits (164), Expect = 2e-14
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG---EVKEIRETPHKRHHKFIEFYDVRA 326
           PS +    G + + NLD S+ N+ L   F A+G     K + +    + + F+ F    A
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 327 AEAALKSLNRSDIAGKRIKLEPSRP 351
           AE A++ +N   +  +++ +   + 
Sbjct: 61  AERAIEKMNGMLLNDRKVFVGRFKS 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 9e-11
 Identities = 12/79 (15%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
              +F++N++ ++++  L   F  +G     + +      +G+  + +    AA  A+  
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 249 LQNKPLRRRKLDIHFSIPK 267
           +    L  RK+ +     +
Sbjct: 68  MNGMLLNDRKVFVGRFKSR 86

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 3e-14
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDV 324
           P+ +  +  T+ V NL       DL+++F  +G +        + T   +   FI F+  
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRP 351
             A  A+  ++        + +E ++P
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKP 87

>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 = 58.9 bits (142), Expect = 2e-11
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTA 245
            + T+ V N++ +  +++L+ LF  +G I  +Y A      + +GF  IS++    A  A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +  +         L++ ++ P  N
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPSTN 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 = 66.2 bits (161), Expect = 4e-14
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK---RHHKFIEFYDVRAAE 328
           + D    TL V NL   V+   + Q+F   G  K  +          + F+EFY+ R A 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARR 356
           AAL ++N   I GK +K+  +    +++
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQK 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 = 59.7 bits (144), Expect = 8e-12
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY---DIRAARTA 245
           +   RTL+V N++ +V +  +  LF Q G  ++     +H       +    + R A  A
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 64

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           + A+  + +  +++ ++++    +
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSS 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 = 65.8 bits (160), Expect = 6e-14
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  L   V ++ L   F  +G++ +I      ET   R   F+EF     A AA+ +
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 334 LNRSDIAGKRIKLEPSRP 351
           +N S++ G+ I++  ++P
Sbjct: 67  MNESELFGRTIRVNLAKP 84

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
             R L+V  +   V+D  L A F  +GDI  +         KHRGF  + +     A  A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
           +  +    L  R + ++ + P 
Sbjct: 64  IDNMNESELFGRTIRVNLAKPM 85

>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 = 65.8 bits (160), Expect = 6e-14
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 327
           D  +       T+    +   ++++ +RQ F  +G++ EIR    ++ + F+ F    +A
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESA 67

Query: 328 EAALKSLNRSDIAGKRIKLEPSRP 351
             A+ S+N + I G  +K    + 
Sbjct: 68  AHAIVSVNGTTIEGHVVKCYWGKE 91

>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 = 58.8 bits (142), Expect = 2e-11
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            + T++   I S + D  +R  F  +G I  +      +G+  + +    +A  A+ ++ 
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVN 75

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
              +    +  ++     + +
Sbjct: 76  GTTIEGHVVKCYWGKESPDMT 96

>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 = 65.4 bits (159), Expect = 7e-14
 Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAARTAM 246
           LF++N+N +  +  L+ +F + G I        +         GF  + Y     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 247 RALQNKPLRRRKLDIHFSIPKDNPS 271
           + LQ   +   KL++  S     P+
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKPA 85

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV--------KEIRETPHKRHHKFIEFYDVRAAEAAL 331
           L + NL+ S + E L+ +F   G +        K            F+E+     A+ AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 332 KSLNRSDIAGKRIKLEPSRPG 352
           K L    + G ++++  S   
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 1e-13
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG-------DIRTLYTACKHRGFVMISYYDIRAARTAM 246
            LF+  I    +  E+     +            +     K+RGF  + Y   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 247 RALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQ 277
           R L    ++    ++ + ++ P+ +  +  +  
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 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 = 55.5 bits (133), Expect = 3e-10
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 9/82 (10%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE-------IRETPHKRHHKFIEFYDVRAAEAAL 331
            L +  +      E++ +      E            +    R   F+E+   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 332 KSLNRSDI--AGKRIKLEPSRP 351
           + L    I   G +I ++ + P
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEP 84

>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 = 64.9 bits (158), Expect = 1e-13
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 269 NPSDKDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 327
             +D       + + NL+   V   D+  IF  YG++         +   F+++ + R A
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNA 63

Query: 328 EAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            AA+   +   IAG+ + +  +      R+
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.1 bits (143), Expect = 1e-11
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 191 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
            +  +F+ N+N+  V+ S++ A+F +YG I        H+GF  + Y + R AR A+   
Sbjct: 14  MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVG---CSVHKGFAFVQYVNERNARAAVAGE 70

Query: 250 QNKPLRRRKLDIHFSIPKDNP 270
             + +  + LDI+ +      
Sbjct: 71  DGRMIAGQVLDINLAAEPKVN 91

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 13/79 (16%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL 334
           L +  L   ++++ ++++  ++G +K         T   + + F E+ D+   + A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 335 NRSDIAGKRIKLEPSRPGG 353
           N   +  K++ ++ +  G 
Sbjct: 64  NGMQLGDKKLLVQRASVGA 82

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 2e-10
 Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAM 246
           +  LF+  + + + D +++ L   +G ++             +G+    Y DI     A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 247 RALQNKPLRRRKLDIHFSIPKDNPS 271
             L    L  +KL +  +      +
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGAKNA 85

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.2 bits (156), Expect = 3e-13
 Identities = 21/94 (22%), Positives = 45/94 (47%), Gaps = 13/94 (13%)

Query: 265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE------VKEIRETPHKRHHKF 318
           +PK   + K      ++V N+    +  ++R++F  +GE       K++  T   R   F
Sbjct: 2   VPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 55

Query: 319 IEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP 351
           ++F   + A+ A  +L + + + G+R+ LE +  
Sbjct: 56  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.7 bits (147), Expect = 4e-12
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC------KHRGFVMISYYDIRAA 242
           +  +  + VRNI       E+R LF  +G+++T+           HRGF  + +   + A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 243 RTAMRALQN-KPLRRRKLDIHFSIPKD 268
           + A  AL +   L  R+L + ++  + 
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 63.2 bits (153), Expect = 4e-13
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
            L+V  L  +++ E+ R +FG+ GE++  +      T     + F+ + D + AE A+ +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN   +  K IK+  +RP
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>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 = 53.6 bits (128), Expect = 1e-09
 Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 192 SRT-LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTA 245
           S+T L V  +  N+   E R+LF   G+I +             G+  ++Y D + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 246 MRALQNKPLRRRKLDIHFSIP 266
           +  L    L+ + + + ++ P
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 1/80 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
            + L+VRN+  +  +  +   F             K R +  + + +   A  AM+AL  
Sbjct: 8   VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 252 KPLRRRKLDIHFSIPKDNPS 271
           K L    +++  + P D  S
Sbjct: 67  KVLDGSPIEVTLAKPVDKDS 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 = 59.3 bits (143), Expect = 1e-11
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL  S S E + + F         R     R + F+ F +   A  A+K+LN   
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 339 IAGKRIKLEPSRP 351
           + G  I++  ++P
Sbjct: 69  LDGSPIEVTLAKP 81

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 334 LNRSDIAGKRIK 345
            N  ++ G+RI+
Sbjct: 71  ANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 3e-10
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTA 245
           P+  L V  ++    + +LR +F +YG I  +      +      F  + + ++  A+ A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 246 MRALQNKPLRRRKLDI 261
                   L  R++ +
Sbjct: 68  KERANGMELDGRRIRV 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 20/89 (22%), Positives = 46/89 (51%), Gaps = 6/89 (6%)

Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F ++G I    +  + K RG   + + ++ +A  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           A+R++Q  P   + + I ++    +   K
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90

>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 = 58.1 bits (140), Expect = 3e-11
 Identities = 16/79 (20%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKE--IRETPHKRHHKFIEFYDVRAAEAALK 332
           T+ + NL+  +  ++L++    IF  +G++ +  +  +   R   F+ F +V +A  AL+
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 333 SLNRSDIAGKRIKLEPSRP 351
           S+       K ++++ ++ 
Sbjct: 65  SMQGFPFYDKPMRIQYAKT 83

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.5 bits (149), Expect = 1e-12
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK-----EIRETPHKRHHKFIEFYDVRAAEAALKS 333
            L V NL  +++++ L  IFG YG +        + T   R   F+ +     A+ A+ +
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 334 LNRSDIAGKRIKLE 347
           LN     G    L 
Sbjct: 68  LNNVIPEGGSQPLS 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 56.5 bits (136), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAM 246
              L+V N+   + D +L  +F +YG I            + RG   + Y     A+ A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 247 RALQNKPL--RRRKLDIHF 263
            AL N       + L +  
Sbjct: 66  SALNNVIPEGGSQPLSVRL 84

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.5 bits (149), Expect = 2e-12
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL P ++ E++R++F  YG+  E+      +   FI       AE A   L+   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELDNMP 68

Query: 339 IAGKRIKLEPSRPGGA 354
           + GK++++  +    +
Sbjct: 69  LRGKQLRVRFACHSAS 84

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.6 bits (144), Expect = 8e-12
 Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           GE  + +     LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A
Sbjct: 1   GEKTFTQR--SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLA 57

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
             A   L N PLR ++L + F+    + +
Sbjct: 58  EIAKVELDNMPLRGKQLRVRFACHSASLT 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 = 61.6 bits (149), Expect = 2e-12
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAA 327
           S+       L V N+     + DLRQ+FG +G++ +   I      +   F+ F +   A
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 328 EAALKSLNRSDIAGKRIKLEPSRP 351
           + A + L+ + + G++I++  +  
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNATA 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 8e-11
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---HRGFVMISYYDIRAARTAMR 247
             + L V NI     D +LR +F Q+G I  +         +GF  +++ +   A  A  
Sbjct: 10  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 69

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
            L    +  RK++++ +  +   +
Sbjct: 70  KLHGTVVEGRKIEVNNATARVMTN 93

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-----KEIRETPHKRHHKF 318
           ++P +    +      L +  L    + E LR  +  +G++          +   R   F
Sbjct: 7   TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           + F  +   +AA+       I G+ ++ + +  
Sbjct: 67  VTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA 98

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 1e-10
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTA 245
             R LF+  ++    +  LR  +EQ+G +              RGF  +++  +     A
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 246 MRALQNKPLRRRKLDIHFSIPKD 268
           M A +   +  R ++   ++ ++
Sbjct: 79  M-AARPHSIDGRVVEPKRAVARE 100

>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 = 60.8 bits (147), Expect = 3e-12
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            + V      ++ ++LR+ F  YG+V ++      R   F+ F D + A++         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLI 64

Query: 339 IAGKRIKLEPSRPGGARRN 357
           I G  + +  + P     +
Sbjct: 65  IKGISVHISNAEPKHNSNS 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 = 58.1 bits (140), Expect = 3e-11
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  +FV     ++ + ELR  F QYGD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 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 = 60.1 bits (145), Expect = 5e-12
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 248
           +F+ N++  +++  L   F  +G I               +G+  I++    A+  A+ A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 249 LQNKPLRRRKLDIHFSIPKDN 269
           +  + L  R + + ++  KD+
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 = 59.8 bits (144), Expect = 7e-12
 Identities = 17/82 (20%), Positives = 40/82 (48%), Gaps = 6/82 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALKS 333
           + + NLDP +  + L   F A+G + +        +T + + + FI F    A++AA+++
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
           +N   +  + I +  +    ++
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 60.2 bits (145), Expect = 5e-12
 Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL + N  PS +  ++R +      V      P  R +      +I+      A   ++ 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN   I G  +  + S P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.8 bits (131), Expect = 3e-10
 Identities = 14/79 (17%), Positives = 22/79 (27%), Gaps = 5/79 (6%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMR 247
            TL++ N   +     +R L +    +              R F  I       AR  + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 248 ALQNKPLRRRKLDIHFSIP 266
            L    +    L    S P
Sbjct: 62  KLNGLKIEGYTLVTKVSNP 80

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 60.1 bits (145), Expect = 6e-12
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK-----EIRETPHKRHHKFIEFYDVRAAEAALKS 333
            L V ++      +++++ F  YGE+K       R T   + +  +E+   + A AA ++
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 334 LNRSDIAGKRIKLEPSRPGG 353
           LN ++I G+ I+++     G
Sbjct: 69  LNGAEIMGQTIQVDWCFVKG 88

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 56.7 bits (136), Expect = 1e-10
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTA 245
               LFV +I+   ++ E++  F  YG+I+ ++          +G+ ++ Y   + A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
             AL    +  + + + +   K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.2 bits (145), Expect = 7e-12
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 13/93 (13%)

Query: 272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKF 318
           D+D +   + V  L+ SV+ +DL   F   G VK               +ET   +    
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           + + D   A+AA++  +  D  G ++K+  +R 
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 52.5 bits (125), Expect = 3e-09
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 13/95 (13%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-------------CKHRGFV 232
           P  +  +  ++V+ +N +V   +L   F+Q G ++                   K +G  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
            +SY D   A+ A+     K  +  KL +  +  K
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 59.7 bits (144), Expect = 8e-12
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKS 333
           N   + V NL P +  +D+  +F  YG +++I  +         F+EF D R AE A+  
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
            +  D  G R+++E  R G   
Sbjct: 73  RDGYDYDGYRLRVEFPRSGRGT 94

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 2e-10
 Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 5/94 (5%)

Query: 176 NGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--CKHRGFVM 233
           +G G + G  P G      ++V N+  ++   ++  +F +YG IR +          F  
Sbjct: 1   SGGGVIRG--PAGN-NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAF 57

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           + + D R A  A+           +L + F    
Sbjct: 58  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 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 = 60.0 bits (145), Expect = 1e-11
 Identities = 20/102 (19%), Positives = 42/102 (41%), Gaps = 9/102 (8%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAM 246
           G+ P   + V N+   V    L  +F ++G + + +     ++   ++ Y D  +A+ A 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 62

Query: 247 RALQNKPL--RRRKLDIHFS------IPKDNPSDKDLNQGTL 280
            +L  + +      L I FS      +  +N   +D  +  L
Sbjct: 63  LSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDL 104

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 6e-11
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 11/96 (11%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVRAAEAALKSLNRSD 338
           ++V NL   V+ + L QIF  +G V +I       +    +++ D  +A+ A  SL+  +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 339 I--AGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           I  A   ++++ S+           LN +   D+SR
Sbjct: 70  IYNACCTLRIDFSKLT--------SLNVKYNNDKSR 97

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH-----HKFIEFYDVRAAEAALKSL 334
           + +  L    + E LR+ FG +GEVKE                F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 335 NRSDIAGKRIK 345
           +R ++  K I 
Sbjct: 62  SRHELDSKTID 72

>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 = 49.2 bits (117), Expect = 3e-08
 Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMRAL 249
           +F+  ++       LR  F Q+G+++             RGF  +++ D       + A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 250 QNKPLRRRKLDI 261
               L  + +D 
Sbjct: 62  SRHELDSKTIDP 73

>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 = 58.4 bits (141), Expect = 2e-11
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L+V  L    + +DL++ F  +GEV  +      +T H +   F+ F +       +  
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
            +   I G+    +      ++
Sbjct: 70  RH--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 = 54.2 bits (130), Expect = 7e-10
 Identities = 11/88 (12%), Positives = 26/88 (29%), Gaps = 7/88 (7%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAA 242
               +  L V  +     + +L+  F  +G++  +           +GF  + + +    
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNP 270
              M       +  R  D      K + 
Sbjct: 64  VKVMSQRHM--IDGRWCDCKLPNSKQSQ 89

>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 = 58.6 bits (141), Expect = 3e-11
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALK 332
           G L V NL  + S EDL ++F AYG + E+               F+ F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            ++     G+ + + PS        
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 = 53.2 bits (127), Expect = 2e-09
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAA 242
           G   S  LFVRN++    + +L  LF  YG +  L+          +GF  +++     A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
             A   +  +  + R L +  S  K   S
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 57.0 bits (137), Expect = 5e-11
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           + V  L  + + ED++  F  +G+V +        T   R   F+ F      E   + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 335 NRSDIAGKRIK 345
           +  +I  K ++
Sbjct: 61  HFHEINNKMVE 71

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.2 bits (101), Expect = 4e-06
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRAL 249
           +FV  ++ N    +++  FEQ+G +         T  +HRGF  +++            +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 250 QNKPLRRRKLDI 261
               +  + ++ 
Sbjct: 61  HFHEINNKMVEC 72

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 6e-11
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALKS 333
            L V  L  +++ ++L Q+F  YG +   R    +         FI F     AE A+K 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 334 LNRSDIAGKRIKLE 347
           LN    +G    + 
Sbjct: 68  LNGQKPSGATEPIT 81

>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 = 53.9 bits (129), Expect = 7e-10
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 7/79 (8%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 247
             L+V  +   +   EL  LF QYG I T            RG   I +     A  A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 248 ALQNKPL--RRRKLDIHFS 264
            L  +        + + F+
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK- 252
            L++ N++  V   +LR LF                G+  + Y D   A  A+  L  K 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 253 PLRRRKLDIHFSIPKDNPS 271
            L  + +++ +S+ K   S
Sbjct: 62  ELHGKIMEVDYSVSKKLRS 80

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN-RS 337
            L + NL P+V+ +DLRQ+FG        +    K  + F+++ D   A  A+++L+ + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ-VLLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 338 DIAGKRIKLEPSRPGGAR 355
           ++ GK ++++ S     R
Sbjct: 62  ELHGKIMEVDYSVSKKLR 79

