Citrus Sinensis ID: 004150

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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-
Protein Sequence
MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHccccccccccccccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHccccHHHccccccccccccccccccccccccccHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccHHHHHHccccccccccccHHHHHHHHHHHccccccccccHHHHHHHHHccccccccccccccccccHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHcccccHHHccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEEcccccccccccEEEccccHHHHHHHHHHHccccccccEEEEEEcHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHcccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccHcHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccEEEccccccccccccccccccHHHcccccccccccccccHHHHcccccccccccccHHHHHHHHHHcccccccccccccccccccccccHHcccccccccccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHccccHHHHHcccccHHHHcHHHHHHHcHHHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
mvrpafpprppgpvgvlpsvarppvpgipgvrpimppvvrpvplptvtpaekpqtkvyvgkiaptadsDFVLSVLKVCGTvkswkraqypsngtpkgfgfcefESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKEtqdagagkedesvqsvekneptkspenlkdnetgnkeshdptnfgvvteeDRKADQEALEKLTCMVEerlktnplpppppqttadgsgisnselpakardgdsdvDMIRNDiaedklddettsdtkasdhdrpetsspdrsrvhdrrgrdkerDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEilydeeededdsRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLsdnavngslaeesaveskgmdvehdyhddsirenhmagdpssqngngdestnvpiaasdmrqsgnvparklgfglvgsgkrtavpsvfhveddddadkdkkmrplvpidysteelqaaqphvsganppnLAAAAEFAKRISnvnskeeksdAERERSRrlhdrssqrekdrsdednnrtrdeHKEKILdrdrdrehgldkvktpdnkklldAKQLIDMIPKTKEELFSYEINWAvydkhelhermrpwISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS
Flexible Loop (DISEMBL)
mvrpafpprppgpvgvlpSVARPPVPGIPGVRPIMPPVVRPVPLPtvtpaekpqtkvYVGKiaptadsdfVLSVLKVCGTVKswkraqypsngtpkgFGFCEFESAEGVLRALRLLNKFnidgqelmlkVDQATREYLERyvdkktentkklketqdagagkedesvqsvekneptkspenlkdnetgnkeshdptnfgvvteEDRKADQEALEKLTCMVEErlktnplpppppqttadgsgisnselpakardgdsdVDMIRNDiaedklddettsdtkasdhdrpetsspdrsrvhdrrgrdkerdlkrekereidryereaerervrkereqrrkieeaereyerclkdweyrererekerqyekekekererkrkkeilydeeededdsrkrwrrsvleekrrkrirekeedladevreeEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAeesaveskgMDVEHDYHDDSIRENHMagdpssqngngdESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPsvfhveddddadkdkkMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRisnvnskeeksdaerersrrlhdrssqrekdrsdednnrtrdehkekildrdrdrehgldkvktpdnkklldakqlIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKkvetglalrsks
Low Complexity Region (SEG)
MvrpafpprppgpvgvlpsvaRppvpgipgvrpimppvvrpvplptvtpAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDkktentkklketQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNplpppppQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHdrrgrdkerdlkrekereidryereaerervrkereqrrkieeaereYERCLKDWeyrererekerqyekekekererkrkkeILYdeeededdSRKRWRRSVLeekrrkrirekeedladevreeeeiavakrraeeeqlqqqqrdalklLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEddddadkdkkMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS
Disordered region (IsUnstruct)
*************************************VV***************TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYV*******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************GFGLV***************************************************************************************************************************************AKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGL******
Disordered Region (DISOPRED)
********************************************************VYVGKIAPTADSDFVLSVLKVCGTVKSWKRA*****GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLE********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************LFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKV***L******
Disordered Region (DISEMBL)
MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKL*****************************LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKL********************************************EIDRY************************EYERCLKDWEYR*********************RKKEILY************WRRSVLEEKRRKRIRE************EEIAVAK*************DALKLLSDNAVNGS*************VEHDYHDDSIRENHM************ESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISN*****************************************KEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS
Disordered Region (DISPRO)
**RPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPV*************KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTE*******************VQSVEKNEPTKSPENLKDNETGNKESHDPTNF*******RKADQEALEKLTCMVEERLKTNPLPPPP*********************************************************************************************ERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQL*QQQRDALKLLS*N***************************************************************PARKLG***V***************************PLV*********************************************************************************LDRDRDREHGL****TPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVET********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDSRKRWRRSVLEEKRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNAVNGSLAEESAVESKGMDVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS
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	771	2.2.26 [Sep-21-2011]
P49756	843	RNA-binding protein 25 OS	yes	no	0.105	0.096	0.451	4e-24
B2RY56	838	RNA-binding protein 25 OS	yes	no	0.105	0.096	0.451	4e-24
Q8IDX6	3130	Reticulocyte-binding prot	no	no	0.162	0.039	0.280	3e-05

>sp|P49756|RBM25_HUMAN RNA-binding protein 25 OS=Homo sapiens GN=RBM25 PE=1 SV=3

 Score =  114 bits (284), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 47/104 (45%), Positives = 72/104 (69%)

Query: 663 KQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSST 722
           K LI+ IP  K ELF+Y ++W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S  
Sbjct: 739 KSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKV 798

Query: 723 QDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLA 766
             H     +L+ +  +LD+EAE+F++KMWR+LI+E +  + GL 
Sbjct: 799 MAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGLV 842

RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5'-splice site (5'-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5'-ss usage through the 5'-CGGGCA-3' RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5' ss in a 5'-CGGGCA-3'-dependent manner. Binds to the exonic splicing enhancer 5'-CGGGCA-3' RNA sequence located within exon 2 of the BCL2L1 pre-mRNA.
Homo sapiens (taxid: 9606)

>sp|B2RY56|RBM25_MOUSE RNA-binding protein 25 OS=Mus musculus GN=Rbm25 PE=1 SV=2

 Score =  114 bits (284), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 47/104 (45%), Positives = 72/104 (69%)

Query: 663 KQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSST 722
           K LI+ IP  K ELF+Y ++W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S  
Sbjct: 734 KSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKV 793

Query: 723 QDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLA 766
             H     +L+ +  +LD+EAE+F++KMWR+LI+E +  + GL 
Sbjct: 794 MAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGLV 837

RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5'-splice site (5'-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5'-ss usage through the 5'-CGGGCA-3' RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5' ss in a 5'-CGGGCA-3'-dependent manner. Binds to the exonic splicing enhancer 5'-CGGGCA-3' RNA sequence located within exon 2 of the BCL2L1 pre-mRNA.

Mus musculus (taxid: 10090)

>sp|Q8IDX6|RBP2A_PLAF7 Reticulocyte-binding protein 2 homolog a OS=Plasmodium falciparum (isolate 3D7) GN=PF13_0198 PE=3 SV=1

 Score = 51.2 bits (121), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/132 (28%), Positives = 76/132 (57%), Gaps = 7/132 (5%)

Query: 313  KEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEK 372
            K +E +R ++E E +R  +ER +R K E+ ++E E   ++ E  ++E   +RQ ++  +K
Sbjct: 2740 KRQEQERLQKEEELKRQEQERLEREKQEQLQKEEELKRQEQERLQKEEALKRQEQERLQK 2799

Query: 373  ERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR-EKEEDLADEVREEEEIAVAK 431
            E E KR+++   + E+ E   ++       E KR+++ R +KEE L  + +E  +     
Sbjct: 2800 EEELKRQEQERLEREKQEQLQKEE------ELKRQEQERLQKEEALKRQEQERLQKEEEL 2853

Query: 432  RRAEEEQLQQQQ 443
            +R E+E+L++++
Sbjct: 2854 KRQEQERLERKK 2865

Involved in reticulocyte adhesion.