>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 = 57.0 bits (137), Expect = 1e-10
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
            L +++L     ++DL Q+F  +G V   +    K+ +      F+ + +  +A+AA++S
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           +N   I  KR+K++  R     +
Sbjct: 80  MNGFQIGMKRLKVQLKRSKNDSK 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 = 52.0 bits (124), Expect = 5e-09
 Identities = 16/93 (17%), Positives = 40/93 (43%), Gaps = 6/93 (6%)

Query: 182 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 236
           AG    G      LF+ ++     D +L  +F  +G++ +            + F  +SY
Sbjct: 9   AGSQKEGP-EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
            +  +A+ A++++    +  ++L +     K++
Sbjct: 68  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 56.3 bits (135), Expect = 2e-10
 Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 6/103 (5%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIR 240
           P  +   R++FV NI     + +L+ +F + G +            K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSD-KDLNQGTLVV 282
            A +AMR L  +    R L +  +  + N  + K L  G  V+
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 1e-09
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYD 323
           +P+  D +  ++ V N+    + E L+ IF   G V   R    +         F E+ D
Sbjct: 1   DPA-VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
              A +A+++LN  + +G+ ++++ +     +  L
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEEL 94

>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 = 3e-10
 Identities = 28/128 (21%), Positives = 54/128 (42%), Gaps = 13/128 (10%)

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 292
           ++S YD       ++ LQ +  +         IP    + +      L+V  +  +V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 293 DLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            LRQ+F  YG ++ ++    +         F++F    +A+ A+  LN  +I  KR+K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 348 PSRPGGAR 355
            +  G  R
Sbjct: 118 LAASGHQR 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 = 49.1 bits (116), Expect = 1e-07
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTA 245
             R L V  I + V++ +LR LFE+YG I ++   C         +  + +    +A+ A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 246 MRALQNKPLRRRKLDIHFSIPKD 268
           +  L    +  ++L +  +    
Sbjct: 101 IAGLNGFNILNKRLKVALAASGH 123

>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 = 55.2 bits (132), Expect = 6e-10
 Identities = 28/104 (26%), Positives = 52/104 (50%), Gaps = 1/104 (0%)

Query: 279 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
            L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  LN  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 63

Query: 338 DIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 381
            + GK I++  S+    +     Q +Q L +D      H+   P
Sbjct: 64  KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 107

>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 = 47.1 bits (111), Expect = 3e-07
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 192 SRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           +  L V N+N   V    L  LF  YGD++ +      +   ++   D   A+ AM  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
              L  + + I  S  ++    ++  +  
Sbjct: 62  GHKLHGKPIRITLSKHQNVQLPREGQEDQ 90

>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 = 53.8 bits (129), Expect = 6e-10
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           + +  L    + +DL+  F  +GEV +        T   R   F+ F +  + +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 335 NRSDIAGKRIK 345
               + GK I 
Sbjct: 61  KEHKLNGKVID 71

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 10/72 (13%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRAL 249
           +F+  ++ +    +L+  F ++G++            + RGF  + + +  +    M   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 250 QNKPLRRRKLDI 261
           +   L  + +D 
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 54.3 bits (130), Expect = 7e-10
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           P+  L+V  +  N   + L   F+++G IRT+    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMR 74

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
             PL      +     K  PS
Sbjct: 75  GFPLGGPDRRLRVDFAKSGPS 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 = 46.2 bits (109), Expect = 5e-07
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V  L P+ S   L + F  +G ++ I          +I++  + AA+AA   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 339 IAG--KRIKLEPSRPG 352
           + G  +R++++ ++ G
Sbjct: 78  LGGPDRRLRVDFAKSG 93

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 8e-10
 Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 5/87 (5%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAA 330
           ++G L V  L    + + L Q+F  YG++ E+       T   R   F+ F ++  A+ A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 331 LKSLNRSDIAGKRIKLEPSRPGGARRN 357
           + ++N   + G++I+++ +      R+
Sbjct: 64  MMAMNGKSVDGRQIRVDQAGKSSDNRS 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 = 48.6 bits (115), Expect = 6e-08
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIRAARTAM 246
              LFV  ++ +  +  L  +F +YG I            + RGF  +++ +I  A+ AM
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 247 RALQNKPLRRRKLDIHFSIPKDN 269
            A+  K +  R++ +  +    +
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSD 87

>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 = 53.2 bits (127), Expect = 1e-09
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDVRAAEAALKSL 334
           L +  L P  +++DL ++   YG++        + T   + + F++F    AA+ A+ +L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 335 NRSDIAGKRIK 345
             S +  +  K
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 = 43.2 bits (101), Expect = 3e-06
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIRAARTAMRAL 249
           L++R +     D +L  L + YG I         T  K +G+  + +    AA+ A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 250 QNKPLRRRKL 259
           +   ++ +  
Sbjct: 61  KASGVQAQMA 70

>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 = 52.7 bits (126), Expect = 2e-09
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 334
           + V  L P    E +R+ FG +GEV+ I      + +K     FI F +    +  ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 335 NRSDIAGKRIK 345
              ++   + +
Sbjct: 61  KYHNVGLSKCE 71

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 12/72 (16%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMRAL 249
           +FV  ++ +  + ++R  F  +G++ ++           RGF  I++ +    +  M   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 250 QNKPLRRRKLDI 261
           +   +   K +I
Sbjct: 61  KYHNVGLSKCEI 72

>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 = 53.2 bits (127), Expect = 2e-09
 Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYD 323
           + S KD     + V  L    ++  LR+ F  +G+++E      ++  K     F+   D
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
             AAE A K  N   I G++  +  +  G   R+L
Sbjct: 62  RAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSL 95

>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 = 45.9 bits (108), Expect = 7e-07
 Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 185 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDI 239
               +     +FV  +  +  D+ LR  FE +GDI            K RG+  ++  D 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
            AA  A +   N  +  RK +++ +     P
Sbjct: 63  AAAERACKDP-NPIIDGRKANVNLAYLGAKP 92

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (126), Expect = 2e-09
 Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 12/93 (12%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
           PSD      T+ + NL      E L ++   +G++K +      +T H +   F +F   
Sbjct: 2   PSDVT-EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 325 RAAEAALKSLNRS------DIAGKRIKLEPSRP 351
            AA+  L + +         + G+++K++ +  
Sbjct: 61  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 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 = 51.0 bits (121), Expect = 1e-08
 Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 11/97 (11%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIR 240
           P      +T+F+RN++ + E+  L  + +Q+GD++ +           +G     +    
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 241 AARTAMRALQ------NKPLRRRKLDIHFSIPKDNPS 271
           AA+  + A           L  R+L +  ++ +D  +
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>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 = 52.9 bits (126), Expect = 3e-09
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 6/90 (6%)

Query: 188 GEHPSRTLFVRNINSNVEDS-----ELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G   S  L     N +V        +  +LF  Y    T +   K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTT-FQYFKSFKRVRINFSNPLSA 59

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSD 272
             A   L       +++ ++F+      S 
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>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 = 48.2 bits (114), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 279 TLVVFNLDPSVSNE-----DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS 333
            L+    +  V +E         +F  Y +    +     +    I F +  +A  A   
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRV-RINFSNPLSAADARLR 65

Query: 334 LNRSDIAGKRIKLEPSRP 351
           L++++  GK +KL  ++ 
Sbjct: 66  LHKTEFLGKEMKLYFAQT 83

>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 = 52.5 bits (125), Expect = 4e-09
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR-----TA 245
           P++ L+++N++  V + +L +LF ++ + +      +     M     I          A
Sbjct: 17  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 76

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPS 271
           +  +    L  + L I F   K   S
Sbjct: 77  LHLVNGYKLYGKILVIEFGKNKKQRS 102

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 9e-09
 Identities = 25/94 (26%), Positives = 36/94 (38%), Gaps = 9/94 (9%)

Query: 267 KDNPSDKDLNQG----TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHK 317
           +  P     N G     L + NL P V+  DL  +F  + E K         T   R   
Sbjct: 4   RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 63

Query: 318 FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           FI F +   A  AL  +N   + GK + +E  + 
Sbjct: 64  FITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 97

>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 = 51.6 bits (123), Expect = 5e-09
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDVRAAEAALKS 333
            L +  L    ++E LR  F  +G + +        T   R   F+ +  V   +AA+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 334 LNRSDIAGKRIK 345
                + G+ ++
Sbjct: 67  ARPHKVDGRVVE 78

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 5e-07
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 247
           R LF+  ++    D  LR+ FEQ+G +              RGF  ++Y  +     AM 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 248 ALQNKPLRRRKLDI 261
           A +   +  R ++ 
Sbjct: 67  A-RPHKVDGRVVEP 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 = 51.7 bits (123), Expect = 8e-09
 Identities = 16/100 (16%), Positives = 42/100 (42%), Gaps = 4/100 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +G H      S  + VR +  +V +++L    E++G I  +      +   ++ +
Sbjct: 1   GSSGSSGSHHKVS-VSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEF 58

Query: 237 YDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKD 274
            +I +A+  +    + P  +  ++   ++S  K      +
Sbjct: 59  ENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGN 98

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 4e-06
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            + V  L  SV   DL +    +G +  +      +    +EF ++ +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 339 --IAGKRIKLEPSRPGGARR 356
             IAG++     S      R
Sbjct: 76  VYIAGQQAFFNYSTSKRITR 95

>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 = 50.5 bits (120), Expect = 2e-08
 Identities = 11/80 (13%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  + V+N+  +    E+  L + Y          +++    ++  +   A+ A++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV--DRNKRTAFVTLLNGEQAQNAIQ 58

Query: 248 ALQNKPLRRRKLDIHFSIPK 267
                  R + L +      
Sbjct: 59  MFHQYSFRGKDLIVQLQPTD 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 = 44.7 bits (105), Expect = 1e-06
 Identities = 9/73 (12%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            ++V NL    + +++  +   Y            +   F+   +   A+ A++  ++  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLK--YCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 339 IAGKRIKLEPSRP 351
             GK + ++    
Sbjct: 65  FRGKDLIVQLQPT 77

>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 = 50.1 bits (119), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           TL + N+ PSVS EDL+ +F + G V +  +     R    I+   V  A  AL  L+  
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 71

Query: 338 DIA-GKRIKLEPSRP 351
           D+     +++  S+ 
Sbjct: 72  DLGENHHLRVSFSKS 86

>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 = 22/76 (28%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAMRAL 249
           PS TL + NI  +V + +L+ LF   G + +      K R   +I    +  A  A+  L
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 250 QNKPLRR-RKLDIHFS 264
            N  L     L + FS
Sbjct: 69  HNHDLGENHHLRVSFS 84

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.7 bits (118), Expect = 2e-08
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 279 TLVVFNLDPSVSNED-LRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEAAL 331
            +++ NL   + +E+ LR+ F  +G +++I      +E        F+ F +  +AE AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 332 KSLNRSDIAGKRIKLEPSRP 351
           + +NRS +  + I +  +  
Sbjct: 66  Q-MNRSLLGNREISVSLADK 84

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.8 bits (113), Expect = 1e-07
 Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 192 SRTLFVRNINSNV-EDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAART 244
            R + +RN+++ + +++ LR  FE +G I  +           +     + + +  +A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 245 AMRALQNKPLRRRKLDIHFSIPK 267
           A+  +    L  R++ +  +  K
Sbjct: 64  AL-QMNRSLLGNREISVSLADKK 85

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 3e-08
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           TL V+  D  ++   LR  F  +G + ++      R+  F+ +  + +A+ A+  LN + 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLS-MDPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 339 IAGKRIKLEPSRP 351
           +   ++K+  +R 
Sbjct: 64  VESVQLKVNIARK 76

>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 = 48.1 bits (114), Expect = 7e-08
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
              TL+V   +  +  + LR  F  +G+I  L           ++Y  + +A  A+  L 
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQAVAELN 60

Query: 251 NKPLRRRKLDIHFSIPK 267
              +   +L ++ +  +
Sbjct: 61  GTQVESVQLKVNIARKQ 77

>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 = 49.8 bits (118), Expect = 4e-08
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 4/83 (4%)

Query: 273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE----VKEIRETPHKRHHKFIEFYDVRAAE 328
           ++ +   L + NL  S+  ++L  +   +G+          +   R   F         E
Sbjct: 14  QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE 73

Query: 329 AALKSLNRSDIAGKRIKLEPSRP 351
           A +   N   I        P+ P
Sbjct: 74  AVIGHFNGKFIKTPPGVSAPTEP 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 5e-07
 Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 4/82 (4%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGD----IRTLYTACKHRGFVMISYYDIRAART 244
           E     L++ N+  ++++ EL  + + +G          ++   RG              
Sbjct: 15  EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 245 AMRALQNKPLRRRKLDIHFSIP 266
            +     K ++        + P
Sbjct: 75  VIGHFNGKFIKTPPGVSAPTEP 96

>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 = 48.9 bits (116), Expect = 5e-08
 Identities = 12/77 (15%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 191 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
             R + + +         +L  L E +G I              I       A+ A+   
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYY 65

Query: 250 QNKP--LRRRKLDIHFS 264
              P  +  + + +H S
Sbjct: 66  TTTPALVFGKPVRVHLS 82

>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 = 42.0 bits (98), Expect = 2e-05
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 4/76 (5%)

Query: 279 TLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLN 335
            + + +          L Q+   +G +       +K +  FIE      A+AA+   +  
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL-ILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 336 RSDIAGKRIKLEPSRP 351
            + + GK +++  S+ 
Sbjct: 69  PALVFGKPVRVHLSQK 84

>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 = 48.3 bits (114), Expect = 8e-08
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           P++ LF+ N+     +  L  LF Q+   + +           + +     +  A  ALQ
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQ 66

Query: 251 NKPL-RRRKLDIHFS 264
              +     + I F+
Sbjct: 67  GFKITPTHAMKITFA 81

>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 = 48.6 bits (115), Expect = 8e-08
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE-----VKEIRETPHKRHHKFIEFYDVRAAEAALKS 333
           T  + NL   V+ E +++ F           +E       +   + EF D+ +  +AL  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           LN   +  KRI+++ +     + 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 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 = 47.8 bits (113), Expect = 2e-07
 Identities = 13/86 (15%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 245
           P  T F+ N+  +V +  ++  F           R      + +GF    + D+ +  +A
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPS 271
           + +L  + L  +++ +  +    +  
Sbjct: 74  L-SLNEESLGNKRIRVDVADQAQDKD 98

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 9e-08
 Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 292 EDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
           EDLR     +G+++++     H      + F D   A+  +++L+     G++I  +   
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

Query: 351 P 351
            
Sbjct: 94  G 94

>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 = 43.4 bits (102), Expect = 6e-06
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 12/91 (13%)

Query: 191 PSRTLFVRNI--NSNVEDS---------ELRALFEQYGDIRTLYTACKH-RGFVMISYYD 238
             R + ++N+    + ED          +LR    ++G IR L    +H  G   +S+ D
Sbjct: 7   HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRD 66

Query: 239 IRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
              A   ++ L  +    R++         +
Sbjct: 67  PEEADYCIQTLDGRWFGGRQITAQAWDGTTD 97

>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 = 48.1 bits (114), Expect = 1e-07
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
                   E   ++   YGEV+E+        H   + +++F     AE A+  LN    
Sbjct: 34  EHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF 93

Query: 340 AGKRIKLEPS 349
            G+ I  E S
Sbjct: 94  NGQPIHAELS 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 = 40.0 bits (93), Expect = 9e-05
 Identities = 9/74 (12%), Positives = 24/74 (32%), Gaps = 4/74 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMRALQ 250
           + ++       +     + E+YG++  +             V + +     A  A+  L 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 251 NKPLRRRKLDIHFS 264
           N+    + +    S
Sbjct: 90  NRWFNGQPIHAELS 103

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V  +        LR  F  YG+++ I     R +  KR   F+ F D  + +  +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 334 LNRSDIAGKRIK 345
                + G   +
Sbjct: 63  QKYHTVNGHNCE 74

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 247
           + +FV  I  + E+  LR  FEQYG I  +           RGF  +++ D  +    + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV- 61

Query: 248 ALQNKPLRRRKLDIHFSI 265
             +   +     ++  ++
Sbjct: 62  IQKYHTVNGHNCEVRKAL 79

>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 = 47.5 bits (112), Expect = 1e-07
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           PSR L +R +   V ++E+ AL   +G +       K +    +      AA T +    
Sbjct: 7   PSRVLHIRKLPGEVTETEVIALGLPFGKVTN-ILMLKGKNQAFLELATEEAAITMVNYYS 65

Query: 251 NKP--LRRRKLDIHFSIPK 267
                LR + + I +S  K
Sbjct: 66  AVTPHLRNQPIYIQYSNHK 84

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 3e-07
 Identities = 12/80 (15%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 190 HPSRTLFVR--NINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           + +++L V    + + V  ++L  + E+ G +  L     ++ +    Y     ++ A  
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYV 74

Query: 248 ALQNKPL---RRRKLDIHFS 264
            L  K +     +K+ ++ +
Sbjct: 75  TLNGKEVVDDLGQKITLYLN 94

>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 = 47.0 bits (111), Expect = 3e-07
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 279 TLVVF--NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +LVV    L   VS   L  +    G V  +   P  + + F  +     ++ A  +LN 
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-MPPNKPYSFARYRTTEESKRAYVTLNG 78

Query: 337 SDI---AGKRIKLEPS 349
            ++    G++I L  +
Sbjct: 79  KEVVDDLGQKITLYLN 94

>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 = 45.9 bits (108), Expect = 7e-07
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 13/87 (14%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----------ETPHKRHHKFIEFYDVRAAE 328
            L V N+   ++ E +   F A   +  +           +    ++  F+EF  V    
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGAR 355
            A+   +     G+ +K+   RP   +
Sbjct: 63  QAMA-FDGIIFQGQSLKI--RRPHDYQ 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 7e-06
 Identities = 14/86 (16%), Positives = 26/86 (30%), Gaps = 13/86 (15%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL----------YTACKHRGFVMISYYDIRAA 242
           R L+V NI   + +  +   F     +  L              + + F  + +  +   
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKD 268
             AM        + + L I    P D
Sbjct: 62  TQAMA-FDGIIFQGQSLKI--RRPHD 84

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 8e-07
 Identities = 16/102 (15%), Positives = 34/102 (33%), Gaps = 3/102 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
                +LD     EDL  +F  +GE+K I      +    +     + A    K  N  +
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 339 IAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGS 380
           +  +  ++      G       +  +++ +D+   L      
Sbjct: 73  LQLRNKEVTWEVLEGEVEK---EALKKIIEDQQESLNKWKSK 111

>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 = 45.2 bits (106), Expect = 2e-06
 Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD-IRAARTAMRALQN 251
              F  +++      +L  LF  +G+I+ +          +I + +  + A    +   N
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANN 70

Query: 252 KPLRRRKLDIHFSIPKD 268
             L+ R  ++ + + + 
Sbjct: 71  GNLQLRNKEVTWEVLEG 87

>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 = 44.3 bits (104), Expect = 2e-06
 Identities = 8/81 (9%), Positives = 27/81 (33%), Gaps = 5/81 (6%)

Query: 273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAE 328
            D+   ++ +       + +D+++     G+V  I+             F+ F  + +A+
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 329 AALKSLNRSDIAGKRIKLEPS 349
             ++           + +   
Sbjct: 62  KFVE-TPGQKYKETDLLILFK 81

>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 = 43.2 bits (101), Expect = 5e-06
 Identities = 8/80 (10%), Positives = 30/80 (37%), Gaps = 5/80 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAART 244
           +  +R+++++   ++    +++   E  G +  +             + + +  I +A+ 
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 62

Query: 245 AMRALQNKPLRRRKLDIHFS 264
            +     +  +   L I F 
Sbjct: 63  FV-ETPGQKYKETDLLILFK 81

>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 = 44.0 bits (103), Expect = 4e-06
 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 2/82 (2%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTA 245
           P        + V  +  +    +L+    + GD+          G V            A
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYL--RKEDMEYA 66

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
           +R L +   R  + +  +    
Sbjct: 67  LRKLDDTKFRSHEGETSYIRVY 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 2/79 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            ++V  L PS S +DL+      G+V        K     +E+      E AL+ L+ + 
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVCYAD--VQKDGMGMVEYLRKEDMEYALRKLDDTK 74

Query: 339 IAGKRIKLEPSRPGGARRN 357
                 +    R    R +
Sbjct: 75  FRSHEGETSYIRVYPERSS 93

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 42.6 bits (99), Expect = 8e-06
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAM 246
               LF+ N+N N   +EL+    +      L       G    F  + +        A+
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71

Query: 247 RALQNKPLRRRKLDIHFSIPK 267
             L    +   ++ +     +
Sbjct: 72  E-LTGLKVFGNEIKLEKPKGR 91

>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 = 42.4 bits (99), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V N+  +VS +++   F  Y  +         E         + F     A AA+  
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 334 LNRSDIAGKRIKLE 347
           LN   I  +++KL 
Sbjct: 71  LNDRPIGSRKVKLV 84

>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 = 38.1 bits (88), Expect = 3e-04
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAA 242
           G+     + V+N+   V   E+   F  Y  I        +      G  M+++     A
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 64

Query: 243 RTAMRALQNKPLRRRKLDI 261
             A+  L ++P+  RK+ +
Sbjct: 65  TAAVIDLNDRPIGSRKVKL 83

>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 = 41.3 bits (96), Expect = 2e-05
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 12/81 (14%)

Query: 277 QGTLV-VFNLDPSVSNEDLRQI------FGAYGEVKEIRETPHKRHHKF-----IEFYDV 324
           Q  LV V  L   +++ ++ +       FG   +V     T +           + +   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 325 RAAEAALKSLNRSDIAGKRIK 345
             A  A++ +N   + G+ +K
Sbjct: 67  EDALRAIQCVNNVVVDGRTLK 87

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 0.001
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 193 RTLFVRNINSNVEDSELRALFE---QYGDI--------RTLYTACKHRGFVMISYYDIRA 241
             +FV  ++  + D E+    E   ++G I         +   +        ++Y     
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 242 ARTAMRALQNKPLRRRKL 259
           A  A++ + N  +  R L
Sbjct: 69  ALRAIQCVNNVVVDGRTL 86

>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 = 41.0 bits (95), Expect = 3e-05
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 2/78 (2%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           +VV  L PS S +DL+                ++     +EF        A++ L+ +  
Sbjct: 3   VVVSGLPPSGSWQDLKDHM--REAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 60

Query: 340 AGKRIKLEPSRPGGARRN 357
                +    R       
Sbjct: 61  RSHEGETAYIRVKVDGPR 78

>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 = 40.7 bits (95), Expect = 5e-05
 Identities = 12/95 (12%), Positives = 31/95 (32%), Gaps = 17/95 (17%)

Query: 191 PSRTLFVRNI------NSNVEDSELR-ALFEQYGDIRTLYTACKHR----------GFVM 233
           P+  L + N+        + E  E+   + ++      + +    R          G + 
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
           + +  +   + AM+ L  +    R +   +  P  
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 7/75 (9%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR-------ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           + +     ED+R     YG VK I                 F+EF  V   + A++ L  
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 337 SDIAGKRIKLEPSRP 351
              A + +  +   P
Sbjct: 81  RKFANRVVVTKYCDP 95

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (89), Expect = 3e-04
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 4/87 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
               +  +N+ +    +E++  F ++G +  +          ++ + +   AR A R L 
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLA 67

Query: 251 NKPLRRRKLDIHFS---IPKDNPSDKD 274
                   L + ++   +    P  KD
Sbjct: 68  YSKFHHVPLYLEWAPIGVFGAAPQKKD 94

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 3e-04
 Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 6/97 (6%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEF 321
           +            + +  L     N+ +   F     V++     +  + K     F+EF
Sbjct: 8   RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 67

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
            +    +AAL   ++  +  + I++ P    G    +
Sbjct: 68  RNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKI 103

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (86), Expect = 4e-04
 Identities = 10/68 (14%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           +++  L   V+N+++  +   Y    +       +   F+   +   AEAA+ + ++S +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY--ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL 58

Query: 340 AGKRIKLE 347
             + + ++
Sbjct: 59  RERELSVQ 66

>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 = 36.8 bits (84), Expect = 8e-04
 Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 3/74 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           + +R +  +V + E+  L   Y          K   FV     +   A  A+       L
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVT--LLNGEQAEAAINTFHQSRL 58

Query: 255 RRRKLDIHFSIPKD 268
           R R+L +    P D
Sbjct: 59  RERELSVQLQ-PTD 71

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {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: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.7 bits (86), Expect = 7e-04
 Identities = 8/83 (9%), Positives = 20/83 (24%), Gaps = 2/83 (2%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
           +   R + + N+  +           +       Y   + +    I       A   +  
Sbjct: 15  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDH 74

Query: 249 LQNKP--LRRRKLDIHFSIPKDN 269
              K    + R + +  S     
Sbjct: 75  CLKKALWFQGRCVKVDLSEKYKK 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	780
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.94
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.66
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.66
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.65
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.65
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.65
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.64
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.64
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.63
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.63
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.63
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.62
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.62
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.62
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.62
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.62
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.61
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.61
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.61
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.61
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.6
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.6
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.6
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.6
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.6
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.6
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.6
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.59
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.59
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.59
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.59
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.59
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.59
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.59
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.59
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.59
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.58
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.58
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.58
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.58
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.58
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.58
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.58
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.58
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.57
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.57
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.57
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.57
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.56
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.56
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.56
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.56
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.56
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.56
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.56
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.55
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.55
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.55
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.55
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.55
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.55
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.55
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.55
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.55
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.55
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.54
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.54
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.54
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.54
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.54
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.54
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.54
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.53
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.53
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.53
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.53
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.52
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.52
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.52
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.52
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.52
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.51
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.51
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.51
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.51
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.51
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.51
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.5
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.5
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.5
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.5
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.5
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.5
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.49
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.49
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.49
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.49
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.49
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.49
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.48
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.48
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.48
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.48
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.47
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.46
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.46
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.46
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.46
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.46
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.45
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.45
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.45
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.45
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.44
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.44
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.43
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.42
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.42
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.42
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.42
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.42
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.4
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.4
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.39
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.38
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.38
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.38
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.37
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.35
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.35
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.33
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.31
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.31
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.26
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.25
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.24
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	99.24
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.21
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.2
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.18
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.15
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.15
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.14
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	99.13
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.12
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.0
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.9
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.84
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.72
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.03
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.24
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.58
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.53
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	92.84
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	89.35

>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=99.94  E-value=1.7e-26  Score=226.66  Aligned_cols=162  Identities=20%  Similarity=0.387  Sum_probs=139.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      |+|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|+.. .+..+..+.+.+....+.
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhhc
Confidence            8999999999999999999999999999887     2678999999999999999999995 566677777777665444


Q ss_pred             CCC--CCCCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 004002          268 DNP--SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (780)
Q Consensus       268 ~~~--s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~  340 (780)
                      ...  .......++|||+|||..+|+++|+++|+.||.|..+.+     ++.++|||||+|.+.++|.+||+ +++..+.
T Consensus        86 ~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~  164 (183)
T d1u1qa_          86 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN  164 (183)
T ss_dssp             TGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEET
T ss_pred             ccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeEC
Confidence            322  123345579999999999999999999999999999865     46788999999999999999997 7999999


Q ss_pred             CceEEEEecCCCchhh
Q 004002          341 GKRIKLEPSRPGGARR  356 (780)
Q Consensus       341 Gr~L~V~~a~~k~~r~  356 (780)
                      |++|+|.+|.++.++.
T Consensus       165 G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         165 GHNCEVRKALSKQEMA  180 (183)
T ss_dssp             TEEEEEEECCCHHHHH
T ss_pred             CEEEEEEecCCccccc
Confidence            9999999998876543

>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=99.75  E-value=1.8e-18  Score=168.74  Aligned_cols=153  Identities=18%  Similarity=0.291  Sum_probs=121.8

Q ss_pred             CceeeeccCCCCCChHHHHHHhcCCCcE---EEeccCccCcccceEEEeecCccccCcc---cccccCCCC-------cc
Q 004002          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGA-------GT  180 (780)
Q Consensus       114 ~~el~V~~Lp~s~~E~el~dlFs~~G~i---~V~~d~~esa~~g~~~v~~~~~~~a~~~---~~~~l~n~~-------~k  180 (780)
                      ++++||++||.+++|.+++++|+.+|.|   .+..+......++++++.|.+...+..+   ....+....       ..
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            3689999999999999999999999997   5666777888889999999987665422   111111110       01


Q ss_pred             cCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          181 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       181 ~~g~~~~~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                      ............++|||+|||+++|+++|+++|+.||.|..+.     .+++++|||||+|.+.++|++|++ +++..+.
T Consensus        86 ~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~  164 (183)
T d1u1qa_          86 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN  164 (183)
T ss_dssp             TGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEET
T ss_pred             ccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeEC
Confidence            1111122345668999999999999999999999999999886     257899999999999999999997 7889999


Q ss_pred             ccccccccCCCC
Q 004002          256 RRKLDIHFSIPK  267 (780)
Q Consensus       256 gr~I~V~~a~pk  267 (780)
                      |++|.|.+|.++
T Consensus       165 G~~i~V~~A~~k  176 (183)
T d1u1qa_         165 GHNCEVRKALSK  176 (183)
T ss_dssp             TEEEEEEECCCH
T ss_pred             CEEEEEEecCCc
Confidence            999999998765

>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=99.66  E-value=6.1e-17  Score=138.29  Aligned_cols=75  Identities=23%  Similarity=0.453  Sum_probs=71.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      +++|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+|++|
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            57899999999999999999999999999987     3678999999999999999999999999999999999999976

>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=99.66  E-value=9.9e-17  Score=136.98  Aligned_cols=76  Identities=28%  Similarity=0.436  Sum_probs=71.1

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|++||+.|||..+.|++|+|++|+|
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            357999999999999999999999999999975     456789999999999999999999999999999999999988


Q ss_pred             C
Q 004002          352 G  352 (780)
Q Consensus       352 k  352 (780)
                      +
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.65  E-value=1.2e-16  Score=136.37  Aligned_cols=75  Identities=23%  Similarity=0.481  Sum_probs=70.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .++|||+|||+++++++|+++|++||+|.+|+     ..++++|||||+|.+.++|++|++.|+|..|.|++|+|.||+|
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            46899999999999999999999999999987     2578999999999999999999999999999999999999986

>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=99.65  E-value=1.5e-16  Score=138.61  Aligned_cols=79  Identities=22%  Similarity=0.336  Sum_probs=73.5

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++||+.|||..+.|++|+|++|
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            35678999999999999999999999999999975     4678999999999999999999999999999999999999


Q ss_pred             CCCc
Q 004002          350 RPGG  353 (780)
Q Consensus       350 ~~k~  353 (780)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            9874

>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=99.65  E-value=2.2e-16  Score=138.42  Aligned_cols=79  Identities=16%  Similarity=0.326  Sum_probs=73.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||.++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|+||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3468999999999999999999999999999987     36889999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8765

>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=99.64  E-value=1.6e-16  Score=138.48  Aligned_cols=79  Identities=23%  Similarity=0.475  Sum_probs=74.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .+.++|||+|||.++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..|.|++|.|.|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            4568999999999999999999999999999987     35789999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8865

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.64  E-value=1.5e-16  Score=138.07  Aligned_cols=79  Identities=20%  Similarity=0.434  Sum_probs=72.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ....++|||+|||.++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..|.|++|.|.|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999987     3578999999999999999999999999999999999999


Q ss_pred             CCCC
Q 004002          264 SIPK  267 (780)
Q Consensus       264 a~pk  267 (780)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9764

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.7e-16  Score=134.17  Aligned_cols=74  Identities=30%  Similarity=0.515  Sum_probs=69.9

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ++|||+|||.++++++|+++|++||.|++|++     .+.++|||||+|.+.++|++|++.|||..+.|++|+|.+|+|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            47999999999999999999999999999975     457789999999999999999999999999999999999987

>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=99.63  E-value=1.3e-16  Score=138.79  Aligned_cols=78  Identities=27%  Similarity=0.502  Sum_probs=73.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.
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            468999999999999999999999999999987     358899999999999999999999999999999999999998


Q ss_pred             CCC
Q 004002          266 PKD  268 (780)
Q Consensus       266 pk~  268 (780)
                      |+.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
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=99.63  E-value=2.9e-16  Score=136.19  Aligned_cols=79  Identities=24%  Similarity=0.388  Sum_probs=72.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ....+|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+||
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            34578999999999999999999999999999875     4667899999999999999999999999999999999999


Q ss_pred             CCCc
Q 004002          350 RPGG  353 (780)
Q Consensus       350 ~~k~  353 (780)
                      .+++
T Consensus        85 ~~kG   88 (88)
T d1rk8a_          85 FVKG   88 (88)
T ss_dssp             EECC
T ss_pred             cCCC
Confidence            8763

>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=99.63  E-value=4e-16  Score=136.77  Aligned_cols=78  Identities=26%  Similarity=0.330  Sum_probs=73.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|++||+.|||..+.|+.|+|.+|+
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            3468999999999999999999999999999975     56789999999999999999999999999999999999998


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            875

>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=99.62  E-value=2.3e-16  Score=137.05  Aligned_cols=78  Identities=27%  Similarity=0.452  Sum_probs=72.9

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|++|+|
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            468999999999999999999999999999975     567899999999999999999999999999999999999998


Q ss_pred             Cch
Q 004002          352 GGA  354 (780)
Q Consensus       352 k~~  354 (780)
                      +..
T Consensus        85 ~~~   87 (89)
T d2cqba1          85 MRI   87 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.62  E-value=5.7e-16  Score=137.15  Aligned_cols=82  Identities=27%  Similarity=0.405  Sum_probs=75.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++||+.|++..|.|++|.|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4568899999999999999999999999999998     35889999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 004002          265 IPKDNPS  271 (780)
Q Consensus       265 ~pk~~~s  271 (780)
                      .++....
T Consensus        86 ~~~~~~~   92 (99)
T d1whwa_          86 TIKKEAS   92 (99)
T ss_dssp             CCCSTTC
T ss_pred             CCCCccC
Confidence            8766443

>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=99.62  E-value=6.3e-16  Score=135.77  Aligned_cols=79  Identities=27%  Similarity=0.519  Sum_probs=73.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcceEEEEEEecHHHHHHHHHHc-cCccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIH  262 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~------tgkskG~aFV~F~~~e~A~~Al~~L-ng~~l~gr~I~V~  262 (780)
                      ..+++|||+|||+++++++|+++|++||.|..|+.      +|+++|||||+|.+.++|++|++.| ++..|.|++|.|.
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            46689999999999999999999999999999872      5789999999999999999999998 8999999999999


Q ss_pred             cCCCCC
Q 004002          263 FSIPKD  268 (780)
Q Consensus       263 ~a~pk~  268 (780)
                      ||.++.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997654