Plasmodium falciparum (isolate 3D7) (taxid: 36329)

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	771
225424679	958	PREDICTED: uncharacterized protein LOC10	0.984	0.792	0.685	0.0
296086551	828	unnamed protein product [Vitis vinifera]	0.987	0.919	0.688	0.0
255568764	948	conserved hypothetical protein [Ricinus	0.976	0.794	0.737	0.0
224111298	894	predicted protein [Populus trichocarpa]	0.981	0.846	0.695	0.0
357485911	771	RNA-binding protein [Medicago truncatula	0.985	0.985	0.645	0.0
356501735	765	PREDICTED: uncharacterized protein LOC10	0.979	0.986	0.667	0.0
356497763	927	PREDICTED: uncharacterized protein LOC10	0.983	0.817	0.679	0.0
449434915	770	PREDICTED: uncharacterized protein LOC10	0.988	0.989	0.673	0.0
449513686	968	PREDICTED: uncharacterized LOC101214372	0.988	0.787	0.673	0.0
307135981	770	RNA binding motif protein [Cucumis melo	0.971	0.972	0.676	0.0

>gi|225424679|ref|XP_002264457.1| PREDICTED: uncharacterized protein LOC100263874 [Vitis vinifera]

 Score =  920 bits (2377), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 540/788 (68%), Positives = 639/788 (81%), Gaps = 29/788 (3%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRPAFPPRPPG +G+LP+++RPPVPG+PGVRPIMPPVVRP  +P   P EKPQT VYVG
Sbjct: 183 MVRPAFPPRPPGAIGMLPALSRPPVPGMPGVRPIMPPVVRPAIVPVAAPTEKPQTTVYVG 242

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIA T ++DF+LS+L+VCG VKSWK AQYP +GTP+G GFCEFES EGVLRALRLL KFN
Sbjct: 243 KIASTVENDFILSLLQVCGPVKSWKHAQYPIDGTPRGLGFCEFESPEGVLRALRLLTKFN 302

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE 180
           +DGQEL+L V+QATREYLERYV+KKTEN+KK +E+   G+ KE ESV  VE+NE  K   
Sbjct: 303 VDGQELVLNVNQATREYLERYVEKKTENSKKPQESDIEGSEKEQESVPGVEQNEILKP-- 360

Query: 181 NLKD-----NETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQ 235
           +L+D     NE  NKE+ D  +FG+VT+EDR+AD+EALEKLT M+EER+KT PLPPPP Q
Sbjct: 361 SLEDSKKDGNELVNKENQDNASFGIVTDEDREADREALEKLTSMMEERIKTKPLPPPPAQ 420

Query: 236 TTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKA-SDHDRPETSSPDR 294
             ADGS  +NSELP K+RD  SDVD++RND AED   DETTS+ K  SD +R E SSPDR
Sbjct: 421 GAADGSENTNSELPTKSRD--SDVDVMRNDAAED---DETTSENKPKSDQERLERSSPDR 475

Query: 295 SRVHDRRGRDKERD--LKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKD 352
           SR +DRR R+++RD  LKREKERE DR ERE ERERVR+E+E+  KIE AE  Y   +K+
Sbjct: 476 SRRYDRRSRERDRDRELKREKEREFDRLERERERERVRREKEREIKIERAENLYRERVKE 535

Query: 353 WEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV--LEEKRRKRI 410
           WEYRERE+E +RQ+EKE+EKERER+R++EI   E ++++D  ++ RR    +EEKR+KR 
Sbjct: 536 WEYREREKEYQRQHEKEREKERERERRREISNQERDNDEDDSRKRRRRSSEVEEKRKKRQ 595

Query: 411 REKEEDLADEVREEEEIAVAKRRAEEEQLQQQQ---RDALKLLSDNAVNGS----LAEES 463
           REKEEDLAD ++E EEIA   RRA EE+ QQQQ    +A+KLL+ +A  GS    L +E+
Sbjct: 596 REKEEDLADRLKEVEEIAETNRRASEEEQQQQQEQQNNAVKLLALHATTGSEKEVLTDET 655

Query: 464 AVESKGMDVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGF 523
             ++K   VE  Y  DS  +NH+ GD   QNG GDES    +AASD+RQS N+PARKLGF
Sbjct: 656 DAQNKDKAVEQAYEGDSSHQNHI-GDGILQNGTGDESAMASLAASDVRQSSNLPARKLGF 714

Query: 524 GLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAA 583
           GLVGSGKRTAV SVFH E+DDDA K+KKMRPLVPIDYSTEELQA QP +SG +P NL AA
Sbjct: 715 GLVGSGKRTAVLSVFHEEEDDDAHKEKKMRPLVPIDYSTEELQAVQPTISGPSPSNLVAA 774

Query: 584 AEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRD 643
           AEFAKRI+NV  K++KSD E+ER+RR +DRSS R  DR+DED NR RDE++EK LDRDRD
Sbjct: 775 AEFAKRITNV--KDDKSDIEKERNRRAYDRSSHR--DRNDEDINRARDENREKFLDRDRD 830

Query: 644 REHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKI 703
           REHG +K++TPDNKKLLDAKQLIDMIPKTKEELFSYEINW VYDKHELHERMRPWISKKI
Sbjct: 831 REHGPEKLRTPDNKKLLDAKQLIDMIPKTKEELFSYEINWGVYDKHELHERMRPWISKKI 890

Query: 704 TEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVET 763
           TEFLGEEE TLVDYIVSSTQ+HVKASQMLELLQ+ILDDEAEMFVLKMWRMLIFEIKKVET
Sbjct: 891 TEFLGEEEATLVDYIVSSTQEHVKASQMLELLQSILDDEAEMFVLKMWRMLIFEIKKVET 950

Query: 764 GLALRSKS 771
           GL+LRSK+
Sbjct: 951 GLSLRSKT 958

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086551|emb|CBI32140.3| unnamed protein product [Vitis vinifera]

 Score =  918 bits (2372), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 541/786 (68%), Positives = 639/786 (81%), Gaps = 25/786 (3%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRPAFPPRPPG +G+LP+++RPPVPG+PGVRPIMPPVVRP  +P   P EKPQT VYVG
Sbjct: 53  MVRPAFPPRPPGAIGMLPALSRPPVPGMPGVRPIMPPVVRPAIVPVAAPTEKPQTTVYVG 112

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIA T ++DF+LS+L+VCG VKSWK AQYP +GTP+G GFCEFES EGVLRALRLL KFN
Sbjct: 113 KIASTVENDFILSLLQVCGPVKSWKHAQYPIDGTPRGLGFCEFESPEGVLRALRLLTKFN 172

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK-SP 179
           +DGQEL+L V+QATREYLERYV+KKTEN+KK +E+   G+ KE ESV  VE+NE  K S 
Sbjct: 173 VDGQELVLNVNQATREYLERYVEKKTENSKKPQESDIEGSEKEQESVPGVEQNEILKPSL 232

Query: 180 ENLK--DNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTT 237
           E+ K   NE  NKE+ D  +FG+VT+EDR+AD+EALEKLT M+EER+KT PLPPPP Q  
Sbjct: 233 EDSKKDGNELVNKENQDNASFGIVTDEDREADREALEKLTSMMEERIKTKPLPPPPAQGA 292

Query: 238 ADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKA-SDHDRPETSSPDRSR 296
           ADGS  +NSELP K+RD  SDVD++RND AED   DETTS+ K  SD +R E SSPDRSR
Sbjct: 293 ADGSENTNSELPTKSRD--SDVDVMRNDAAED---DETTSENKPKSDQERLERSSPDRSR 347

Query: 297 VHDRRGRDKERD--LKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 354
            +DRR R+++RD  LKREKERE DR ERE ERERVR+E+E+  KIE AE  Y   +K+WE
Sbjct: 348 RYDRRSRERDRDRELKREKEREFDRLERERERERVRREKEREIKIERAENLYRERVKEWE 407

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV--LEEKRRKRIRE 412
           YRERE+E +RQ+EKE+EKERER+R++EI   E ++++D  ++ RR    +EEKR+KR RE
Sbjct: 408 YREREKEYQRQHEKEREKERERERRREISNQERDNDEDDSRKRRRRSSEVEEKRKKRQRE 467

Query: 413 KEEDLADEVREEEEIAVAKRRAEEEQLQQQQ---RDALKLLSDNAVNGS----LAEESAV 465
           KEEDLAD ++E EEIA   RRA EE+ QQQQ    +A+KLL+ +A  GS    L +E+  
Sbjct: 468 KEEDLADRLKEVEEIAETNRRASEEEQQQQQEQQNNAVKLLALHATTGSEKEVLTDETDA 527

Query: 466 ESKGMDVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGL 525
           ++K   VE  Y  DS  +NH+ GD   QNG GDES    +AASD+RQS N+PARKLGFGL
Sbjct: 528 QNKDKAVEQAYEGDSSHQNHI-GDGILQNGTGDESAMASLAASDVRQSSNLPARKLGFGL 586

Query: 526 VGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAE 585
           VGSGKRTAV SVFH E+DDDA K+KKMRPLVPIDYSTEELQA QP +SG +P NL AAAE
Sbjct: 587 VGSGKRTAVLSVFHEEEDDDAHKEKKMRPLVPIDYSTEELQAVQPTISGPSPSNLVAAAE 646

Query: 586 FAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDRE 645
           FAKRI+NV  K++KSD E+ER+RR +DRSS R  DR+DED NR RDE++EK LDRDRDRE
Sbjct: 647 FAKRITNV--KDDKSDIEKERNRRAYDRSSHR--DRNDEDINRARDENREKFLDRDRDRE 702

Query: 646 HGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITE 705
           HG +K++TPDNKKLLDAKQLIDMIPKTKEELFSYEINW VYDKHELHERMRPWISKKITE
Sbjct: 703 HGPEKLRTPDNKKLLDAKQLIDMIPKTKEELFSYEINWGVYDKHELHERMRPWISKKITE 762

Query: 706 FLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGL 765
           FLGEEE TLVDYIVSSTQ+HVKASQMLELLQ+ILDDEAEMFVLKMWRMLIFEIKKVETGL
Sbjct: 763 FLGEEEATLVDYIVSSTQEHVKASQMLELLQSILDDEAEMFVLKMWRMLIFEIKKVETGL 822

Query: 766 ALRSKS 771
           +LRSK+
Sbjct: 823 SLRSKT 828

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568764|ref|XP_002525353.1| conserved hypothetical protein [Ricinus communis] gi|223535316|gb|EEF36991.1| conserved hypothetical protein [Ricinus communis]

 Score =  917 bits (2370), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 576/781 (73%), Positives = 651/781 (83%), Gaps = 28/781 (3%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRP FPPRP G +G+LP+ +R  VPGIPGVRP+  P+VRP  +P+VTPAEKP T VYVG
Sbjct: 186 MVRPMFPPRPLGALGILPAASRLLVPGIPGVRPV--PIVRPG-VPSVTPAEKPLTTVYVG 242

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIAPT D+DF+LS+L+ CG VKSWKR Q P++GTP+GFGFCEFESAEGVLRALRLL+KFN
Sbjct: 243 KIAPTVDNDFMLSLLRFCGPVKSWKRPQDPNDGTPRGFGFCEFESAEGVLRALRLLSKFN 302

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK--S 178
           IDGQEL+L V+QATREYLERYV+KKTEN K LKE Q  GA KED    + EK+EP K   
Sbjct: 303 IDGQELVLNVNQATREYLERYVEKKTENLKNLKENQAPGAAKED---GTAEKSEPPKIIG 359

Query: 179 PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTA 238
            ++ KD +  NKE++DP NFG+VT+ED++ D+EALEKLT M+EERLKTNPLPPPPPQT A
Sbjct: 360 EDSNKDGDKVNKENNDPANFGIVTDEDKEGDKEALEKLTSMIEERLKTNPLPPPPPQTPA 419

Query: 239 DGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSD-TKASDHDRPETSSPDRSR- 296
            GSG +NSE PAK+RDGDSD D  R   AEDK DDET SD   A++ DRP T SPDRS  
Sbjct: 420 HGSG-TNSEFPAKSRDGDSDADTTRQ--AEDKNDDETISDHIPATEQDRPGTCSPDRSSR 476

Query: 297 --VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 354
                 R RD+ERDLKREKEREI+RYEREAERER+RKEREQRRKIEEAEREYE  LKDWE
Sbjct: 477 KYDRRSRERDRERDLKREKEREIERYEREAERERIRKEREQRRKIEEAEREYEERLKDWE 536

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 414
           YRERE+EK+RQY+KEK+KER+RKR+KEILYDEE D+DDSRK+WRRS L++KRRK+ REKE
Sbjct: 537 YREREKEKQRQYDKEKDKERDRKRRKEILYDEEGDDDDSRKKWRRSALDDKRRKKQREKE 596

Query: 415 EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKGM 470
           +D+AD ++EEEE+A AKRRAEEE++QQQQ DA KL  D  +NG+    L EE  VESK  
Sbjct: 597 DDMADRLKEEEEMAEAKRRAEEERIQQQQTDAFKLSFDQVMNGTEMKVLVEEVYVESKDK 656

Query: 471 DVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGK 530
            VE D   D        GD   QNG  DEST   +  SD+RQSGN PARKLGFGLVGSGK
Sbjct: 657 VVEQDNEGD-------LGDGVLQNGTVDESTVTSMTESDIRQSGNAPARKLGFGLVGSGK 709

Query: 531 RTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRI 590
           R AVPSVFH EDDDDADKDKKMRPLVPIDYSTEELQA QP VSGA PP +AAAAEFAKRI
Sbjct: 710 RAAVPSVFHEEDDDDADKDKKMRPLVPIDYSTEELQAVQPTVSGAQPP-IAAAAEFAKRI 768

Query: 591 SNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDK 650
           SNV  KEEK D ERERSRR HDRSSQR++DR+DED  R RDE K+KIL+RDR+REHGLDK
Sbjct: 769 SNVTPKEEKPDMERERSRRSHDRSSQRDRDRNDEDAIRMRDE-KDKILERDRNREHGLDK 827

Query: 651 VKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEE 710
           VKTPD +KLLDAKQLIDMIPKTK+ELFSYEINWAVYD+HELHERMRPWISKKITEFLGEE
Sbjct: 828 VKTPDKQKLLDAKQLIDMIPKTKDELFSYEINWAVYDRHELHERMRPWISKKITEFLGEE 887

Query: 711 ETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSK 770
           ETTLVDYIVSST+DHVKASQMLE+LQ+ILDDEAEMFVLKMWRMLIFEIKKVETGLALRS+
Sbjct: 888 ETTLVDYIVSSTRDHVKASQMLEMLQSILDDEAEMFVLKMWRMLIFEIKKVETGLALRSR 947

Query: 771 S 771
           S
Sbjct: 948 S 948

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111298|ref|XP_002315807.1| predicted protein [Populus trichocarpa] gi|222864847|gb|EEF01978.1| predicted protein [Populus trichocarpa]

 Score =  869 bits (2246), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 544/782 (69%), Positives = 640/782 (81%), Gaps = 25/782 (3%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRP FPPRPPG + V+P+V RP VPGIPGVRP+M P++RPV +P+VTPAEKPQT VY+G
Sbjct: 127 MVRPLFPPRPPGALSVVPAVPRPLVPGIPGVRPVMYPIIRPV-IPSVTPAEKPQTTVYIG 185

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIAP+ ++DF++S+L+ CG VKSWKR Q P+NGTP+GFGFCEFESAEGVLRALRLL KFN
Sbjct: 186 KIAPSVENDFMMSLLQFCGPVKSWKRPQDPANGTPRGFGFCEFESAEGVLRALRLLTKFN 245

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSP- 179
           IDGQELML V+QAT+EYLERYV+KKTEN+K  KETQ A  GKED +    +K E +KS  
Sbjct: 246 IDGQELMLNVNQATKEYLERYVEKKTENSKNFKETQVADTGKEDGTGIDGKKGEFSKSSA 305

Query: 180 -ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKT--NPLPPPPPQT 236
            ++  D++ GNKE+HD  NFG+VT+ED+  D+EA+EKLT M+EERLKT   P PPPP   
Sbjct: 306 EDSNNDSDKGNKENHDLANFGIVTDEDKAGDREAIEKLTSMIEERLKTKPLPPPPPPSLA 365

Query: 237 TADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKA-SDHDRPETSSPDRS 295
            ADGSG SN ELP+K+RDGD+D D++R+   E K DDET+SD KA S+ DRPETSSPDRS
Sbjct: 366 PADGSGNSNLELPSKSRDGDTDADIMRS--VEGKNDDETSSDNKAASEQDRPETSSPDRS 423