>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=99.62  E-value=4.7e-16  Score=136.35  Aligned_cols=79  Identities=25%  Similarity=0.428  Sum_probs=73.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..+++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..|.|++|.|.|+
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            3578999999999999999999999999999987     36789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      ....
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>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=99.62  E-value=1.4e-16  Score=138.57  Aligned_cols=80  Identities=23%  Similarity=0.383  Sum_probs=72.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~---g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..++|||+|||.++++++|+++|++||.|+.+++.   +.++|||||+|.+.++|++||+.|||..+.|++|+|.+++++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            34589999999999999999999999999999862   346799999999999999999999999999999999999987


Q ss_pred             chh
Q 004002          353 GAR  355 (780)
Q Consensus       353 ~~r  355 (780)
                      .+|
T Consensus        87 ~~R   89 (89)
T d1cvja2          87 KER   89 (89)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            643

>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=99.62  E-value=5.1e-16  Score=138.43  Aligned_cols=80  Identities=25%  Similarity=0.432  Sum_probs=73.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||.++++++|+++|++||.|+++++     ++.++|||||+|.+.++|++||+.|||..|.|++|+|++++
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            3468999999999999999999999999999864     56778999999999999999999999999999999999999


Q ss_pred             CCchh
Q 004002          351 PGGAR  355 (780)
Q Consensus       351 ~k~~r  355 (780)
                      ++.++
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            98754

>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=99.62  E-value=8.3e-16  Score=139.33  Aligned_cols=100  Identities=21%  Similarity=0.411  Sum_probs=82.2

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      .++|||+|||.++++++|+++|++||.|+.|++  ++.++|||||+|.+.++|.+||+.|||..|.|+.|+|.++.+...
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~   86 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRA   86 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCch
Confidence            468999999999999999999999999999986  567789999999999999999999999999999999999875432


Q ss_pred             hhhHhhhhchhccHHHHHHHHhhhCC
Q 004002          355 RRNLMLQLNQELEQDESRILQHQVGS  380 (780)
Q Consensus       355 r~~~l~ql~~~~~~~~~~~~~~~~Gs  380 (780)
                      .    ........++++.....++|.
T Consensus        87 ~----~~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          87 F----QKMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             T----TTSCHHHHHHHHHHHHHHHCC
T ss_pred             h----hhhHHHHHHHHHHHHHHHhCC
Confidence            2    222223344556666666664

>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=99.61  E-value=4.2e-16  Score=138.97  Aligned_cols=79  Identities=16%  Similarity=0.387  Sum_probs=73.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      +.++|||+|||+++|+++|+++|++||.|.+++     .+++++|||||+|.+.++|++||++|+|..|.|++|+|+|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            457899999999999999999999999998876     367899999999999999999999999999999999999998


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8764

>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=99.61  E-value=2.5e-16  Score=134.18  Aligned_cols=75  Identities=19%  Similarity=0.227  Sum_probs=66.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .+||||+|||+++|+++|+++|++||.|..++     ..++++|||||+|.+.++|++|++.|+|..+.|++|.|+++.|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            37999999999999999999999999997665     3688999999999999999999999999999999999999987

>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=99.61  E-value=2.5e-16  Score=142.77  Aligned_cols=101  Identities=25%  Similarity=0.404  Sum_probs=84.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      .+++|||+|||.++|+++|+++|++||+|.+|+  .+++++|||||+|.+.++|.+|++.|+|..|.|++|.|.++.+..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   85 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANR   85 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            568999999999999999999999999999988  467889999999999999999999999999999999999986432


Q ss_pred             CCCCCCCCccceeecCCCCCCChhHHHHHhcccCC
Q 004002          269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE  303 (780)
Q Consensus       269 ~~s~~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~  303 (780)
                      ...            .......+++++.+..+||.
T Consensus        86 ~~~------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          86 AFQ------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HTT------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             hhh------------hhHHHHHHHHHHHHHHHhCC
Confidence            111            11222346778888888774

>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=99.61  E-value=5.4e-16  Score=132.00  Aligned_cols=73  Identities=29%  Similarity=0.375  Sum_probs=68.9

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      +|||+|||..+|+++|+++|++||+|++|++     +++++|||||+|.++++|.+|++.|||..+.|++|+|.+++.
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            6999999999999999999999999999986     467789999999999999999999999999999999999863

>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=99.61  E-value=1.1e-15  Score=134.26  Aligned_cols=78  Identities=24%  Similarity=0.477  Sum_probs=72.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe------CCCcccEEEEEEcCHHHHHHHHHHh-CCCccCCceEEEEe
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~L-nG~~i~Gr~L~V~~  348 (780)
                      ...+|||+|||.++++++|+++|++||.|+.|++      ++.++|||||+|.+.++|++||+.| ||..+.|++|+|++
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            4568999999999999999999999999999986      4567899999999999999999999 89999999999999


Q ss_pred             cCCCc
Q 004002          349 SRPGG  353 (780)
Q Consensus       349 a~~k~  353 (780)
                      |+++.
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98765

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.61  E-value=4.2e-16  Score=137.32  Aligned_cols=82  Identities=21%  Similarity=0.335  Sum_probs=76.9

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ....++|||+|||.++|+++|+++|++||.|..++.++.+++||||+|.+.++|++|++.|||..+.|++|+|.++.++.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            33567999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             hh
Q 004002          354 AR  355 (780)
Q Consensus       354 ~r  355 (780)
                      .+
T Consensus        93 ~~   94 (96)
T d1fjca_          93 GT   94 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.60  E-value=8.2e-16  Score=134.76  Aligned_cols=79  Identities=23%  Similarity=0.306  Sum_probs=72.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|++||+.|||..+.|+.|+|+|+.
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            3568999999999999999999999999999975     56678999999999999999999999999999999999997


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ....
T Consensus        86 ~~~~   89 (93)
T d1h2vz_          86 GFKE   89 (93)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            6554

>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=99.60  E-value=8.8e-16  Score=133.61  Aligned_cols=81  Identities=30%  Similarity=0.384  Sum_probs=73.1

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ...++|||+|||.++|+++|+++|++||.|+.|++   ....++||||+|.+.++|++|++.|||..+.|+.|+|.+|++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            34578999999999999999999999999999986   234578999999999999999999999999999999999987


Q ss_pred             Cchh
Q 004002          352 GGAR  355 (780)
Q Consensus       352 k~~r  355 (780)
                      +..+
T Consensus        86 ~~~~   89 (90)
T d2cqia1          86 PSSQ   89 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            6543

>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=99.60  E-value=9e-16  Score=144.03  Aligned_cols=81  Identities=23%  Similarity=0.453  Sum_probs=74.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++||+.|+|..|.|++|+|+|+
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            44579999999999999999999999999998872     5889999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      .++..+
T Consensus       120 ~~~~~~  125 (139)
T d1u6fa1         120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            876543

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=6.7e-16  Score=132.70  Aligned_cols=75  Identities=24%  Similarity=0.456  Sum_probs=68.3

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----C---CCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          195 LFVRNINSNVEDSELRALFEQYGDIRTLYT-----A---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       195 LfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----t---gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      |||+|||+++|+++|+++|++||+|.+++.     +   +++||||||+|.+.++|++|++.|+|..|.|++|.|+|+.+
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            899999999999999999999999998872     1   25799999999999999999999999999999999999876


Q ss_pred             CCC
Q 004002          267 KDN  269 (780)
Q Consensus       267 k~~  269 (780)
                      ...
T Consensus        81 ~~k   83 (85)
T d2cpfa1          81 ATK   83 (85)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            543

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.7e-15  Score=132.59  Aligned_cols=80  Identities=21%  Similarity=0.389  Sum_probs=72.8

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      .....+|||+|||.++++++|+++|++||.|+.|++   ...++|||||+|.+.++|++||+.|||..+.|++|+|++|+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            344568999999999999999999999999999976   33468999999999999999999999999999999999999


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            864

>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=99.60  E-value=5.3e-16  Score=134.79  Aligned_cols=79  Identities=23%  Similarity=0.476  Sum_probs=73.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++|+++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|+|..|.|++|.|+++.
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            458899999999999999999999999999886     357899999999999999999999999999999999999998


Q ss_pred             CCCC
Q 004002          266 PKDN  269 (780)
Q Consensus       266 pk~~  269 (780)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.60  E-value=6.2e-16  Score=133.31  Aligned_cols=76  Identities=18%  Similarity=0.421  Sum_probs=71.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      .+|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.++++|++|++.|+|..|.|++|.|.|+.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4799999999999999999999999999987     35899999999999999999999999999999999999999765


Q ss_pred             C
Q 004002          268 D  268 (780)
Q Consensus       268 ~  268 (780)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.60  E-value=1e-15  Score=129.77  Aligned_cols=73  Identities=25%  Similarity=0.395  Sum_probs=68.7

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      +.|||+|||.++++++|+++|++||.|++|++    +++++|||||+|.+.++|++|++.|||+.+.|++|+|+++.
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            36999999999999999999999999999986    56678999999999999999999999999999999999885

>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=99.60  E-value=1.6e-15  Score=129.99  Aligned_cols=77  Identities=22%  Similarity=0.325  Sum_probs=71.3

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRP  351 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~~  351 (780)
                      .+.++|||+|||.++++++|+++|++||.|+.|++...++|+|||+|.+.++|++|++.|||..+. |++|+|+||+.
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~akk   83 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK   83 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEecC
Confidence            345799999999999999999999999999999998778899999999999999999999999884 68999999973

>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=99.59  E-value=1.9e-15  Score=132.28  Aligned_cols=79  Identities=23%  Similarity=0.405  Sum_probs=72.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      ...++|||+|||+++|+++|+++|++||+|..|+.   ...++|||||+|.+.++|++|++.|++..|.|++|+|.||.+
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            45679999999999999999999999999999872   455799999999999999999999999999999999999987


Q ss_pred             CC
Q 004002          267 KD  268 (780)
Q Consensus       267 k~  268 (780)
                      +.
T Consensus        89 r~   90 (93)
T d2cq3a1          89 RV   90 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.59  E-value=7.1e-16  Score=134.00  Aligned_cols=79  Identities=24%  Similarity=0.503  Sum_probs=72.8

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++++++|+++|++||.|..+.+     ++.++|||||+|.++++|++||+.|||..+.|++|+|+++.+
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            467999999999999999999999999999864     567899999999999999999999999999999999999988


Q ss_pred             Cchh
Q 004002          352 GGAR  355 (780)
Q Consensus       352 k~~r  355 (780)
                      +..+
T Consensus        85 ~~~~   88 (90)
T d1x5sa1          85 SSDN   88 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.2e-15  Score=132.81  Aligned_cols=79  Identities=19%  Similarity=0.436  Sum_probs=72.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .+.++|||+|||.++|+++|+++|++||+|.+|+.   ....+|||||+|.+.++|++|++.|+|..|.|++|+|.|+.+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            45689999999999999999999999999999873   344689999999999999999999999999999999999986


Q ss_pred             CC
Q 004002          267 KD  268 (780)
Q Consensus       267 k~  268 (780)
                      +.
T Consensus        86 ~~   87 (90)
T d2cqia1          86 PS   87 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.59  E-value=7.5e-16  Score=131.12  Aligned_cols=72  Identities=17%  Similarity=0.364  Sum_probs=68.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            699999999999999999999999999988     358899999999999999999999999999999999999985

>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=99.59  E-value=1.4e-15  Score=130.81  Aligned_cols=74  Identities=24%  Similarity=0.455  Sum_probs=68.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccc--ccccccc
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHF  263 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~I~V~~  263 (780)
                      ..++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|..+.|  ++|+|+|
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            457899999999999999999999999999987     358899999999999999999999999999976  8899988


Q ss_pred             C
Q 004002          264 S  264 (780)
Q Consensus       264 a  264 (780)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.59  E-value=2.1e-15  Score=133.40  Aligned_cols=79  Identities=28%  Similarity=0.415  Sum_probs=73.0

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+.|||..+.|+.|+|.+++
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            3567999999999999999999999999999986     56778999999999999999999999999999999999999


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            8653

>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=99.59  E-value=1e-15  Score=131.90  Aligned_cols=75  Identities=17%  Similarity=0.402  Sum_probs=70.9

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      +|||+|||..+|+++|+++|++||+|++|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++|.++.
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~~~~   82 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            6999999999999999999999999999975     57789999999999999999999999999999999999998764

>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=99.59  E-value=8e-16  Score=131.03  Aligned_cols=74  Identities=22%  Similarity=0.287  Sum_probs=66.5

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ++|||+|||.++|+++|+++|++||.|..+.+     .+.++|||||+|.+.++|++|++.|||..+.|++|+|++++|
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            58999999999999999999999999987653     567889999999999999999999999999999999999987

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=1.8e-15  Score=133.00  Aligned_cols=81  Identities=21%  Similarity=0.469  Sum_probs=72.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHcc------Ccccccc
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQ------NKPLRRR  257 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Ln------g~~l~gr  257 (780)
                      ....++|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+      |..+.|+
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            34568999999999999999999999999999887     356789999999999999999999886      5678899


Q ss_pred             ccccccCCCCCC
Q 004002          258 KLDIHFSIPKDN  269 (780)
Q Consensus       258 ~I~V~~a~pk~~  269 (780)
                      +|+|.|+.++.+
T Consensus        85 ~l~v~~a~~k~~   96 (98)
T d1x4ha1          85 QLKVDLAVTRDE   96 (98)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCc
Confidence            999999987654

>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=99.59  E-value=6.1e-16  Score=136.28  Aligned_cols=80  Identities=23%  Similarity=0.397  Sum_probs=75.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      .+.++|||+|||+++|+++|+++|++||.|..++.+++++|||||+|.+.++|++|++.|++..|.|++|.|.|+.++..
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            45689999999999999999999999999998888999999999999999999999999999999999999999988754

>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=99.58  E-value=1.8e-15  Score=130.09  Aligned_cols=75  Identities=24%  Similarity=0.434  Sum_probs=68.8

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEE
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLE  347 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G--r~L~V~  347 (780)
                      ...++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++||+.|||..+.|  ++|+|+
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            34568999999999999999999999999999975     46788999999999999999999999999977  889999


Q ss_pred             ec
Q 004002          348 PS  349 (780)
Q Consensus       348 ~a  349 (780)
                      +|
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.58  E-value=2.8e-15  Score=133.24  Aligned_cols=78  Identities=13%  Similarity=0.263  Sum_probs=71.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +...++|||+|||+++|+++|+++|++||+|..++    .+++++|||||+|.+.++|++|++.|||..|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34568999999999999999999999999998876    36788999999999999999999999999999999999887


Q ss_pred             CC
Q 004002          265 IP  266 (780)
Q Consensus       265 ~p  266 (780)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.58  E-value=1.6e-15  Score=130.59  Aligned_cols=74  Identities=30%  Similarity=0.425  Sum_probs=67.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEe
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G--r~L~V~~  348 (780)
                      +.++|||+|||.++|+++|+++|++||.|+++++     ++.++|||||+|.+.++|++|++.|||..+.|  ++|+|+|
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            4568999999999999999999999999999975     46788999999999999999999999999998  5699988


Q ss_pred             c
Q 004002          349 S  349 (780)
Q Consensus       349 a  349 (780)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.58  E-value=7.8e-16  Score=133.67  Aligned_cols=78  Identities=17%  Similarity=0.360  Sum_probs=71.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~---tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ..+|||+|||+++|+++|+++|++||+|..++.   .+.++|||||+|.+.++|++|++.|+|..|.|++|.|.++.+++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            468999999999999999999999999999873   45578999999999999999999999999999999999998765


Q ss_pred             C
Q 004002          269 N  269 (780)
Q Consensus       269 ~  269 (780)
                      +
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.58  E-value=3.7e-16  Score=139.56  Aligned_cols=79  Identities=24%  Similarity=0.450  Sum_probs=72.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|++..|.|++|+|.|+
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3457999999999999999999999999999887     36889999999999999999999999999999999999998


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .++.
T Consensus        86 ~~~~   89 (104)
T d1p1ta_          86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCCC
Confidence            7643

>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=99.58  E-value=8.9e-16  Score=132.30  Aligned_cols=78  Identities=21%  Similarity=0.323  Sum_probs=72.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP  270 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~~  270 (780)
                      .++|||+|||+++|+++|+++|++||.|..++. ++++|||||+|.+.++|++|++.|+|..|.|++|.|+|++|++..
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~~   85 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKD   85 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCCC
Confidence            479999999999999999999999999877653 678999999999999999999999999999999999999987643

>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=99.58  E-value=1.6e-15  Score=130.61  Aligned_cols=73  Identities=25%  Similarity=0.412  Sum_probs=67.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccc--cccccccC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFS  264 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~I~V~~a  264 (780)
                      .++|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|  ++|.|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            47899999999999999999999999999987     257899999999999999999999999999987  45888875

>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=99.58  E-value=1.6e-15  Score=142.29  Aligned_cols=78  Identities=28%  Similarity=0.457  Sum_probs=72.3

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|++||+.|||..|.|++|+|+++++
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            357999999999999999999999999999875     467899999999999999999999999999999999999987


Q ss_pred             Cch
Q 004002          352 GGA  354 (780)
Q Consensus       352 k~~  354 (780)
                      +..
T Consensus       122 ~~~  124 (139)
T d1u6fa1         122 GHQ  124 (139)
T ss_dssp             CCC
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=99.58  E-value=2.6e-15  Score=131.92  Aligned_cols=78  Identities=18%  Similarity=0.349  Sum_probs=72.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      .++++|||+|||+++|+++|+++|++||.|..++.  ...++|||||+|.+.++|++||+.|++..|.|++|+|+|+++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            45689999999999999999999999999998873  5678999999999999999999999999999999999998764