Query: 296 RVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRR--KIEEAEREYERCLKDW 353
           R +DRR RD++R+   ++E+E +    E E ER R  +E+ +  KIEEAEREYE  L+DW
Sbjct: 424 RGYDRRSRDRDRERDLKREKEREIERYERETERERVRKEREQRRKIEEAEREYEERLRDW 483

Query: 354 EYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREK 413
           EYRERE+EK+RQYEKE++KERERKR+KEIL+DEE+++DDSRKRWRRS LE++RRKR+REK
Sbjct: 484 EYREREKEKQRQYEKERDKERERKRRKEILHDEEDEDDDSRKRWRRSALEDRRRKRLREK 543

Query: 414 EEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKG 469
           E+DLAD ++EEEEIA +KRR EEE+LQ++Q+D LKLLS + +N S    LAE   VESK 
Sbjct: 544 EDDLADRLKEEEEIAESKRRDEEEKLQEKQKDELKLLSGHVLNESEMTNLAEGPIVESKD 603

Query: 470 MDVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSG 529
             +E DY  DS  EN +AGD   QNGNGDES    +A  D R +G+ PARKLGFGLVGSG
Sbjct: 604 EAIEKDYDGDSGNEN-LAGDEVLQNGNGDESNMALMAEPDTRHNGSAPARKLGFGLVGSG 662

Query: 530 KRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKR 589
           KR AVPSVFH E+DDDA K+KKMRPLVPIDYSTEELQA QP VSGA PPNL AAAEFAKR
Sbjct: 663 KRAAVPSVFHEEEDDDARKEKKMRPLVPIDYSTEELQAVQPAVSGAQPPNLVAAAEFAKR 722

Query: 590 ISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLD 649
           ISNV  KEEK D ERERSRR HDRSSQR++D+          +  E+  DRDR+R+HGLD
Sbjct: 723 ISNVAPKEEKPDVERERSRRSHDRSSQRDRDQ----------KVPERDRDRDRNRDHGLD 772

Query: 650 KVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGE 709
           KVKTPD +KLLDAKQLIDMIPKTKEELF YEINWAVYDKHELHERMRPWISKKITEFLGE
Sbjct: 773 KVKTPDKQKLLDAKQLIDMIPKTKEELFLYEINWAVYDKHELHERMRPWISKKITEFLGE 832

Query: 710 EETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRS 769
           EETTLVDYIVSSTQ+HVKASQMLE+LQ ILDDEAEMFVLKMWRMLIFEIKKVETGL+LRS
Sbjct: 833 EETTLVDYIVSSTQEHVKASQMLEMLQAILDDEAEMFVLKMWRMLIFEIKKVETGLSLRS 892

Query: 770 KS 771
           KS
Sbjct: 893 KS 894

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357485911|ref|XP_003613243.1| RNA-binding protein [Medicago truncatula] gi|355514578|gb|AES96201.1| RNA-binding protein [Medicago truncatula]

 Score =  852 bits (2201), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 505/782 (64%), Positives = 615/782 (78%), Gaps = 22/782 (2%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRP +PPR PG + VLP V+RPPV GIP +RPI+PPVVRPV  P+VTPAEK  T VY+G
Sbjct: 1   MVRPVYPPRLPGAINVLP-VSRPPVAGIPSIRPIIPPVVRPVVPPSVTPAEKQHTTVYIG 59

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIAPT +++F+LS+LK+CG +KSWKR Q  S+GTPK FGF EF++AEGVLRALRLL K N
Sbjct: 60  KIAPTVENEFMLSLLKLCGNIKSWKRPQDLSSGTPKSFGFYEFDTAEGVLRALRLLTKLN 119

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE 180
           IDGQEL++ VD+A R YLERYV KKT+N+K+ KETQ A  GK D+  ++ + NE  K   
Sbjct: 120 IDGQELVINVDEAMRNYLERYVQKKTDNSKE-KETQAAEVGK-DQVAKTSDVNEEAKPDV 177

Query: 181 NLKDNETGN----KESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQT 236
              + E GN    K++HD   FG+VT+EDR+ D++ALEK+  M+EERL + PLPPPPP  
Sbjct: 178 EHSNKEEGNDSVNKKTHDVATFGIVTDEDREVDRDALEKIKQMIEERLNSRPLPPPPPLP 237

Query: 237 TADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRS 295
           T DGS  S SE P K R+GDSDVD  +N+  E+K + ET  D K  S+HDRPET  PDR 
Sbjct: 238 TGDGSVDSTSEQPTKTREGDSDVD-TKNESGEEKNERETNGDKKPTSEHDRPET--PDRR 294

Query: 296 RVHDR--RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW 353
             HDR  R RD+ER+LKREKER ++RYEREAER+R+RKEREQ+R+IEE ER++E  LK+W
Sbjct: 295 --HDRKSRERDRERELKREKERVLERYEREAERDRIRKEREQKRRIEEVERQFELQLKEW 352

Query: 354 EYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREK 413
           EYRERE+EKERQYEKEKEK+RERKR+KEILYDEE+D+ DSRKRWRR+ +EEKR KR+REK
Sbjct: 353 EYREREKEKERQYEKEKEKDRERKRRKEILYDEEDDDGDSRKRWRRNAIEEKRNKRLREK 412

Query: 414 EEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNG---SLAEESAVESKGM 470
           E+DLAD+ +EEEEIA AK+R EE+Q  ++QRDALKLL+++ VNG   ++A          
Sbjct: 413 EDDLADKQKEEEEIAEAKKRTEEDQQLKRQRDALKLLTEHIVNGRDETMATREITNEMNN 472

Query: 471 DVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGK 530
            V      D++ + +  GD +  N   DEST   +A +D + SGN P +KLGFGLVGSGK
Sbjct: 473 IV---AVQDTVADFNHEGDANVLNTTHDESTMASVATTDTQSSGNAPLKKLGFGLVGSGK 529

Query: 531 RTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRI 590
           RT VPSVFH ++DDDA KDKK+RPLVPIDYSTEELQA +   SG  PPNLAAAAEFAKRI
Sbjct: 530 RTTVPSVFHEDEDDDAHKDKKLRPLVPIDYSTEELQAVESTPSGPTPPNLAAAAEFAKRI 589

Query: 591 SNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDK 650
           S+ N KEE+ D ER+RSR  +++S+ R++DRSDED    RDEH+E+  DRDRDR+HGL+K
Sbjct: 590 SSTNFKEERLDGERDRSRHSNEKSNHRDRDRSDEDGTNHRDEHRERNSDRDRDRDHGLEK 649

Query: 651 VKTPDN-KKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGE 709
            KT DN ++LLDAKQLIDMIPKTKEELFSYEI+WA YDKH+LH+RMRPWISKKI EFLGE
Sbjct: 650 HKTYDNSRRLLDAKQLIDMIPKTKEELFSYEIDWAAYDKHQLHQRMRPWISKKIKEFLGE 709

Query: 710 EETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRS 769
           EE TL DYIVSSTQ+HV+ASQMLE LQ ILD+EAEMFVLKMWRMLIFEIKKVETGLA +S
Sbjct: 710 EENTLTDYIVSSTQEHVQASQMLERLQVILDEEAEMFVLKMWRMLIFEIKKVETGLASKS 769

Query: 770 KS 771
           KS
Sbjct: 770 KS 771

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356501735|ref|XP_003519679.1| PREDICTED: uncharacterized protein LOC100803051 [Glycine max]

 Score =  822 bits (2123), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 521/781 (66%), Positives = 619/781 (79%), Gaps = 26/781 (3%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRP FP RPPG V + P+++RPPV GIP VRPI+PPVVRPV  P+VTPAEKPQ  VY+G
Sbjct: 1   MVRPVFPARPPGAVNI-PTISRPPVAGIPAVRPIIPPVVRPVVAPSVTPAEKPQNTVYIG 59

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIAPT +++F+LS+L++CGT+K+WKR Q  S GTP  FGF EFESAEGVLRALRLL K N
Sbjct: 60  KIAPTVENEFMLSLLQLCGTIKTWKRPQDLSTGTPTSFGFYEFESAEGVLRALRLLTKLN 119

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKS-- 178
           IDGQEL + V+QA +E LERY   KTEN K  K+TQ AG G+++E  Q    N+  K+  
Sbjct: 120 IDGQELKVNVNQAMKENLERYDKTKTENLKN-KKTQ-AGVGEKNEGEQPSNANKDAKADT 177