>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=99.58  E-value=2.7e-15  Score=128.52  Aligned_cols=77  Identities=18%  Similarity=0.349  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccc-cccccccccCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL-RRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l-~gr~I~V~~a~  265 (780)
                      ..|+++|||+|||.++|+++|+++|++||+|.+|+.....+|||||+|.+.++|++|++.|+|..| .|++|+|.||+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            346799999999999999999999999999999987667789999999999999999999999988 46899999985

>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=99.58  E-value=1.2e-15  Score=129.16  Aligned_cols=72  Identities=22%  Similarity=0.442  Sum_probs=68.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      +|||+|||+++++++|+++|++||.|.+++    .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+++.
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            699999999999999999999999999998    368899999999999999999999999999999999999874

>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=99.57  E-value=1.6e-15  Score=129.82  Aligned_cols=72  Identities=22%  Similarity=0.447  Sum_probs=67.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      .++++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|+++|+|..|.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4568999999999999999999999999999887     35889999999999999999999999999999999876

>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=99.57  E-value=2.3e-15  Score=131.26  Aligned_cols=78  Identities=14%  Similarity=0.325  Sum_probs=70.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||+++|+++|+++|++||+|.+|+     .++++||||||+|.+.++|++||+.  ...|.|+.|.|+++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            3568999999999999999999999999999987     3689999999999999999999995  44789999999999


Q ss_pred             CCCCC
Q 004002          265 IPKDN  269 (780)
Q Consensus       265 ~pk~~  269 (780)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87653

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.4e-15  Score=130.14  Aligned_cols=76  Identities=29%  Similarity=0.442  Sum_probs=70.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-eCCCcceEEEEEEecHHHHHHHHHHccCccc-cccccccccCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPL-RRRKLDIHFSIP  266 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l-~gr~I~V~~a~p  266 (780)
                      |+++|||+|||.++|+++|+++|++||.|..++ ..++.+|||||+|.+.++|.+|+..|+|..| .|++|+|.|+++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            678999999999999999999999999998765 5677899999999999999999999999988 589999999875

>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=99.57  E-value=1.7e-15  Score=130.16  Aligned_cols=74  Identities=24%  Similarity=0.397  Sum_probs=67.6

Q ss_pred             eeecCCCCCCChhHHHHHhcccCCeeEEEeC-----C---CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----P---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       280 L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~-----g---~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      |||+|||.++|+++|+++|++||.|++|++.     +   .++|||||+|.+.++|++|++.|||..+.|+.|+|+++++
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            7999999999999999999999999998751     1   3579999999999999999999999999999999999976


Q ss_pred             Cc
Q 004002          352 GG  353 (780)
Q Consensus       352 k~  353 (780)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.57  E-value=3.3e-15  Score=133.31  Aligned_cols=79  Identities=24%  Similarity=0.386  Sum_probs=71.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.+++ .|.|++|.|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3457899999999999999999999999999998     3578999999999999999999998875 799999999998


Q ss_pred             CCCCC
Q 004002          265 IPKDN  269 (780)
Q Consensus       265 ~pk~~  269 (780)
                      .++..
T Consensus        87 ~~~~~   91 (103)
T d2cqda1          87 YLGAK   91 (103)
T ss_dssp             TTTCC
T ss_pred             CCCCC
Confidence            76544

>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=99.56  E-value=2e-15  Score=134.63  Aligned_cols=78  Identities=23%  Similarity=0.391  Sum_probs=72.3

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++++++|+++|++||+|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999875     566789999999999999999999999999999999999987


Q ss_pred             Cch
Q 004002          352 GGA  354 (780)
Q Consensus       352 k~~  354 (780)
                      +..
T Consensus        88 ~~~   90 (104)
T d1p1ta_          88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            653

>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=99.56  E-value=1.8e-15  Score=136.13  Aligned_cols=77  Identities=13%  Similarity=0.268  Sum_probs=71.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      +.+++|||+|||+++++++|+++|++||+|..|.+ .+.+|||||+|.+.++|++|++.|||..|.|++|.|.|+...
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            35589999999999999999999999999999975 578999999999999999999999999999999999998654

>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=99.56  E-value=1.5e-15  Score=129.84  Aligned_cols=75  Identities=23%  Similarity=0.401  Sum_probs=68.6

Q ss_pred             eeecCCCCCCChhHHHHHhcccCCeeEE-Ee-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-RE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       280 L~V~NLp~~vteedL~~~Fs~yG~I~~v-~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      |||+|||.++|+++|+++|++||.|..+ ++     +++++|||||+|.+.++|++||+.|||..+.|++|+|.++.++.
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            7999999999999999999999998654 33     56778999999999999999999999999999999999999875


Q ss_pred             h
Q 004002          354 A  354 (780)
Q Consensus       354 ~  354 (780)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.56  E-value=3.1e-15  Score=133.50  Aligned_cols=80  Identities=28%  Similarity=0.358  Sum_probs=71.9

Q ss_pred             CCCCccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       273 ~~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ++...++|||+|||..+++++|+++|++||.|++|++     ++.++|||||+|.+.++|++||+.+|+ .+.|++|+|+
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            4445568999999999999999999999999999986     467899999999999999999999886 7999999999


Q ss_pred             ecCCCc
Q 004002          348 PSRPGG  353 (780)
Q Consensus       348 ~a~~k~  353 (780)
                      ++..+.
T Consensus        85 ~a~~~~   90 (103)
T d2cqda1          85 LAYLGA   90 (103)
T ss_dssp             ESTTTC
T ss_pred             EcCCCC
Confidence            998654

>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=99.56  E-value=2.9e-15  Score=132.05  Aligned_cols=76  Identities=24%  Similarity=0.389  Sum_probs=71.2

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..+|||+|||.++++++|+++|++||.|++|++.. .+|||||+|++.++|++||..|||..|.|+.|+|.|++++.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~-~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe-cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            46899999999999999999999999999999864 48999999999999999999999999999999999998754

>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=99.56  E-value=8.4e-16  Score=131.49  Aligned_cols=75  Identities=20%  Similarity=0.481  Sum_probs=68.6

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcCCCEEEE-E-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          195 LFVRNINSNVEDSELRALFEQYGDIRTL-Y-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       195 LfVgNLp~~vteeeLr~lF~~yG~I~sv-~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      |||+|||+++|+++|+++|++||.|..+ +     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.+++
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            7999999999999999999999998553 2     357899999999999999999999999999999999999998765


Q ss_pred             C
Q 004002          269 N  269 (780)
Q Consensus       269 ~  269 (780)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.56  E-value=3.8e-15  Score=127.41  Aligned_cols=71  Identities=28%  Similarity=0.518  Sum_probs=66.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEE
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  346 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V  346 (780)
                      ..++|||+|||.++|+++|+++|++||.|++|++     +++++|||||+|.+.++|++|++.|||..+.|++|+|
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            4578999999999999999999999999999875     4677899999999999999999999999999999987

>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=99.56  E-value=1.1e-15  Score=136.06  Aligned_cols=77  Identities=21%  Similarity=0.440  Sum_probs=70.4

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|+.||+|++|++     +++++|||||+|.+.++|++|+. |||..+.|+.|+|.+++
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            4468999999999999999999999999999976     57789999999999999999995 99999999999999986


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      ++.
T Consensus        96 ~~~   98 (101)
T d2cq4a1          96 AEK   98 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>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=99.56  E-value=5.2e-15  Score=129.93  Aligned_cols=77  Identities=31%  Similarity=0.508  Sum_probs=71.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~--~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..++|||+|||.++|+++|+++|++||.|+.+++  +...++||||+|.+.++|++||+.|||+.+.|++|+|+++++.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            3457999999999999999999999999999876  4567899999999999999999999999999999999999875

>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=99.55  E-value=2.5e-15  Score=129.64  Aligned_cols=76  Identities=22%  Similarity=0.390  Sum_probs=67.4

Q ss_pred             CccceeecCCCCCCCh-hHHHHHhcccCCeeEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 004002          276 NQGTLVVFNLDPSVSN-EDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (780)
Q Consensus       276 ~~~~L~V~NLp~~vte-edL~~~Fs~yG~I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~  348 (780)
                      ..++|||+|||.++++ ++|+++|++||.|+.|++      +++++|||||+|.+.++|++||+ |||..+.|+.|+|++
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            3568999999999865 569999999999999975      45678999999999999999995 999999999999999


Q ss_pred             cCCC
Q 004002          349 SRPG  352 (780)
Q Consensus       349 a~~k  352 (780)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=99.55  E-value=4e-15  Score=131.71  Aligned_cols=75  Identities=21%  Similarity=0.363  Sum_probs=68.6

Q ss_pred             CccceeecCCC-CCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLD-PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp-~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ...+|||+||| ..+++++|+++|++||.|+.|++   ++|||||+|++.++|++||+.|||+.+.|++|+|++++++.
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            34679999997 56788999999999999999998   48999999999999999999999999999999999997653

>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=99.55  E-value=2.3e-15  Score=133.27  Aligned_cols=82  Identities=22%  Similarity=0.364  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE--------E-----eCCCcceEEEEEEecHHHHHHHHHHccCccc
Q 004002          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL--------Y-----TACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (780)
Q Consensus       188 ~e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv--------~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l  254 (780)
                      .+...++|||+|||.++|+++|+++|++||.|..+        .     .+++++|||||+|.+.++|++|++.|+|..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            34467899999999999999999999999988543        2     2478899999999999999999999999999


Q ss_pred             cccccccccCCCCCC
Q 004002          255 RRRKLDIHFSIPKDN  269 (780)
Q Consensus       255 ~gr~I~V~~a~pk~~  269 (780)
                      .|++|+|+++.++..
T Consensus        84 ~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          84 QGSKLKVSLARKKPP   98 (101)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCEEEEEEEcCCCCC
Confidence            999999999987543

>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=99.55  E-value=1.8e-15  Score=130.63  Aligned_cols=76  Identities=18%  Similarity=0.396  Sum_probs=67.4

Q ss_pred             CCcEEEEeCCCCCCC-HHHHHHHhhcCCCEEEEE------eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          191 PSRTLFVRNINSNVE-DSELRALFEQYGDIRTLY------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       191 ~s~tLfVgNLp~~vt-eeeLr~lF~~yG~I~sv~------~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      ..++|||+|||+++| +++|+++|++||+|.+|+      .+++++|||||+|.+.++|++|++ |++..|.|++|.|.+
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            458999999999986 566999999999999997      257889999999999999999996 999999999999999


Q ss_pred             CCCC
Q 004002          264 SIPK  267 (780)
Q Consensus       264 a~pk  267 (780)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>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=99.55  E-value=1.9e-15  Score=131.68  Aligned_cols=79  Identities=23%  Similarity=0.593  Sum_probs=71.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHH----HhhcCCCEEEEEe--CCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRA----LFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~----lF~~yG~I~sv~~--tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      +|+++|||+|||++++++||++    +|++||+|.+|+.  +++++|||||+|.+.++|.+|++.|+|..+.|++|.|.|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3679999999999999999864    6899999999983  467899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 004002          264 SIPKD  268 (780)
Q Consensus       264 a~pk~  268 (780)
                      +.++.
T Consensus        81 ak~~~   85 (91)
T d1nu4a_          81 AKTDS   85 (91)
T ss_dssp             CSSCC
T ss_pred             eCCCc
Confidence            98654

>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=99.55  E-value=1.2e-15  Score=132.22  Aligned_cols=79  Identities=24%  Similarity=0.459  Sum_probs=73.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~~  269 (780)
                      ..+++|||+|||+++|+++|+++|++||+|.+|+...+++|||||+|.+.++|++|+.  ++..|.|++|.|.++.++..
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            4578999999999999999999999999999999888899999999999999999996  78899999999999987664


Q ss_pred             C
Q 004002          270 P  270 (780)
Q Consensus       270 ~  270 (780)
                      .
T Consensus        81 ~   81 (88)
T d1wf0a_          81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.55  E-value=9.7e-16  Score=136.04  Aligned_cols=81  Identities=21%  Similarity=0.397  Sum_probs=74.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .++++|||+|||.++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.|+|..|.|++|.|.|+
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            4678999999999999999999999999876653     46899999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 004002          265 IPKDNP  270 (780)
Q Consensus       265 ~pk~~~  270 (780)
                      .+++.+
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            887643

>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=99.55  E-value=4.3e-15  Score=127.92  Aligned_cols=76  Identities=26%  Similarity=0.269  Sum_probs=71.0

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      .++|||+|||.++++++|+++|++||.|..+++ +.++|||||+|.++++|.+|+..|||..+.|++|+|.+++|+.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            468999999999999999999999999988776 4578999999999999999999999999999999999999875

>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=99.55  E-value=9.7e-16  Score=130.53  Aligned_cols=76  Identities=28%  Similarity=0.367  Sum_probs=69.5

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC-ccCCceEEEEecCCCchh
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-DIAGKRIKLEPSRPGGAR  355 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~-~i~Gr~L~V~~a~~k~~r  355 (780)
                      +|||+|||.++|+++|+++|++||.|..+++. .++|||||+|.+.++|++|++.|||. .+.|++|+|+++.++.++
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~-~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe-cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            69999999999999999999999999876653 46899999999999999999999996 699999999999997654

>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=99.55  E-value=6.9e-16  Score=131.49  Aligned_cols=77  Identities=22%  Similarity=0.359  Sum_probs=69.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCc-cccccccccccCCCCCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK-PLRRRKLDIHFSIPKDNP  270 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~-~l~gr~I~V~~a~pk~~~  270 (780)
                      .+|||+|||.++|+++|+++|++||.|.+++ ..+.+|||||+|.+.++|++|++.|+|. .+.|++|+|+|+.|+..+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~-~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ-VLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSC-EEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeE-EecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            4799999999999999999999999987654 3467899999999999999999999996 599999999999987643

>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=99.55  E-value=4e-15  Score=130.83  Aligned_cols=82  Identities=21%  Similarity=0.336  Sum_probs=71.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCC-EEEEEe------CCCcceEEEEEEecHHHHHHHHHHccC--ccccccccccc
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGD-IRTLYT------ACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIH  262 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~-I~sv~~------tgkskG~aFV~F~~~e~A~~Al~~Lng--~~l~gr~I~V~  262 (780)
                      +++|||+|||.++|+++|+++|++||+ |..++.      +++++|||||+|.+.++|.+|++.|++  ..+.|++|.|.
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            378999999999999999999999996 888872      478999999999999999999999965  45579999999


Q ss_pred             cCCCCCCCCCC
Q 004002          263 FSIPKDNPSDK  273 (780)
Q Consensus       263 ~a~pk~~~s~~  273 (780)
                      ||.|+..+.++
T Consensus        81 ~A~p~~~~~~~   91 (96)
T d2disa1          81 WAEPEIDVDED   91 (96)
T ss_dssp             ESCSSCSTTTC
T ss_pred             EcCCCCCCChH
Confidence            99987766543

>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=99.55  E-value=3.8e-15  Score=128.58  Aligned_cols=76  Identities=25%  Similarity=0.425  Sum_probs=71.0

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..+|||+|||.++++++|+++|++||.|.+|++. +.++||||+|++.++|++|++.|||..+.|++|+|++|.++.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~-~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeee-cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3579999999999999999999999999999985 457999999999999999999999999999999999998764

>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=99.55  E-value=4.3e-15  Score=133.25  Aligned_cols=76  Identities=29%  Similarity=0.522  Sum_probs=70.7

Q ss_pred             ccceeecCCCC-CCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 004002          277 QGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       277 ~~~L~V~NLp~-~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k  352 (780)
                      ..+|||+|||+ .+|+++|+++|++||.|+.|++...++|+|||+|+++++|++||+.|||..+.|+.|+|++++..
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~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            35899999965 59999999999999999999988778999999999999999999999999999999999998754

>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=99.54  E-value=6.5e-15  Score=127.33  Aligned_cols=77  Identities=29%  Similarity=0.371  Sum_probs=69.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEE-eCCCcccEEEEEEcCHHHHHHHHHHhCCCcc-CCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI-AGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i-~Gr~L~V~~a~~k  352 (780)
                      +.++|||+|||.++++++|+++|++||.|..++ ..++.+++|||+|.+.++|.+|+..|||..+ +|+.|+|+++++.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            356899999999999999999999999998765 4667789999999999999999999999988 5899999999864

>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=99.54  E-value=7.7e-15  Score=131.59  Aligned_cols=77  Identities=25%  Similarity=0.380  Sum_probs=70.9

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          192 SRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       192 s~tLfVgNLp~-~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      +++|||+|||+ .+|+++|+++|++||+|..|++....+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+....
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~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            57999999965 599999999999999999999766679999999999999999999999999999999999986543

>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=99.54  E-value=4.5e-15  Score=133.48  Aligned_cols=77  Identities=18%  Similarity=0.282  Sum_probs=71.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++||+|+.|.+ +..+|||||+|.+.++|++||+.|||..|.|++|+|+++....
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            3468999999999999999999999999999998 4678999999999999999999999999999999999986543

>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=99.54  E-value=5.5e-15  Score=130.26  Aligned_cols=77  Identities=14%  Similarity=0.325  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ..++|||+|||.++++++|+++|++||+|.+|+. .+.||||||+|.+.++|++|++.|+|..|.|++|+|.|++++.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i-~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEE-EecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            3579999999999999999999999999999985 3569999999999999999999999999999999999997643

>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=99.54  E-value=3.3e-15  Score=133.50  Aligned_cols=77  Identities=17%  Similarity=0.306  Sum_probs=71.1

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .++|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++||+ ++|..|.|+.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            368999999999999999999999999999976     45789999999999999999996 799999999999999998


Q ss_pred             Cch
Q 004002          352 GGA  354 (780)
Q Consensus       352 k~~  354 (780)
                      +.+
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.54  E-value=5.9e-15  Score=124.02  Aligned_cols=70  Identities=14%  Similarity=0.389  Sum_probs=65.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +|||+|||+++|+++|+++|++||+|..++     .+++++|||||+|.+.++|++|++ +++..|.|+.|.|+.|
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            589999999999999999999999999998     368899999999999999999998 7999999999999754

>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=99.54  E-value=4.4e-15  Score=126.04  Aligned_cols=74  Identities=22%  Similarity=0.424  Sum_probs=68.7

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      .++|||+|++  +|+++|+++|++||.|.+|++. +.++||||+|.+.++|.+|++.|||..+.|++|+|.+++++.
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~-~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeec-cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            4689999996  9999999999999999999985 567999999999999999999999999999999999998753

>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=99.54  E-value=4.5e-15  Score=131.31  Aligned_cols=81  Identities=26%  Similarity=0.383  Sum_probs=71.8

Q ss_pred             CCCccceeecCCCCCCChhHHHHHhcccCCeeEEE-------------eCCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 004002          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-------------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (780)
Q Consensus       274 ~~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-------------~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~  340 (780)
                      +....+|||+|||..+|+++|+++|+.||.|..+.             .+++++|||||+|.++++|++||+.|||..+.
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            34567999999999999999999999999986432             14677899999999999999999999999999


Q ss_pred             CceEEEEecCCCch
Q 004002          341 GKRIKLEPSRPGGA  354 (780)
Q Consensus       341 Gr~L~V~~a~~k~~  354 (780)
                      |++|+|++++++..
T Consensus        85 gr~i~V~~a~~~~p   98 (101)
T d2cpea1          85 GSKLKVSLARKKPP   98 (101)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CEEEEEEEcCCCCC
Confidence            99999999998654

>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=99.53  E-value=7.4e-15  Score=127.94  Aligned_cols=77  Identities=21%  Similarity=0.391  Sum_probs=69.6

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|++||+.  ...++|+.|.|+++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            3468999999999999999999999999999975     578899999999999999999985  458999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8653

>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=99.53  E-value=6.6e-15  Score=126.51  Aligned_cols=74  Identities=23%  Similarity=0.450  Sum_probs=68.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++|+++|+++|++||+|..++     .+++++|||||+|.+.++|++|++ +++..|.|+.|+|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            347999999999999999999999999999987     368899999999999999999998 69999999999998774

>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=99.53  E-value=5.7e-15  Score=131.19  Aligned_cols=77  Identities=21%  Similarity=0.278  Sum_probs=70.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ..++|||+|||.++++++|+++|++||.|+.+++    ++.++|||||+|.+.++|++||+.|||+.|.|+++.|.+++|
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            3468999999999999999999999999988864    556789999999999999999999999999999999988876


Q ss_pred             C
Q 004002          352 G  352 (780)
Q Consensus       352 k  352 (780)
                      -
T Consensus        97 l   97 (101)
T d1x5oa1          97 L   97 (101)
T ss_dssp             B
T ss_pred             c
Confidence            3

>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=99.53  E-value=5.2e-15  Score=127.73  Aligned_cols=76  Identities=32%  Similarity=0.564  Sum_probs=70.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      .++|||+|||.++++++|+++|++||+|.+|+. .+.+|||||+|.+.++|++|++.|+|..|.|++|+|+||.++.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~-~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE-ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeee-ecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            468999999999999999999999999999985 3578999999999999999999999999999999999998654

>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=99.53  E-value=2.6e-15  Score=130.15  Aligned_cols=77  Identities=19%  Similarity=0.333  Sum_probs=71.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCch
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~  354 (780)
                      ..++|||+|||.++|+++|+++|++||.|.+|++...+++||||+|++.++|++||.  ++..|.|++|+|++++++..
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            356899999999999999999999999999999988899999999999999999995  88899999999999987653

>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=99.53  E-value=1.4e-14  Score=127.27  Aligned_cols=78  Identities=22%  Similarity=0.391  Sum_probs=70.7

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhC------CCccCCceEE
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN------RSDIAGKRIK  345 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~Ln------G~~i~Gr~L~  345 (780)
                      .++|||+|||.++|+++|+++|++||.|.++++     ++.++|||||+|.+.++|.+||+.||      |..+.|++|+
T Consensus         8 ~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~   87 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLK   87 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEE
Confidence            468999999999999999999999999999875     45678999999999999999999987      6678999999


Q ss_pred             EEecCCCch
Q 004002          346 LEPSRPGGA  354 (780)
Q Consensus       346 V~~a~~k~~  354 (780)
                      |.++.++.+
T Consensus        88 v~~a~~k~~   96 (98)
T d1x4ha1          88 VDLAVTRDE   96 (98)
T ss_dssp             EECCCCCCC
T ss_pred             EEECCCCCc
Confidence            999988753

>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=99.53  E-value=3.8e-15  Score=133.06  Aligned_cols=77  Identities=18%  Similarity=0.436  Sum_probs=71.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-----tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      .++|||+|||+++|+++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ +++..|.|++|.|+++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            379999999999999999999999999999873     57899999999999999999997 799999999999999988


Q ss_pred             CCC
Q 004002          267 KDN  269 (780)
Q Consensus       267 k~~  269 (780)
                      ++.
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.53  E-value=7.4e-15  Score=124.21  Aligned_cols=72  Identities=24%  Similarity=0.482  Sum_probs=66.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      .++|||+|||+++|+++|+++|++||.|..++     .+++++|||||+|.+.++|++|++ ++|..|.|++|.|+.|
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            37999999999999999999999999999887     367899999999999999999996 8999999999999876

>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=99.52  E-value=2.1e-15  Score=127.58  Aligned_cols=71  Identities=17%  Similarity=0.422  Sum_probs=66.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      |+|||+|||+++|+++|+++|++||+|.+++     .++++||||||+|.+.++|++|++ +++..|.|++|.|+.|
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            6899999999999999999999999998876     368899999999999999999998 7999999999999875

>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=99.52  E-value=1.4e-14  Score=124.38  Aligned_cols=73  Identities=19%  Similarity=0.340  Sum_probs=67.9

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      .++|||+|||.++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|++||+ +++..|.|++|+|+.|.
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            468999999999999999999999999999875     57889999999999999999997 69999999999998875

>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=99.52  E-value=1e-14  Score=122.51  Aligned_cols=70  Identities=20%  Similarity=0.371  Sum_probs=64.9

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .|||+|||.++|+++|+++|++||.|..|++     +++++|||||+|.+.++|++||+ +++..+.|+.|.|+.|
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            4899999999999999999999999999975     56789999999999999999997 7999999999999754

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=1.5e-14  Score=121.66  Aligned_cols=72  Identities=15%  Similarity=0.335  Sum_probs=65.9

Q ss_pred             eeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       280 L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      |||+|||.++++++|+++|++|| ++.+++ ++++|+|||+|.+.++|++|++.|||..+.|++|+|++++...
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 555555 4678999999999999999999999999999999999997653

>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=99.52  E-value=7.2e-15  Score=127.98  Aligned_cols=79  Identities=22%  Similarity=0.432  Sum_probs=71.2

Q ss_pred             ccceeecCCCCCCChhHHHH----HhcccCCeeEEEeC--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~----~Fs~yG~I~~v~~~--g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      .++|||+|||.+++++||++    +|++||+|.+|++.  ++++|||||+|.+.++|.+|++.|||..+.|+.|+|.+|+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak   82 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   82 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            46899999999999999864    68999999999873  4568999999999999999999999999999999999999


Q ss_pred             CCchh
Q 004002          351 PGGAR  355 (780)
Q Consensus       351 ~k~~r  355 (780)
                      ++.+.
T Consensus        83 ~~~~~   87 (91)
T d1nu4a_          83 TDSDI   87 (91)
T ss_dssp             SCCTH
T ss_pred             CCchh
Confidence            87654

>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=99.52  E-value=2e-15  Score=134.46  Aligned_cols=75  Identities=17%  Similarity=0.390  Sum_probs=69.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++|+++|+++|+.||+|.+|+     .+++++|||||+|.+.++|++|++ |+|..|.|++|.|+++.
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            457999999999999999999999999999987     368899999999999999999996 99999999999999875


Q ss_pred             C
Q 004002          266 P  266 (780)
Q Consensus       266 p  266 (780)
                      +
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.51  E-value=1.2e-14  Score=128.46  Aligned_cols=76  Identities=28%  Similarity=0.520  Sum_probs=69.1

Q ss_pred             CCCcEEEEeCCC-CCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          190 HPSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       190 ~~s~tLfVgNLp-~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ...++|||+||| ..+++++|+++|++||+|.+|++   +||||||+|.+.++|++|++.|+|+.|.|++|+|.|+.++.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            345789999997 57889999999999999999986   68999999999999999999999999999999999997643

>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=99.51  E-value=6.7e-15  Score=127.58  Aligned_cols=75  Identities=13%  Similarity=0.290  Sum_probs=66.6

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ..+|||+|||.+++++||+++|++|| ++.+.+ +..++||||+|.+.++|++||+.|||..+.|++|+|++++++.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            46899999999999999999999999 333333 4568999999999999999999999999999999999997654

>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=99.51  E-value=7.3e-15  Score=124.66  Aligned_cols=75  Identities=20%  Similarity=0.366  Sum_probs=69.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      ...++|||+||+  +|+++|+++|++||+|.+++. .+.+|||||+|.+.++|.+|+++|+|..+.|++|+|.|++++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~-~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeee-ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            346899999985  999999999999999999975 567899999999999999999999999999999999999765

>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=99.51  E-value=1.1e-14  Score=130.90  Aligned_cols=80  Identities=21%  Similarity=0.282  Sum_probs=71.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEe-CCCcceEEEEEEecHHHHHHHHHHccCccc--cccccccccCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIP  266 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~-tgkskG~aFV~F~~~e~A~~Al~~Lng~~l--~gr~I~V~~a~p  266 (780)
                      .+..+|||+|||+++|+++|+++|++||+|.+|+. ..+.+|||||+|.+.++|++|++.|+|..|  .+++|+|.|+.+
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~   84 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL   84 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSS
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCC
Confidence            45688999999999999999999999999999873 346789999999999999999999999998  578899999877


Q ss_pred             CCC
Q 004002          267 KDN  269 (780)
Q Consensus       267 k~~  269 (780)
                      +..
T Consensus        85 ~~~   87 (108)
T d2adba1          85 TSL   87 (108)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            553

>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=99.51  E-value=4.9e-15  Score=131.38  Aligned_cols=80  Identities=29%  Similarity=0.343  Sum_probs=73.2

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++||+.|||..+.|++|+|++++
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            4568999999999999999999999999877643     67889999999999999999999999999999999999999


Q ss_pred             CCchh
Q 004002          351 PGGAR  355 (780)
Q Consensus       351 ~k~~r  355 (780)
                      ++.++
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            87654

>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=99.51  E-value=6.2e-15  Score=124.71  Aligned_cols=71  Identities=28%  Similarity=0.443  Sum_probs=66.1

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ++|||+|||.++|+++|+++|++||.|+++++     ++++||||||+|.+.++|++||+ +|++.++|+.|+|+.|
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            36999999999999999999999999998875     57789999999999999999997 7999999999999876

>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=99.50  E-value=1.9e-14  Score=121.60  Aligned_cols=71  Identities=18%  Similarity=0.359  Sum_probs=65.8

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ++|||+|||.++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++ |||+.|.|+.|+|+.|
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            58999999999999999999999999999875     56678999999999999999995 8999999999999876

>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=99.50  E-value=3.3e-15  Score=130.40  Aligned_cols=76  Identities=24%  Similarity=0.335  Sum_probs=69.6

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ...+|||+|||.++|+++|+++|++||.|..+++    +++++|||||+|.+.++|++||+ |||..+.|++|+|++|+.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            4568999999999999999999999999877654    67889999999999999999996 999999999999999986


Q ss_pred             C
Q 004002          352 G  352 (780)
Q Consensus       352 k  352 (780)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.50  E-value=2.4e-14  Score=127.43  Aligned_cols=79  Identities=16%  Similarity=0.389  Sum_probs=69.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE------eCCCcceEEEEEEecHHHHHHHHHHccCcccccccccccc
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~------~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~  263 (780)
                      .+.++|||+|||+++|+++|+++|++|| |..++      .+++++|||||+|.+.++|++|++ |++..|.|++|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4668999999999999999999999999 55555      357789999999999999987775 999999999999999


Q ss_pred             CCCCCCC
Q 004002          264 SIPKDNP  270 (780)
Q Consensus       264 a~pk~~~  270 (780)
                      +.++...
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.50  E-value=2.1e-15  Score=131.62  Aligned_cols=77  Identities=16%  Similarity=0.216  Sum_probs=69.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...++|||+|||+++|+++|+++|++||.|..++    .+++++|||||+|.+.++|++||+ |+|..|.|++|.|.++.
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            3557999999999999999999999999876654    468999999999999999999996 99999999999999987


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      .+
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>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=99.50  E-value=1.4e-14  Score=121.15  Aligned_cols=70  Identities=20%  Similarity=0.340  Sum_probs=65.1

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .|||+|||.++|+++|+++|++||.|..+.+     ++.++++|||+|.+.++|++|++ |||+.+.|++|+|.+|
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            4899999999999999999999999999864     56778999999999999999996 9999999999999876

>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=99.50  E-value=8.5e-15  Score=122.40  Aligned_cols=70  Identities=17%  Similarity=0.419  Sum_probs=65.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +|||+|||+++|+++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++ ++|..|.|++|.|++|
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            599999999999999999999999999886     357899999999999999999997 9999999999999875

>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=99.49  E-value=7.1e-15  Score=127.41  Aligned_cols=76  Identities=14%  Similarity=0.309  Sum_probs=67.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      .+++|||+|||++++++||+++|++||. ..+. .++++|||||+|.+.++|++|++.|++..|.|++|.|+|+.++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~-~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCY-VDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEE-EEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeee-eeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4689999999999999999999999992 2232 36789999999999999999999999999999999999986543

>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=99.49  E-value=9.1e-15  Score=123.10  Aligned_cols=70  Identities=19%  Similarity=0.476  Sum_probs=64.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++||+ +++..|.|+.|.|+.|
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            699999999999999999999999999998     368899999999999999999997 5788899999998764

>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=99.49  E-value=3.3e-14  Score=125.28  Aligned_cols=77  Identities=22%  Similarity=0.409  Sum_probs=70.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~k~  353 (780)
                      ..++|||+|||.++++++|+++|++||.|+.|++. +.+++|||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~-~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeee-ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            45789999999999999999999999999999985 457899999999999999999999999987  589999998764

>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=99.49  E-value=3.2e-14  Score=125.30  Aligned_cols=78  Identities=28%  Similarity=0.505  Sum_probs=70.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccc--cccccccCCCC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPK  267 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~g--r~I~V~~a~pk  267 (780)
                      .++++|||+|||+++++++|+++|++||+|..++. .+.++||||+|.+.++|++|++.|++..|.|  ++|+|.|+++.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~-~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEE-CSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEee-eccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            46799999999999999999999999999999985 4568999999999999999999999999976  57999998764


Q ss_pred             C
Q 004002          268 D  268 (780)
Q Consensus       268 ~  268 (780)
                      .
T Consensus        94 ~   94 (97)
T d1whya_          94 P   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.49  E-value=2.7e-14  Score=126.23  Aligned_cols=78  Identities=14%  Similarity=0.223  Sum_probs=71.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      ....++|||+|||+++++++|+++|++||+|..++.  ..+|||||+|.+.++|++||+.|||..|.|+.|+|.++.++.
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i--~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV--QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEE--ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccc--cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            345689999999999999999999999999999875  357999999999999999999999999999999999987654

>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=99.49  E-value=1.8e-14  Score=121.08  Aligned_cols=71  Identities=18%  Similarity=0.450  Sum_probs=65.1

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCC
Q 004002          195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (780)
Q Consensus       195 LfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk  267 (780)
                      |||+|||+++++++|+++|++|| +..++ .++.+|||||+|.+.++|++|++.|||..+.|++|.|+|+...
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-LKYCF-VDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE-EETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee-ecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 55554 4778999999999999999999999999999999999998643

>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=99.48  E-value=1.8e-14  Score=124.47  Aligned_cols=73  Identities=15%  Similarity=0.182  Sum_probs=67.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCCCCC
Q 004002          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (780)
Q Consensus       194 tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~pk~  268 (780)
                      +|||+|||+++|+++|+++|++||+|..++..  .+|||||+|.+.++|++||+.|+|..|.|+.|.|.++.++.
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 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            69999999999999999999999999999753  45999999999999999999999999999999999876543

>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=99.48  E-value=2.5e-14  Score=123.08  Aligned_cols=73  Identities=12%  Similarity=0.345  Sum_probs=67.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ..++|||+|||.++|+++|+++|+.||.|..|+    .+++++|||||+|.+.++|++|++ +++..+.|+.|.|.|.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            358999999999999999999999999999987    357899999999999999999997 7999999999999875

>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=99.48  E-value=1.2e-14  Score=125.52  Aligned_cols=73  Identities=21%  Similarity=0.187  Sum_probs=67.5