Query: 179 -PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTT 237
            P N +  E+ NKESHD  NFG+VT+EDR+AD+EALEK++ M+EERLK  PLP P  Q T
Sbjct: 178 EPSNKEVLESSNKESHDVANFGIVTDEDREADREALEKISKMIEERLKIRPLPAPSAQLT 237

Query: 238 ADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRSR 296
            DGS    SE P KARDGDS VD  +N+ AE+K + ET +D K  S+H+R  T SPDR  
Sbjct: 238 GDGSVNLTSEQPVKARDGDSVVDTEKNESAENKNEKETNNDNKPTSEHER--TESPDRR- 294

Query: 297 VHDR--RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 354
            HDR  R RD++R+LKREK+RE++RYEREAERERVRKEREQRR++EE ER+YE  LKDWE
Sbjct: 295 -HDRKSRERDRDRELKREKDRELERYEREAERERVRKEREQRRRVEETERQYETYLKDWE 353

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 414
           YRERE+EKERQYEKEKEKERERKR+KEILYDEE++++DSRKRWRRSV+E+KR+KR+REKE
Sbjct: 354 YREREKEKERQYEKEKEKERERKRRKEILYDEEDEDEDSRKRWRRSVIEDKRKKRLREKE 413

Query: 415 EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKGM 470
           +DL D  +EEEEIA  K++AEEEQ  +QQRDALKLLS++ VN      + EE  +E K +
Sbjct: 414 DDLVDRQKEEEEIAETKKKAEEEQ--KQQRDALKLLSEHVVNAGKENMITEEITIEVKSI 471

Query: 471 DVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGK 530
             E D   D   E H+ GD  S N   DES    +A +D +  GN P +KLGFGLVGSGK
Sbjct: 472 VAEQDTVADYHHEYHI-GDGDSINVINDESIIASVATTDAQSGGNAPTKKLGFGLVGSGK 530

Query: 531 RTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRI 590
           RT+V SVFH EDD++A   KKMRPLVPIDYSTEELQA QP VSG  PPNLAAAAEFAKRI
Sbjct: 531 RTSVRSVFHEEDDNEA---KKMRPLVPIDYSTEELQAVQPTVSGPTPPNLAAAAEFAKRI 587

Query: 591 SNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDK 650
           S+ N KEEK D ER+RSRR +++S+ R  DRSD D    RDE+KE+I  RDRDR+HG +K
Sbjct: 588 SSTNFKEEKLDGERDRSRRSNEKSNHR--DRSD-DGTHNRDENKERIPGRDRDRDHGSEK 644

Query: 651 VKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEE 710
           ++T DNK+LLDAKQLIDMIPKTKEELFSYEI+WAVYDKH+LH+RMRPWISKKI EFLGEE
Sbjct: 645 LRTSDNKRLLDAKQLIDMIPKTKEELFSYEIDWAVYDKHQLHDRMRPWISKKIQEFLGEE 704

Query: 711 ETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSK 770
           ETTL+DYIVSSTQ+HVKASQMLE LQ ILD+EAEMFVLKMWRMLIFEIKKVE+GLALRSK
Sbjct: 705 ETTLIDYIVSSTQEHVKASQMLERLQIILDEEAEMFVLKMWRMLIFEIKKVESGLALRSK 764

Query: 771 S 771
           S
Sbjct: 765 S 765

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497763|ref|XP_003517728.1| PREDICTED: uncharacterized protein LOC100809428 [Glycine max]

 Score =  809 bits (2090), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 531/781 (67%), Positives = 625/781 (80%), Gaps = 23/781 (2%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRP FP RPPG V + P+++RPPV GIP VRPI+PPVVRPV  P+VTPAEKPQ  VY+G
Sbjct: 160 MVRPVFPARPPGAVNI-PTISRPPVAGIPAVRPIIPPVVRPVVAPSVTPAEKPQNTVYIG 218

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIAPT +++F+LS+L++CGT+K+WKR Q  S GTP  FGF EFESAEGVLRALRLL K N
Sbjct: 219 KIAPTVENEFMLSLLQLCGTIKTWKRPQDLSTGTPTSFGFYEFESAEGVLRALRLLTKLN 278

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK--- 177
           IDGQEL + V+QA +E LE YV  KTEN K  KETQ+ G   E E  Q    NE  K   
Sbjct: 279 IDGQELKVNVNQAMKEILELYVKTKTENLKN-KETQEVGEKNEGE--QPSNANEDAKVDT 335

Query: 178 SPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTT 237
            P N + +E+ NKESHD  NFG+VT+EDR+AD EALEK+T M+EERLKT PLP PP Q T
Sbjct: 336 EPSNKEASESSNKESHDVANFGIVTDEDREADCEALEKITKMIEERLKTRPLPTPPAQPT 395

Query: 238 ADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRSR 296
            DGS    SE P KARDGDS VD  +N+ AE+K + ET +D K  S+H+R  T SPDR  
Sbjct: 396 GDGSVNLTSEQPVKARDGDSVVDTEKNESAENKNEKETNNDNKPTSEHER--TESPDRR- 452

Query: 297 VHDR--RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 354
            HDR  R RD++R+LKREK+RE++RYEREAERERVRKEREQRR++EEAER+YE  LKDWE
Sbjct: 453 -HDRKSRERDRDRELKREKDRELERYEREAERERVRKEREQRRRVEEAERQYETYLKDWE 511

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 414
           YRERE+EKERQYEKEKEKERERKR+KEILYDEE++++DSRKRWRRSV+EEKR+KR+REKE
Sbjct: 512 YREREKEKERQYEKEKEKERERKRRKEILYDEEDEDEDSRKRWRRSVIEEKRKKRLREKE 571

Query: 415 EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKGM 470
           +DL D  R++EE  +A+ + + E+ Q++QRDALKLLS++ VNG     + EE   E K +
Sbjct: 572 DDLVD--RQKEEEEIAEAKKKAEEEQKRQRDALKLLSEHVVNGGKENMITEEITNEVKSI 629

Query: 471 DVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGK 530
            VE D   D  RE+H+ GD +S N   DEST   +A +D +  GN P +KLGFGLVGSGK
Sbjct: 630 VVEQDTVADYSREDHI-GDGNSINVIIDESTIASVAPTDAQSGGNAPTKKLGFGLVGSGK 688

Query: 531 RTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRI 590
           RT+VPSVFH EDDDDA KDKKMRPLVPIDYSTEELQA QP VSG  PPNLAAAAEFAKRI
Sbjct: 689 RTSVPSVFHEEDDDDAHKDKKMRPLVPIDYSTEELQAVQPTVSGPTPPNLAAAAEFAKRI 748

Query: 591 SNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDK 650
           S+ N KEEK D ER+RSRR +++S+ R  DRSDED    RDE+KE+I  RDRDR+HG +K
Sbjct: 749 SSTNFKEEKLDGERDRSRRSNEKSNHR--DRSDEDGTHNRDENKERIPGRDRDRDHGSEK 806

Query: 651 VKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEE 710
           +KT DNK+LLDAKQLIDMIPKTKEELFSYEI+WAVYDKH+LH+RMRPWISKKI EFLGEE
Sbjct: 807 LKTSDNKRLLDAKQLIDMIPKTKEELFSYEIDWAVYDKHQLHDRMRPWISKKIKEFLGEE 866

Query: 711 ETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSK 770
           ETTL+DYIVSSTQ+HVKASQMLE LQ ILD+EAEMFVLKMWRMLIFEIKKVE+GLALRSK
Sbjct: 867 ETTLIDYIVSSTQEHVKASQMLERLQIILDEEAEMFVLKMWRMLIFEIKKVESGLALRSK 926

Query: 771 S 771
           S
Sbjct: 927 S 927

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434915|ref|XP_004135241.1| PREDICTED: uncharacterized protein LOC101214372 [Cucumis sativus]

 Score =  798 bits (2062), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 525/779 (67%), Positives = 635/779 (81%), Gaps = 17/779 (2%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           M+R  FPPRPPG +G++P + RPP+PGIPGVRPI+PPVVRP  LP++TPAEKPQT +Y+G
Sbjct: 1   MIRTPFPPRPPGAMGMVPGMPRPPIPGIPGVRPIIPPVVRPAILPSITPAEKPQTTIYIG 60

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           +IA + D+DF+LS+L++CG VKSWKRAQ PS+GTP+ FGFCEFESAEGVLRALRLL K N
Sbjct: 61  RIAQSVDNDFMLSLLQLCGPVKSWKRAQDPSDGTPRTFGFCEFESAEGVLRALRLLTKLN 120

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK-SP 179
           IDGQEL LK  QATR+YL+RYV+KK EN+KKLKETQ +   +E+    +V K E +K S 
Sbjct: 121 IDGQELGLKGTQATRDYLKRYVEKKAENSKKLKETQASETKEEETDTTNVAKKETSKPSA 180

Query: 180 ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTAD 239
           E+ K++    ++  D     V+++EDR AD+EA EKLT  +EER+K+ PLPPPP  TT D
Sbjct: 181 EDSKEDHDSGEKDFDIACSAVLSDEDRDADREAKEKLTNALEERMKSRPLPPPPLLTTTD 240

Query: 240 GSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRSRVH 298
            S  S+ E  AK +DG++D D  + D A+D+ D++TTSD K AS+HD+PETSSP+RSR +
Sbjct: 241 VSDNSSVEPSAKPKDGEADGDTSKPDAADDRNDEDTTSDHKQASEHDKPETSSPERSRRY 300

Query: 299 DRRGRDKERD--LKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYR 356
           DRR R+++R+  LKR+KEREI+RYERE ERER RKEREQRRK EEAER+YE CLK+WEYR
Sbjct: 301 DRRSRERDRERDLKRDKEREIERYERETERERARKEREQRRKFEEAERQYEECLKEWEYR 360

Query: 357 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 416
           EREREK+RQYEKE+EKE+ERKRKKEILYDE++++DDSR++WRR  LEEKR+KR REKE+D
Sbjct: 361 EREREKQRQYEKEREKEKERKRKKEILYDEDDEDDDSRRKWRRGALEEKRKKRSREKEDD 420

Query: 417 LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKGMDV 472
             D  REEEEIA AKR+AEEEQLQ+  RD  KLL    ++ S     AEES +E K +  
Sbjct: 421 SFDRQREEEEIAEAKRKAEEEQLQKL-RDPPKLLPSQTISVSEKTVTAEESTIEIKVVAS 479

Query: 473 EHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRT 532
           E +   DS  +NH+ GD   QNG+GDE   +P   S+ RQSG +P ++LGFGLVGSGKRT
Sbjct: 480 ERESEIDSSCDNHI-GDGILQNGSGDELNTIP---SETRQSGGLPGKRLGFGLVGSGKRT 535

Query: 533 AVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISN 592
           AVPSVFH E+DD+A K+KKMRPLVPIDYS EELQA QP  +GA PPNLAAAAEFAKRISN
Sbjct: 536 AVPSVFHEEEDDEAHKEKKMRPLVPIDYSAEELQAVQPPSTGALPPNLAAAAEFAKRISN 595

Query: 593 VNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVK 652
           VNSKEEK D+ERER RR  ++S  R  DR+DED +R++DE+K    DRDR+R+H LDKVK
Sbjct: 596 VNSKEEKPDSERERGRRPSEKSGHR--DRNDEDTHRSKDENK--ATDRDRERDHVLDKVK 651

Query: 653 TPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEET 712
           TPDNKKLLDAKQLIDMIPKTKEELFSY+INWA+Y+KH LHERMRPWISKKITEFLGEEET
Sbjct: 652 TPDNKKLLDAKQLIDMIPKTKEELFSYDINWAIYEKHALHERMRPWISKKITEFLGEEET 711

Query: 713 TLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS 771
           TLVDYIVSSTQ+HVKASQMLELLQ+ILD+EAEMFVLKMWRMLIFEIKKVETGLA R+K+
Sbjct: 712 TLVDYIVSSTQEHVKASQMLELLQSILDEEAEMFVLKMWRMLIFEIKKVETGLAFRTKA 770

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449513686|ref|XP_004164394.1| PREDICTED: uncharacterized LOC101214372 [Cucumis sativus]

 Score =  795 bits (2053), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 525/779 (67%), Positives = 635/779 (81%), Gaps = 17/779 (2%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           M+R  FPPRPPG +G++P + RPP+PGIPGVRPI+PPVVRP  LP++TPAEKPQT +Y+G
Sbjct: 199 MIRTPFPPRPPGAMGMVPGMPRPPIPGIPGVRPIIPPVVRPAILPSITPAEKPQTTIYIG 258

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           +IA + D+DF+LS+L++CG VKSWKRAQ PS+GTP+ FGFCEFESAEGVLRALRLL K N
Sbjct: 259 RIAQSVDNDFMLSLLQLCGPVKSWKRAQDPSDGTPRTFGFCEFESAEGVLRALRLLTKLN 318

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK-SP 179
           IDGQEL LK  QATR+YL+RYV+KK EN+KKLKETQ +   +E+    +V K E +K S 
Sbjct: 319 IDGQELGLKGTQATRDYLKRYVEKKAENSKKLKETQASETKEEETDTTNVAKKETSKPSA 378

Query: 180 ENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTAD 239
           E+ K++    ++  D     V+++EDR AD+EA EKLT  +EER+K+ PLPPPP  TT D
Sbjct: 379 EDSKEDHDSGEKDFDIACSAVLSDEDRDADREAKEKLTNALEERMKSRPLPPPPLLTTTD 438

Query: 240 GSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRSRVH 298
            S  S+ E  AK +DG++D D  + D A+D+ D++TTSD K AS+HD+PETSSP+RSR +
Sbjct: 439 VSDNSSVEPSAKPKDGEADGDTSKPDAADDRNDEDTTSDHKQASEHDKPETSSPERSRRY 498

Query: 299 DRRGRDKERD--LKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYR 356
           DRR R+++R+  LKR+KEREI+RYERE ERER RKEREQRRK EEAER+YE CLK+WEYR
Sbjct: 499 DRRSRERDRERDLKRDKEREIERYERETERERARKEREQRRKFEEAERQYEECLKEWEYR 558

Query: 357 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 416
           EREREK+RQYEKE+EKE+ERKRKKEILYDE++++DDSR++WRR  LEEKR+KR REKE+D
Sbjct: 559 EREREKQRQYEKEREKEKERKRKKEILYDEDDEDDDSRRKWRRGALEEKRKKRSREKEDD 618

Query: 417 LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESKGMDV 472
             D  REEEEIA AKR+AEEEQLQ+  RD  KLL    ++ S     AEES +E K +  
Sbjct: 619 SFDRQREEEEIAEAKRKAEEEQLQKL-RDPPKLLPSQTISVSEKTVTAEESTIEIKVVAS 677

Query: 473 EHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRT 532
           E +   DS  +NH+ GD   QNG+GDE   +P   S+ RQSG +P ++LGFGLVGSGKRT
Sbjct: 678 ERESEIDSSCDNHI-GDGILQNGSGDELNTIP---SETRQSGGLPGKRLGFGLVGSGKRT 733

Query: 533 AVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISN 592
           AVPSVFH E+DD+A K+KKMRPLVPIDYS EELQA QP  +GA PPNLAAAAEFAKRISN
Sbjct: 734 AVPSVFHEEEDDEAHKEKKMRPLVPIDYSAEELQAVQPPSTGALPPNLAAAAEFAKRISN 793

Query: 593 VNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVK 652
           VNSKEEK D+ERER RR  ++S  R  DR+DED +R++DE+K    DRDR+R+H LDKVK
Sbjct: 794 VNSKEEKPDSERERGRRPSEKSGHR--DRNDEDTHRSKDENK--ATDRDRERDHVLDKVK 849

Query: 653 TPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEET 712
           TPDNKKLLDAKQLIDMIPKTKEELFSY+INWA+Y+KH LHERMRPWISKKITEFLGEEET
Sbjct: 850 TPDNKKLLDAKQLIDMIPKTKEELFSYDINWAIYEKHALHERMRPWISKKITEFLGEEET 909

Query: 713 TLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS 771
           TLVDYIVSSTQ+HVKASQMLELLQ+ILD+EAEMFVLKMWRMLIFEIKKVETGLA R+K+
Sbjct: 910 TLVDYIVSSTQEHVKASQMLELLQSILDEEAEMFVLKMWRMLIFEIKKVETGLAFRTKA 968