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      +|||+|||.++++++|+++|++||.|+.+++.  ++|||||+|.+.++|++||+.|||..+.|+.|+|.+++++.
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 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            59999999999999999999999999999984  35999999999999999999999999999999998876543

>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=99.48  E-value=5.4e-14  Score=121.52  Aligned_cols=79  Identities=24%  Similarity=0.346  Sum_probs=70.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHc--cCccccccccccccCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~L--ng~~l~gr~I~V~~a~p  266 (780)
                      ..|+++|||+|||.++++++|+++|++||.|.+++. .+.+|||||+|.+.++|++|++.+  ++..+.|++|+|.|+..
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~-~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccc-cccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            458899999999999999999999999999999974 467899999999999999999976  45689999999999976


Q ss_pred             CC
Q 004002          267 KD  268 (780)
Q Consensus       267 k~  268 (780)
                      +.
T Consensus        84 ~~   85 (88)
T d2cq1a1          84 KE   85 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.47  E-value=2.1e-14  Score=119.35  Aligned_cols=66  Identities=24%  Similarity=0.447  Sum_probs=62.3

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccc
Q 004002          195 LFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (780)
Q Consensus       195 LfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~  260 (780)
                      |||+|||+++|+++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.|+|..|.|+.|+
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            79999999999999999999999999987     3678999999999999999999999999999999875

>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=99.46  E-value=3e-14  Score=127.95  Aligned_cols=78  Identities=26%  Similarity=0.317  Sum_probs=69.6

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCcc--CCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDI--AGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i--~Gr~L~V~~a~~k  352 (780)
                      ...+|||+|||.++|+++|+++|++||.|+.|++ ..+++|+|||+|.++++|++||+.|||..|  .|++|+|.+++++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            3467999999999999999999999999999876 334689999999999999999999999988  5789999999875


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        86 ~   86 (108)
T d2adba1          86 S   86 (108)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.46  E-value=1.9e-14  Score=121.13  Aligned_cols=70  Identities=23%  Similarity=0.453  Sum_probs=64.5

Q ss_pred             ceeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       279 ~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      +|||+|||.++|+++|+++|++||.|+.|++     +++++|||||+|.+.++|++||+ +++..+.|+.|.|+.|
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            4899999999999999999999999999975     56789999999999999999997 5788999999999865

>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=99.46  E-value=3.7e-14  Score=123.05  Aligned_cols=72  Identities=14%  Similarity=0.385  Sum_probs=63.9

Q ss_pred             CccceeecCCCCCCChhHH---HHHhcccCCeeEEEeC-----C---CcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 004002          276 NQGTLVVFNLDPSVSNEDL---RQIFGAYGEVKEIRET-----P---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL---~~~Fs~yG~I~~v~~~-----g---~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L  344 (780)
                      ...+|||+|||+++++++|   +++|++||.|+.|++.     +   ..+|||||+|.+.++|++||+.|||..+.|+.|
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            3457999999999999999   7789999999999762     2   234899999999999999999999999999999


Q ss_pred             EEE
Q 004002          345 KLE  347 (780)
Q Consensus       345 ~V~  347 (780)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.46  E-value=3.7e-14  Score=122.00  Aligned_cols=74  Identities=9%  Similarity=0.166  Sum_probs=67.9

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ..++|||+|||.++|+++|+++|+.||.|+.|++    ++.++|||||+|.+.++|++||+ ++|..+.|+.|.|.+++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999976    46678999999999999999996 79999999999998864

>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=99.46  E-value=4.9e-14  Score=123.80  Aligned_cols=78  Identities=19%  Similarity=0.229  Sum_probs=68.9

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCC-eeEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCC--ccCCceEEEEe
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEP  348 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~-I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~LnG~--~i~Gr~L~V~~  348 (780)
                      +.|||+|||.++++++|+++|++||+ |+.+++      +++++|||||+|.++++|.+|++.|++.  .+.|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            46999999999999999999999996 888876      3567899999999999999999999754  55799999999


Q ss_pred             cCCCchh
Q 004002          349 SRPGGAR  355 (780)
Q Consensus       349 a~~k~~r  355 (780)
                      |+|+.+.
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9987643

>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=99.45  E-value=1.9e-13  Score=121.90  Aligned_cols=79  Identities=15%  Similarity=0.253  Sum_probs=70.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHcc--CccccccccccccCCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLDIHFSIP  266 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Ln--g~~l~gr~I~V~~a~p  266 (780)
                      ..++++|||+|||.++|+++|+++|++||.|..++. .+.||+|||+|.+.++|++|++.|+  +..+.|++|+|.|+..
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~-~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEE-EecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            347899999999999999999999999999999975 5689999999999999999999885  4567899999999976


Q ss_pred             CC
Q 004002          267 KD  268 (780)
Q Consensus       267 k~  268 (780)
                      ++
T Consensus        91 ~~   92 (104)
T d1wexa_          91 KR   92 (104)
T ss_dssp             SS
T ss_pred             Cc
Confidence            54

>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=99.45  E-value=1.8e-14  Score=119.67  Aligned_cols=66  Identities=24%  Similarity=0.439  Sum_probs=61.6

Q ss_pred             eeecCCCCCCChhHHHHHhcccCCeeEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 004002          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (780)
Q Consensus       280 L~V~NLp~~vteedL~~~Fs~yG~I~~v~~-----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~  345 (780)
                      |||+|||.++|+++|+++|++||.|..+++     ++.++|+|||+|.+.++|++|++.|||+.+.|+.|+
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            799999999999999999999999999875     566889999999999999999999999999998764

>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=99.45  E-value=9.8e-14  Score=123.43  Aligned_cols=77  Identities=23%  Similarity=0.364  Sum_probs=67.3

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~------~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...+|||+|||.++|+++|+++|++|| |+++++      ++.++|||||+|.+.++|++|+ .||+..|.|++|+|.++
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            347899999999999999999999999 666653      4567899999999999998777 59999999999999999


Q ss_pred             CCCch
Q 004002          350 RPGGA  354 (780)
Q Consensus       350 ~~k~~  354 (780)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T d1wi8a_          92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.45  E-value=3.1e-14  Score=125.84  Aligned_cols=76  Identities=21%  Similarity=0.186  Sum_probs=70.1

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~  353 (780)
                      ...+|||+|||.++++++|+++|++||+|+.+++.  ++|||||+|.+.++|++||+.|||..+.|+.|+|.+++.+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            34579999999999999999999999999999884  46999999999999999999999999999999999987654

>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=99.44  E-value=7.5e-14  Score=117.25  Aligned_cols=71  Identities=20%  Similarity=0.199  Sum_probs=64.3

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~---~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .+|||+|||.++++++|+++|+.||.|+.|++   ....+++|||+|++.++|++|+. ||++.|+|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            37999999999999999999999999999976   33456799999999999999995 8999999999999864

>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=99.44  E-value=1.8e-13  Score=118.21  Aligned_cols=78  Identities=15%  Similarity=0.180  Sum_probs=70.4

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~k  352 (780)
                      .+.++|||+|||.++++++|+++|++||.|..+++. ..+++|||+|.+.++|++|++.+  ++..+.|++|+|.+++.+
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~-~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc-ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            456799999999999999999999999999999885 45799999999999999999976  567899999999999876


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        85 ~   85 (88)
T d2cq1a1          85 E   85 (88)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.43  E-value=3.6e-14  Score=121.98  Aligned_cols=74  Identities=22%  Similarity=0.296  Sum_probs=66.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEE---EE--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRT---LY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~s---v~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...+|||+|||+++++++|+++|+.||.|..   +.  .+++++|+|||+|.+.++|++|++.|++..|.|++|+|.++
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            4568999999999999999999999998743   12  46889999999999999999999999999999999999764

>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=99.42  E-value=7.9e-14  Score=119.76  Aligned_cols=74  Identities=22%  Similarity=0.282  Sum_probs=66.4

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeE-EE----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~-v~----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      ...+|||+|||.+++++||+++|+.||.|.. +.    .++.++|+|||+|.+.++|++||+.|||+.+.|++|+|+++
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            3457999999999999999999999998854 22    36778999999999999999999999999999999999875

>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=99.42  E-value=2.3e-13  Score=121.22  Aligned_cols=78  Identities=12%  Similarity=0.164  Sum_probs=70.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ....+|||+|||+++|+++|+++|..+|.|..+.     .+++++|||||+|.++++|++|++ +++..|.||.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            3456899999999999999999999999987754     467899999999999999999997 8999999999999998


Q ss_pred             CCCC
Q 004002          265 IPKD  268 (780)
Q Consensus       265 ~pk~  268 (780)
                      .+++
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7664

>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=99.42  E-value=1.8e-13  Score=121.10  Aligned_cols=78  Identities=19%  Similarity=0.178  Sum_probs=69.6

Q ss_pred             CCccceeecCCCCC-CChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHH--HhCCCccCCceEEEEecCC
Q 004002          275 LNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       275 ~~~~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~--~LnG~~i~Gr~L~V~~a~~  351 (780)
                      ...++|||+|||.+ +|+++|+++|++||.|..|++. ..+|+|||+|.+.++|.+|++  .+++..+.|++|+|.+++.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~-~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEe-ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            34578999999985 8999999999999999999985 457999999999999999998  5788899999999999976


Q ss_pred             Cc
Q 004002          352 GG  353 (780)
Q Consensus       352 k~  353 (780)
                      +.
T Consensus        95 ~~   96 (99)
T d1x4fa1          95 YK   96 (99)
T ss_dssp             CS
T ss_pred             cc
Confidence            54

>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=99.42  E-value=1.1e-13  Score=116.12  Aligned_cols=71  Identities=17%  Similarity=0.261  Sum_probs=64.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~---~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ++|||+|||+++++++|+++|+.||+|..++   .....+|||||+|.+.++|++|++ ++++.|.|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999887   234567899999999999999996 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=99.42  E-value=3.6e-13  Score=119.97  Aligned_cols=78  Identities=18%  Similarity=0.185  Sum_probs=70.4

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~k  352 (780)
                      ...++|||+|||.++|+++|+++|++||.|+.|++. +.|++|||+|++.++|++|++.|  ++..+.|++|+|.+++.+
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~-~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE-ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            356799999999999999999999999999999985 56899999999999999999988  556789999999999765


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        92 ~   92 (104)
T d1wexa_          92 R   92 (104)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.40  E-value=2e-13  Score=121.26  Aligned_cols=79  Identities=10%  Similarity=0.224  Sum_probs=68.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE--E-eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL--Y-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv--~-~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .....+|||+|||+++|+++|+++|+.||.+...  + ..++.+|||||+|.+.++|++|++ |++..|.||.|+|.++.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            3455799999999999999999999999854322  1 467899999999999999999987 89999999999999987


Q ss_pred             CCC
Q 004002          266 PKD  268 (780)
Q Consensus       266 pk~  268 (780)
                      ++.
T Consensus        91 ~~~   93 (102)
T d1weza_          91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.40  E-value=8.5e-14  Score=120.73  Aligned_cols=71  Identities=18%  Similarity=0.324  Sum_probs=63.2

Q ss_pred             CcEEEEeCCCCCCCHHHH---HHHhhcCCCEEEEEe-----C---CCcceEEEEEEecHHHHHHHHHHccCccccccccc
Q 004002          192 SRTLFVRNINSNVEDSEL---RALFEQYGDIRTLYT-----A---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeL---r~lF~~yG~I~sv~~-----t---gkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~  260 (780)
                      .++|||+|||+++++++|   +++|++||+|..|+.     +   ...+|||||+|.+.++|++|++.|||..|.|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999   678999999999972     2   23459999999999999999999999999999998


Q ss_pred             cc
Q 004002          261 IH  262 (780)
Q Consensus       261 V~  262 (780)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            73

>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=99.39  E-value=6e-13  Score=118.44  Aligned_cols=78  Identities=23%  Similarity=0.247  Sum_probs=69.2

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEE-e----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-E----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~-~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .+..+|||+|||+++|++||+++|+.||.|..+. +    ++.++|+|||+|.+.++|++|++ +|+..|.||.|+|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            3456899999999999999999999999987743 2    56788999999999999999996 9999999999999999


Q ss_pred             CCCc
Q 004002          350 RPGG  353 (780)
Q Consensus       350 ~~k~  353 (780)
                      .+..
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            8764

>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=99.38  E-value=2.4e-13  Score=120.67  Aligned_cols=78  Identities=13%  Similarity=0.196  Sum_probs=67.8

Q ss_pred             CCccceeecCCCCCCChhHHHHHhcccCCeeEEE----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       275 ~~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~----~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ....+|||+|||+++|++||+++|+.||.+ .|+    .++.++|||||+|.+.++|++|++ ||++.|.||.|+|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            344689999999999999999999999854 443    256778999999999999999986 89999999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      ++..
T Consensus        91 ~~~~   94 (102)
T d1weza_          91 TAGT   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.38  E-value=2.3e-13  Score=120.41  Aligned_cols=79  Identities=16%  Similarity=0.212  Sum_probs=69.8

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHH--HccCccccccccccccCC
Q 004002          189 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR--ALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~-vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~--~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++++|||+|||.+ +|+++|+++|++||.|..++. .+.+|||||+|.+.++|.+|++  .+++..+.|++|.|.|+.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~-~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~   93 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE   93 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEE-eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcC
Confidence            346789999999985 899999999999999999875 4678999999999999999998  467888999999999996


Q ss_pred             CCC
Q 004002          266 PKD  268 (780)
Q Consensus       266 pk~  268 (780)
                      .+.
T Consensus        94 ~~~   96 (99)
T d1x4fa1          94 KYK   96 (99)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            543

>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=99.38  E-value=5.1e-13  Score=115.85  Aligned_cols=77  Identities=17%  Similarity=0.233  Sum_probs=68.8

Q ss_pred             CccceeecCCCCC-CChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 004002          276 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (780)
Q Consensus       276 ~~~~L~V~NLp~~-vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~k  352 (780)
                      ..++|||+|||.. +|++||+++|++||.|..|++. ..+++|||+|++.++|++|++.|  ++..+.|++|+|.++++.
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~-~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEee-ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            4578999999986 8899999999999999999985 45689999999999999999966  677899999999999864


Q ss_pred             c
Q 004002          353 G  353 (780)
Q Consensus       353 ~  353 (780)
                      .
T Consensus        86 ~   86 (89)
T d1x4da1          86 K   86 (89)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.37  E-value=4.6e-13  Score=116.12  Aligned_cols=78  Identities=14%  Similarity=0.146  Sum_probs=69.3

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHc--cCccccccccccccCC
Q 004002          189 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLDIHFSI  265 (780)
Q Consensus       189 e~~s~tLfVgNLp~~-vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~L--ng~~l~gr~I~V~~a~  265 (780)
                      ..++++|||+|||.. +|++||+++|++||+|..++. .+.+++|||+|.+.++|++|++.|  ++..+.|++|+|.|+.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i-~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~   83 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   83 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-CSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEe-eccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECC
Confidence            457899999999986 889999999999999999985 456789999999999999999976  5667999999999987


Q ss_pred             CC
Q 004002          266 PK  267 (780)
Q Consensus       266 pk  267 (780)
                      ..
T Consensus        84 ~~   85 (89)
T d1x4da1          84 KY   85 (89)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>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=99.35  E-value=1.5e-13  Score=122.70  Aligned_cols=79  Identities=19%  Similarity=0.217  Sum_probs=70.3

Q ss_pred             CCCcEEEEeCCCCCC-CH----HHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          190 HPSRTLFVRNINSNV-ED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       190 ~~s~tLfVgNLp~~v-te----eeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      ...++|||+||+.++ ++    ++|+.+|++||+|.+++. .+++|||||+|.+.++|++|++.|||..|.|++|+|.|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~-~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   81 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFA   81 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEE-ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEE-ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeec
Confidence            356899999999987 33    569999999999999974 578999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 004002          265 IPKDN  269 (780)
Q Consensus       265 ~pk~~  269 (780)
                      .+...
T Consensus        82 ~~~~~   86 (104)
T d1weya_          82 QTLHI   86 (104)
T ss_dssp             CCSSC
T ss_pred             ccCCC
Confidence            77654

>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=99.35  E-value=1.9e-13  Score=122.06  Aligned_cols=78  Identities=18%  Similarity=0.225  Sum_probs=69.4

Q ss_pred             CccceeecCCCCCC-Ch----hHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSV-SN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~v-te----edL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+||+.++ ++    ++|+++|++||.|+++++. +++++|||+|.+.++|++|++.|||..|.|++|+|.|++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            34689999999986 33    5699999999999999885 568999999999999999999999999999999999998


Q ss_pred             CCch
Q 004002          351 PGGA  354 (780)
Q Consensus       351 ~k~~  354 (780)
                      +...
T Consensus        83 ~~~~   86 (104)
T d1weya_          83 TLHI   86 (104)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            7653

>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=99.33  E-value=4.1e-13  Score=119.20  Aligned_cols=75  Identities=12%  Similarity=0.161  Sum_probs=66.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeE-EEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~-v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||.++|+++|+++|+.||.|.. +.+    ++.++|+|||+|.+.++|++||+ |||..|.|+.|.|.++.
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            3468999999999999999999999998865 332    56789999999999999999996 99999999999999875


Q ss_pred             C
Q 004002          351 P  351 (780)
Q Consensus       351 ~  351 (780)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.31  E-value=3.3e-13  Score=119.84  Aligned_cols=74  Identities=16%  Similarity=0.192  Sum_probs=66.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE-E----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL-Y----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv-~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ...+|||+|||+++|+++|+++|..||.|..+ .    .+++++|||||+|.+.++|++|++ |++..|.|+.|.|.++.
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            45789999999999999999999999987542 2    468899999999999999999996 89999999999998764