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307135981|gb|ADN33840.1| RNA binding motif protein [Cucumis melo subsp. melo]

 Score =  763 bits (1970), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 518/766 (67%), Positives = 626/766 (81%), Gaps = 17/766 (2%)

Query: 14  VGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLS 73
           +G++P++ RPP+PGIPGVRPI+PPVVRP  LP+VTPAEKPQT +Y+G+IA + D+DF+LS
Sbjct: 14  MGMVPAMPRPPIPGIPGVRPIIPPVVRPAVLPSVTPAEKPQTTIYIGRIAQSVDNDFMLS 73

Query: 74  VLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA 133
           +L++CG VKSWKRAQ PS+GTP+ FGFCEFESAEGVLRALRLL K NIDGQEL LK  QA
Sbjct: 74  LLQLCGPVKSWKRAQDPSDGTPRTFGFCEFESAEGVLRALRLLTKLNIDGQELGLKGTQA 133

Query: 134 TREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK-SPENLKDNETGNKES 192
           TR+YL+RYV+KK EN+KKLKETQ +   +E+    +V K E +K S E+ K++    ++ 
Sbjct: 134 TRDYLKRYVEKKAENSKKLKETQISETKEEEADTANVAKKETSKPSAEDSKEDHDSGEKD 193

Query: 193 HDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKA 252
            D     V+++EDR AD+EA EK+T  +EERLK+ PLPPPP  TT D S  S+ E  AK 
Sbjct: 194 FDIACSAVLSDEDRDADREAKEKITNALEERLKSRPLPPPPLLTTTDVSDNSSVEPSAKL 253

Query: 253 RDGDSDVDMIRNDIAEDKLDDETTSDTK-ASDHDRPETSSPDRSRVHDRRGRDKERD--L 309
           +DG++D D ++ D A+D+ D++TTSD K AS+HD+PETSSPDRSR +DRR R+++R+  L
Sbjct: 254 KDGEADGDTLKPDAADDRNDEDTTSDHKQASEHDKPETSSPDRSRRYDRRSRERDRERDL 313

Query: 310 KREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKE 369
           KR+KEREI+RYERE ERER RKEREQRRK EEAER+YE CLK+WEYREREREK+RQYEKE
Sbjct: 314 KRDKEREIERYERETERERARKEREQRRKFEEAERQYEECLKEWEYREREREKQRQYEKE 373

Query: 370 KEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAV 429
           +EKE+ERKRKKEILYDE++++DDSR++WRR  LEEKR+KR REKE+D  D  +EEEEIA 
Sbjct: 374 REKEKERKRKKEILYDEDDEDDDSRRKWRRGALEEKRKKRSREKEDDSFDREKEEEEIAE 433

Query: 430 AKRRAEEEQLQQQQRDALKLL--SDNAVN--GSLAEESAVESKGMDVEHDYHDDSIRENH 485
           AKR+AEEEQLQ+  RD  KLL     ++N    +AEES  E K M  E +   DS  +NH
Sbjct: 434 AKRKAEEEQLQKL-RDPPKLLPGQTTSINEKTVIAEESTNEIKVMASERESELDSSCDNH 492

Query: 486 MAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDD 545
           + GD  SQNG+GDE   +P   S+ RQSG +P ++LGFGLVGSGKRTAVPSVFH E+DD+
Sbjct: 493 I-GDGISQNGSGDELNTIP---SETRQSGGLPGKRLGFGLVGSGKRTAVPSVFHEEEDDE 548

Query: 546 ADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERE 605
           A K+KKMRPLVPIDYS EELQA QP  +GA PPNLAAAAEFAKRISN NSKEEK D+ERE
Sbjct: 549 AHKEKKMRPLVPIDYSAEELQAVQPASTGALPPNLAAAAEFAKRISNANSKEEKPDSERE 608

Query: 606 RSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQL 665
           R RR  ++S  R  DR+DED  R++DE+K    DRDR+R+H LDKVKTPDNKKLLDAKQL
Sbjct: 609 RGRRPSEKSGHR--DRNDEDTYRSKDENK--ATDRDRERDHVLDKVKTPDNKKLLDAKQL 664

Query: 666 IDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDH 725
           IDMIPKTKEELFSY+INWA+Y+KH LHERMRPWISKKITEFLGEEETTLVDYIVSSTQ+H
Sbjct: 665 IDMIPKTKEELFSYDINWAIYEKHALHERMRPWISKKITEFLGEEETTLVDYIVSSTQEH 724

Query: 726 VKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS 771
           VKASQMLELLQ+ILD+EAEMFVLKMWRMLIFEIKKVETGLA R+K+
Sbjct: 725 VKASQMLELLQSILDEEAEMFVLKMWRMLIFEIKKVETGLAFRTKA 770

Source: Cucumis melo subsp. melo

Species: Cucumis melo

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	771
TAIR|locus:2195568	899	AT1G60200 [Arabidopsis thalian	0.369	0.317	0.591	6.4e-136
MGI|MGI:1914289	838	Rbm25 "RNA binding motif prote	0.182	0.168	0.395	5.2e-39
UNIPROTKB|E1BSR5	782	RBM25 "Uncharacterized protein	0.182	0.180	0.402	1.2e-38
UNIPROTKB|E1BHM5	843	RBM25 "Uncharacterized protein	0.182	0.167	0.395	1.4e-38
UNIPROTKB|P49756	843	RBM25 "RNA-binding protein 25"	0.182	0.167	0.395	1.4e-38
ZFIN|ZDB-GENE-030131-5547	833	rbm25 "RNA binding motif prote	0.289	0.267	0.297	8.4e-36
WB|WBGene00012245	707	W04D2.6 [Caenorhabditis elegan	0.169	0.185	0.364	1.7e-35
FB|FBgn0028474	998	CG4119 [Drosophila melanogaste	0.217	0.168	0.352	6.2e-32
RGD|1308755	354	Rbm25 "RNA binding motif prote	0.182	0.398	0.395	1.7e-29
DICTYBASE|DDB_G0269926	724	DDB_G0269926 "splicing factor	0.215	0.229	0.335	1.2e-26

TAIR|locus:2195568 AT1G60200 [Arabidopsis thaliana (taxid:3702)]

 Score = 837 (299.7 bits), Expect = 6.4e-136, Sum P(3) = 6.4e-136
 Identities = 175/296 (59%), Positives = 216/296 (72%)

Query:   479 DSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVF 538
             +S  E+H A D   +NG+G+ES  +    ++     + P++KLGFGLVGSGKRT+VPSVF
Sbjct:   612 ESANEHH-AAD-FEENGSGNESMAID---NNSGSEAHAPSKKLGFGLVGSGKRTSVPSVF 666

Query:   539 HVEXXXXXXXXXXMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEE 598
             + E          M+PLVPIDYSTEE +A     SG  PP+LA AAEFAKRIS+ N KEE
Sbjct:   667 YEEDEDEARKAKKMKPLVPIDYSTEEQEAVAHGGSGNTPPHLALAAEFAKRISSTNPKEE 726

Query:   599 KSDAERERSRRLHDRSSQREKDRS---DEDNNRTRDEHKEKILDRDRDREHGLDKVKTPD 655
               + E++RSRR HD++S R+++R    D D +R RD            +E G  K K  D
Sbjct:   727 TIETEKQRSRRSHDKASHRDRERERERDRDRDRVRDRGDGHSGPTKDAKESG--KAKIID 784

Query:   656 NKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLV 715
              K  LDAKQLID IPKTKE+LFSYEINWA+YDKH++HERMRPWISKKI EFLGEEE TLV
Sbjct:   785 TK-FLDAKQLIDTIPKTKEDLFSYEINWAMYDKHQVHERMRPWISKKIMEFLGEEEATLV 843

Query:   716 DYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS 771
             D+IVS+TQ HV+ASQMLELLQ+ILD+EAEMFVLKMWRMLIFEIK+VE G+ ++SK+
Sbjct:   844 DFIVSNTQQHVQASQMLELLQSILDEEAEMFVLKMWRMLIFEIKRVEAGVPVKSKA 899