>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=99.31  E-value=4.9e-14  Score=122.25  Aligned_cols=72  Identities=17%  Similarity=0.317  Sum_probs=63.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----------eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccc
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY----------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----------~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~  262 (780)
                      |+|||+|||.++|+++|+++|++||.|..+.          .+++++|||||+|.+.++|++|++ |+|..+.|++|+|+
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            7899999999999999999999999765432          346789999999999999999995 99999999999997


Q ss_pred             cCC
Q 004002          263 FSI  265 (780)
Q Consensus       263 ~a~  265 (780)
                      .+.
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.26  E-value=1.5e-12  Score=117.46  Aligned_cols=77  Identities=17%  Similarity=0.203  Sum_probs=67.8

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEE-----EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v-----~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      ...+|||+|||+++|+++|+++|+.||.|..+     ..++.++|+|||+|.+.++|++|++ |||..|+|+.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            34589999999999999999999999987542     2367889999999999999999996 99999999999999886


Q ss_pred             CCc
Q 004002          351 PGG  353 (780)
Q Consensus       351 ~k~  353 (780)
                      +..
T Consensus        96 ~~~   98 (112)
T d1wela1          96 KKG   98 (112)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            654

>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=99.25  E-value=1.3e-13  Score=119.44  Aligned_cols=71  Identities=18%  Similarity=0.327  Sum_probs=62.8

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe----------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----------~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~  347 (780)
                      ++|||+|||.++|+++|+++|+.||.|..+.+          ++.++|||||+|.+.++|++|++ |||..+.|++|+|+
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            47999999999999999999999998766532          34678999999999999999985 99999999999997


Q ss_pred             ec
Q 004002          348 PS  349 (780)
Q Consensus       348 ~a  349 (780)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.24  E-value=1.1e-12  Score=118.31  Aligned_cols=75  Identities=9%  Similarity=0.177  Sum_probs=66.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhcCCCEEEE---E--eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL---Y--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       191 ~s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv---~--~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      ..++|||+|||+++|+++|+++|+.||.|..+   .  ..|+++|||||+|.+.++|++|++ |++..|+|+.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            45799999999999999999999999987432   1  578999999999999999999997 89999999999998764


Q ss_pred             C
Q 004002          266 P  266 (780)
Q Consensus       266 p  266 (780)
                      +
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.24  E-value=6.8e-13  Score=118.42  Aligned_cols=72  Identities=24%  Similarity=0.272  Sum_probs=67.6

Q ss_pred             cceeecCCCCCCChhHHHHHhcccCCeeEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 004002          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (780)
Q Consensus       278 ~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~----~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a  349 (780)
                      .+++|.+++.++++++|+++|++||+|++|++    +++++|+|||+|.+.++|.+|++.|||++++|++|+|+++
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            47999999999999999999999999999986    5677899999999999999999999999999999999875

>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=99.21  E-value=9.5e-12  Score=112.37  Aligned_cols=78  Identities=21%  Similarity=0.170  Sum_probs=67.6

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCH-HHHHHHHHHhCCCccCCceEEEEecCCCchh
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV-RAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~-e~A~~Ai~~LnG~~i~Gr~L~V~~a~~k~~r  355 (780)
                      .-.+||+|||.++|+++|+++|++||+|..|++. +.+|+|||+|.+. ++|.+|+..||+..+.++.+.|.++..+...
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~~~   89 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEV   89 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHHH
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccchh
Confidence            3467999999999999999999999999999986 5689999999985 7899999999999998877777777665443

>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=99.20  E-value=1e-11  Score=110.02  Aligned_cols=66  Identities=18%  Similarity=0.329  Sum_probs=59.7

Q ss_pred             CCCCcEEEEeC--CCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccc
Q 004002          189 EHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (780)
Q Consensus       189 e~~s~tLfVgN--Lp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~  255 (780)
                      ..++++|+|.|  ||.++|+++|+++|++||.|..++. .+.+|||||+|.+.++|++|+++|+|+.|.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~-~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC-CTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEee-ccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            35678999966  9999999999999999999999974 457899999999999999999999999873

>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=99.18  E-value=1.3e-11  Score=109.25  Aligned_cols=63  Identities=22%  Similarity=0.326  Sum_probs=56.9

Q ss_pred             CccceeecC--CCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 004002          276 NQGTLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (780)
Q Consensus       276 ~~~~L~V~N--Lp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i  339 (780)
                      +..+|+|.|  ||.++|+++|+++|++||.|+.|++. ..++||||+|.+.++|++|++.|||+.+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~-~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeec-cCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345788855  99999999999999999999999985 4578999999999999999999999977

>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=99.15  E-value=2.1e-11  Score=107.50  Aligned_cols=82  Identities=18%  Similarity=0.289  Sum_probs=70.7

Q ss_pred             CCCCCCcEEEEeCC--CCCCC---------HHHHHHHhhcCCCEEEEE-eCCCcceEEEEEEecHHHHHHHHHHccCccc
Q 004002          187 YGEHPSRTLFVRNI--NSNVE---------DSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (780)
Q Consensus       187 ~~e~~s~tLfVgNL--p~~vt---------eeeLr~lF~~yG~I~sv~-~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l  254 (780)
                      .....+++|+|+|+  |.++.         +++|++.|++||.|..|+ .....+|+|||+|.+.++|.+|++.|+|..+
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            34457899999999  65432         368999999999999987 4667889999999999999999999999999


Q ss_pred             cccccccccCCCCC
Q 004002          255 RRRKLDIHFSIPKD  268 (780)
Q Consensus       255 ~gr~I~V~~a~pk~  268 (780)
                      .||+|.|.|..++.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987654

>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=99.15  E-value=2.4e-11  Score=103.37  Aligned_cols=75  Identities=16%  Similarity=0.197  Sum_probs=64.7

Q ss_pred             CccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce-EEEEecCCCc
Q 004002          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-IKLEPSRPGG  353 (780)
Q Consensus       276 ~~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~-L~V~~a~~k~  353 (780)
                      +...|+|+|+|++.+++.| +.|++||+|.++++. ..++||||+|.++++|++||+ +||..++|+. |.|.++..+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k~   78 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   78 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCChh
Confidence            4567999999999987655 579999999999974 668999999999999999996 9999999974 6799887653

>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=99.14  E-value=3.1e-11  Score=106.42  Aligned_cols=78  Identities=17%  Similarity=0.299  Sum_probs=68.0

Q ss_pred             CccceeecCC--CCCCC---------hhHHHHHhcccCCeeEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce
Q 004002          276 NQGTLVVFNL--DPSVS---------NEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  343 (780)
Q Consensus       276 ~~~~L~V~NL--p~~vt---------eedL~~~Fs~yG~I~~v~~-~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~  343 (780)
                      ..++|+|.||  |.++.         ++||++.|++||.|..|++ .+..+|+|||+|.+.++|.+|+..|||+.++|++
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~   86 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQ   86 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCEE
Confidence            4578999999  54432         3689999999999999986 5567899999999999999999999999999999


Q ss_pred             EEEEecCCCc
Q 004002          344 IKLEPSRPGG  353 (780)
Q Consensus       344 L~V~~a~~k~  353 (780)
                      |+|++..++.
T Consensus        87 i~v~~~~g~~   96 (99)
T d2dita1          87 ITAQAWDGTT   96 (99)
T ss_dssp             CEEEECCSCC
T ss_pred             EEEEEeCCcC
Confidence            9999987654

>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=99.13  E-value=2.8e-12  Score=114.34  Aligned_cols=72  Identities=14%  Similarity=0.219  Sum_probs=67.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcceEEEEEEecHHHHHHHHHHccCccccccccccccC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~----~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a  264 (780)
                      +.++|++++.+++|++|+++|++||+|.+|+    .+++++|||||+|.+.++|.+|++.|+|+.+.|++|.|.|+
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            4688999999999999999999999999998    36789999999999999999999999999999999999885

>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=99.12  E-value=4.3e-11  Score=107.98  Aligned_cols=73  Identities=15%  Similarity=0.243  Sum_probs=65.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecH-HHHHHHHHHccCccccccccccccCCC
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI-RAARTAMRALQNKPLRRRKLDIHFSIP  266 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~-e~A~~Al~~Lng~~l~gr~I~V~~a~p  266 (780)
                      ..+||+|||.++|+++|+++|++||+|..|+. .+.+|||||.|.+. ++|..|+..|++..+.++.+.|.+...
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i-~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC-CTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEE-ecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            46699999999999999999999999999985 35789999999995 789999999999999988888877654

>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=99.00  E-value=1.2e-10  Score=98.91  Aligned_cols=72  Identities=18%  Similarity=0.207  Sum_probs=62.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCccccccc-cccccCCC
Q 004002          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK-LDIHFSIP  266 (780)
Q Consensus       192 s~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~-I~V~~a~p  266 (780)
                      .+.|+|.++|++.+++.| ++|++||+|.+++. ++.+|||||+|.+.++|++||+ +||..|.|+. |.|..+..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            478999999999997655 57999999999974 6789999999999999999996 8999999985 56776543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=2e-09  Score=95.39  Aligned_cols=76  Identities=24%  Similarity=0.326  Sum_probs=64.6

Q ss_pred             CccceeecCC--CCCCC--------hhHHHHHhcccCCeeEEEeC-------CCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 004002          276 NQGTLVVFNL--DPSVS--------NEDLRQIFGAYGEVKEIRET-------PHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (780)
Q Consensus       276 ~~~~L~V~NL--p~~vt--------eedL~~~Fs~yG~I~~v~~~-------g~srG~aFV~F~~~e~A~~Ai~~LnG~~  338 (780)
                      +++.|.|.||  +.++.        .+||++.|++||.|++|.+.       ...+|++||+|.+.++|.+|++.|||+.
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            3567999999  55543        36799999999999999862       2345899999999999999999999999


Q ss_pred             cCCceEEEEecCC
Q 004002          339 IAGKRIKLEPSRP  351 (780)
Q Consensus       339 i~Gr~L~V~~a~~  351 (780)
                      ++||.|.+.+..+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.84  E-value=9.8e-10  Score=97.41  Aligned_cols=76  Identities=16%  Similarity=0.353  Sum_probs=65.2

Q ss_pred             CCcEEEEeCC--CCCCC--------HHHHHHHhhcCCCEEEEEe-------CCCcceEEEEEEecHHHHHHHHHHccCcc
Q 004002          191 PSRTLFVRNI--NSNVE--------DSELRALFEQYGDIRTLYT-------ACKHRGFVMISYYDIRAARTAMRALQNKP  253 (780)
Q Consensus       191 ~s~tLfVgNL--p~~vt--------eeeLr~lF~~yG~I~sv~~-------tgkskG~aFV~F~~~e~A~~Al~~Lng~~  253 (780)
                      |++.|.|+|+  |.++.        .++|++.|++||.|.+|++       .....|++||+|.+.++|.+|++.|+|+.
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            6899999999  55543        3578999999999999983       12356899999999999999999999999


Q ss_pred             ccccccccccCCC
Q 004002          254 LRRRKLDIHFSIP  266 (780)
Q Consensus       254 l~gr~I~V~~a~p  266 (780)
                      +.||+|.|.|..+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999998753

>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=98.72  E-value=1.2e-08  Score=87.94  Aligned_cols=75  Identities=20%  Similarity=0.277  Sum_probs=61.9

Q ss_pred             eeEEEecCCCCCCHHHHHHHHhhcCCCcceeEE-eeccccCCcc-eeeEEeccCCccchHHHHHHhcCceeEEEEeeCCC
Q 004002          695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLY-LPIDFKNKCN-VGYAFINMLSPLHIIPFYEVLFSCAIGILFFNNNN  772 (780)
Q Consensus       695 tt~mirniPn~~~~~~l~~~i~~~~~~~ydf~y-lp~d~~~~~n-~gyafin~~~~~~~~~f~~~f~~~~~~~~~~~~~~  772 (780)
                      |.|+||++|+.+|++++++.|+  ..+++||+| .|=+...+-+ -..|||||.+++++..|.+.|+|+.     |-|+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~--~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~-----F~D~~   74 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQ--PMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV-----FLDNK   74 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHC--SCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE-----EECTT
T ss_pred             ceEEEecCCCCCCHHHHHHHhC--CcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcE-----EEcCC
Confidence            8999999999999999999998  468899987 5555554433 3569999999999999999999997     65555


Q ss_pred             ceee
Q 004002          773 NYYY  776 (780)
Q Consensus       773 ~~~~  776 (780)
                      +..|
T Consensus        75 g~~~   78 (91)
T d1uw4a_          75 GQEY   78 (91)
T ss_dssp             CCEE
T ss_pred             CCEe
Confidence            5444

>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=97.03  E-value=0.00072  Score=54.22  Aligned_cols=59  Identities=25%  Similarity=0.426  Sum_probs=52.0

Q ss_pred             hHHHHHhcccCCeeEEEeCCCccc--EEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 004002          292 EDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (780)
Q Consensus       292 edL~~~Fs~yG~I~~v~~~g~srG--~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  350 (780)
                      +-|..+|+++|.|..+.+.+.+.+  .|-|...+..+|.-|+..|+.++|++++|.|.++.
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 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345577899999999998766655  69999999999999999999999999999999874

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.24  E-value=0.0022  Score=53.81  Aligned_cols=56  Identities=21%  Similarity=0.452  Sum_probs=49.4

Q ss_pred             hHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 004002          292 EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (780)
Q Consensus       292 edL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  351 (780)
                      .+|.+.|..||+|+-||+..   +...|+|.+-+.|.+|++ |+|.++.|+.|+|....+
T Consensus        39 ~~Llq~l~~~GeViLvRFv~---d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~~   94 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQ---GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEET---TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCCC
T ss_pred             HHHHHHHhhCCeEEEEEEeC---CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCCC
Confidence            56889999999999999863   568999999999999998 899999999999986543

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.58  E-value=0.015  Score=49.10  Aligned_cols=64  Identities=5%  Similarity=0.050  Sum_probs=53.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE-eCCC------cceEEEEEEecHHHHHHHHHHccCccccc
Q 004002          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK------HRGFVMISYYDIRAARTAMRALQNKPLRR  256 (780)
Q Consensus       193 ~tLfVgNLp~~vteeeLr~lF~~yG~I~sv~-~tgk------skG~aFV~F~~~e~A~~Al~~Lng~~l~g  256 (780)
                      ++|.||.||+.+||+++.+.+...|++...+ ..|+      .-.-|+|.|.+.++...-.+..+|+.+.+
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            5899999999999999999999999887655 1111      22469999999999999999999998854

>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=95.53  E-value=0.0085  Score=47.87  Aligned_cols=58  Identities=12%  Similarity=0.219  Sum_probs=50.4

Q ss_pred             HHHHHhhcCCCEEEEEeCCCcce--EEEEEEecHHHHHHHHHHccCccccccccccccCC
Q 004002          208 ELRALFEQYGDIRTLYTACKHRG--FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (780)
Q Consensus       208 eLr~lF~~yG~I~sv~~tgkskG--~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V~~a~  265 (780)
                      .|...|.++|.|.++.....+.|  .|-|...+.++|..|+..|+..+|++++|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            35578899999999986555544  69999999999999999999999999999998864

>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=92.84  E-value=0.039  Score=46.05  Aligned_cols=69  Identities=19%  Similarity=0.331  Sum_probs=55.1

Q ss_pred             CCcEEEEeCCCCCCCH---------HHHHHHhhcCCCEEEEEeCCCcceEEEEEEecHHHHHHHHHHccCcccccccccc
Q 004002          191 PSRTLFVRNINSNVED---------SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (780)
Q Consensus       191 ~s~tLfVgNLp~~vte---------eeLr~lF~~yG~I~sv~~tgkskG~aFV~F~~~e~A~~Al~~Lng~~l~gr~I~V  261 (780)
                      +..||.|.=..++.++         .+|.+.|..||+|.-+|.-   .+-..|+|.+-+.|-+|++ ++|.++.|+.|+|
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv---~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~I   89 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRIN---QGQMLVTFADSHSALSVLD-VDGMKVKGRAVKI   89 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEE---TTEEEEECSCSHHHHHHHH-GGGSEETTEEEEE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEe---CCeEEEEECCcHHHHHHhc-cCCeEEcceEEEE
Confidence            5678888655544433         3688899999999888732   2458899999999999999 8999999999998


Q ss_pred             cc
Q 004002          262 HF  263 (780)
Q Consensus       262 ~~  263 (780)
                      .-
T Consensus        90 t~   91 (95)
T d1ufwa_          90 SG   91 (95)
T ss_dssp             EC
T ss_pred             ec
Confidence            64

>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=89.35  E-value=0.32  Score=40.99  Aligned_cols=56  Identities=14%  Similarity=0.284  Sum_probs=47.0

Q ss_pred             ccceeecCCCCCCChhHHHHHhcccCCeeEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 004002          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (780)
Q Consensus       277 ~~~L~V~NLp~~vteedL~~~Fs~yG~I~~v~~~g~srG~aFV~F~~~e~A~~Ai~~Ln  335 (780)
                      ..-+|.-..|..+...||.++|++||.|.-..+...   -|||.-.+.++|+.+++.++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIddT---Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDT---SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEETT---EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEecCc---eEEEEecCHHHHHHHHHHhc
Confidence            346888889999999999999999999877666433   59999999999999987554