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0006397 "mRNA processing" evidence=IEA

MGI|MGI:1914289 Rbm25 "RNA binding motif protein 25" [Mus musculus (taxid:10090)]

 Score = 288 (106.4 bits), Expect = 5.2e-39, Sum P(4) = 5.2e-39
 Identities = 57/144 (39%), Positives = 90/144 (62%)

Query:   623 DEDNNRTRDEHKEKILDRDRDREHGLD-KVKTPDNKKLLDAKQLIDMIPKTKEELFSYEI 681
             DED++    + K   LD   D ++     V T + +K +  K LI+ IP  K ELF+Y +
Sbjct:   695 DEDSDDVPRKRKLVPLDYGEDDKNATKGTVNTEEKRKHI--KSLIEKIPTAKPELFAYPL 752

Query:   682 NWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDD 741
             +W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S    H     +L+ +  +LD+
Sbjct:   753 DWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDE 812

Query:   742 EAEMFVLKMWRMLIFEIKKVETGL 765
             EAE+F++KMWR+LI+E +  + GL
Sbjct:   813 EAEVFIVKMWRLLIYETEAKKIGL 836

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006915 "apoptotic process" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=ISO

UNIPROTKB|E1BSR5 RBM25 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 295 (108.9 bits), Expect = 1.2e-38, Sum P(4) = 1.2e-38
 Identities = 58/144 (40%), Positives = 91/144 (63%)

Query:   623 DEDNNRTRDEHKEKILDR-DRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEI 681
             DED++    + K   LD  D D+ +    V T + +K +  K LI+ IP  K ELF+Y +
Sbjct:   639 DEDSDDVPRKRKLVPLDYGDEDKSNIKGSVNTEEKRKHI--KSLIEKIPTAKPELFAYPL 696

Query:   682 NWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDD 741
             +W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S    H     +L+ +  +LD+
Sbjct:   697 DWSIVDSTLMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDE 756

Query:   742 EAEMFVLKMWRMLIFEIKKVETGL 765
             EAE+F++KMWR+LI+E +  + GL
Sbjct:   757 EAEVFIVKMWRLLIYETEAKKIGL 780

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|E1BHM5 RBM25 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 288 (106.4 bits), Expect = 1.4e-38, Sum P(4) = 1.4e-38
 Identities = 57/144 (39%), Positives = 90/144 (62%)

Query:   623 DEDNNRTRDEHKEKILDRDRDREHGLD-KVKTPDNKKLLDAKQLIDMIPKTKEELFSYEI 681
             DED++    + K   LD   D ++     V T + +K +  K LI+ IP  K ELF+Y +
Sbjct:   700 DEDSDDVPRKRKLVPLDYGEDDKNAAKGTVNTEEKRKHI--KSLIEKIPTAKPELFAYPL 757

Query:   682 NWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDD 741
             +W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S    H     +L+ +  +LD+
Sbjct:   758 DWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDE 817

Query:   742 EAEMFVLKMWRMLIFEIKKVETGL 765
             EAE+F++KMWR+LI+E +  + GL
Sbjct:   818 EAEVFIVKMWRLLIYETEAKKIGL 841

GO:0016607 "nuclear speck" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P49756 RBM25 "RNA-binding protein 25" [Homo sapiens (taxid:9606)]

 Score = 288 (106.4 bits), Expect = 1.4e-38, Sum P(4) = 1.4e-38
 Identities = 57/144 (39%), Positives = 90/144 (62%)

Query:   623 DEDNNRTRDEHKEKILDRDRDREHGLD-KVKTPDNKKLLDAKQLIDMIPKTKEELFSYEI 681
             DED++    + K   LD   D ++     V T + +K +  K LI+ IP  K ELF+Y +
Sbjct:   700 DEDSDDVPRKRKLVPLDYGEDDKNATKGTVNTEEKRKHI--KSLIEKIPTAKPELFAYPL 757

Query:   682 NWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDD 741
             +W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S    H     +L+ +  +LD+
Sbjct:   758 DWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDE 817

Query:   742 EAEMFVLKMWRMLIFEIKKVETGL 765
             EAE+F++KMWR+LI+E +  + GL
Sbjct:   818 EAEVFIVKMWRLLIYETEAKKIGL 841

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

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

GO:0016607 "nuclear speck" evidence=IDA

GO:0003729 "mRNA binding" evidence=IDA

GO:0006915 "apoptotic process" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

ZFIN|ZDB-GENE-030131-5547 rbm25 "RNA binding motif protein 25" [Danio rerio (taxid:7955)]

 Score = 278 (102.9 bits), Expect = 8.4e-36, Sum P(3) = 8.4e-36
 Identities = 71/239 (29%), Positives = 122/239 (51%)

Query:   532 TAVPSVFHVEXXXXXXXXXXMRP---LVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAK 588
             TA PSV                P   ++P + S +E+   +      N P +  +     
Sbjct:   604 TAAPSVSSASGNATPNTPREESPCGIIIPHENSPQEMLLPEE-----NRPKIGLSL---- 654

Query:   589 RISNVNSKEEKSDAERERS--RRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREH 646
             ++ +  S  + S A+R++     + +R    E D +         +++++    D     
Sbjct:   655 KLGSSGSPGQPSVAKRKKLPVESVFNRFDDDEVDEAPRKRKLVPLDYEDEEKAVDGATVA 714

Query:   647 GLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEF 706
             G   V T + +K +  K LI+ IP  K ELF+Y ++W+V D   + +R+RPWI+KKI E+
Sbjct:   715 GGKGVNTEEKRKHI--KSLIEKIPTAKPELFNYPLDWSVVDTALMEKRIRPWINKKIVEY 772

Query:   707 LGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGL 765
             +GEEE TLVD++ S    H     +L+ +  +LD+EAE+F++KMWR+LI+E +  + GL
Sbjct:   773 IGEEEATLVDFVCSKVMAHSTPQGILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGL 831

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

WB|WBGene00012245 W04D2.6 [Caenorhabditis elegans (taxid:6239)]

 Score = 258 (95.9 bits), Expect = 1.7e-35, Sum P(2) = 1.7e-35
 Identities = 50/137 (36%), Positives = 86/137 (62%)

Query:   622 SDEDNNRTRDEH-KEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYE 680
             +D+D +   D H K+K+   +  RE  +  +   + ++L   KQ+I  IP TK+ELF + 
Sbjct:   567 NDDDED---DVHSKKKLKPFEITREERMQVMSAEEKREL--TKQIIKTIPATKDELFVHR 621

Query:   681 INWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILD 740
             I W   D   +++R+RPW++KK+T+FLGEE+ +  D+I    +      ++L+ +  I+D
Sbjct:   622 IEWDQLDGKWMNDRIRPWVAKKVTQFLGEEDKSFCDFICDQIEKQATPQEILKDVAVIID 681

Query:   741 DEAEMFVLKMWRMLIFE 757
             ++AE FV+KMWR+LI+E
Sbjct:   682 EDAEQFVIKMWRLLIYE 698

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0018991 "oviposition" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

FB|FBgn0028474 CG4119 [Drosophila melanogaster (taxid:7227)]

 Score = 264 (98.0 bits), Expect = 6.2e-32, Sum P(4) = 6.2e-32
 Identities = 62/176 (35%), Positives = 97/176 (55%)

Query:   591 SNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDK 650
             SN +  +         S   H+ +S+  K+ +      + D     I  +D   E+G   
Sbjct:   829 SNASGGKNNGGGSSSSSNNKHNSNSKHGKNEAAASAGSSADAAAANI-KKD---ENG--- 881

Query:   651 VKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEE 710
              K  D K+    K +ID IP  KEELF+Y+++    D   +  ++RPWI+KKI E++GE 
Sbjct:   882 AKVYDEKRR-HIKSIIDRIPTQKEELFNYKLDRNEIDSGLMERKIRPWINKKIIEYIGEP 940

Query:   711 ETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLA 766
             E TLVD+I S          +L+ +Q +LD+EAE+FV+KMWR+LI+E+   ++GLA
Sbjct:   941 EPTLVDFICSKVLAGSPPQSILDDVQMVLDEEAEVFVVKMWRLLIYELDAKKSGLA 996

GO:0003729 "mRNA binding" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IC

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

RGD|1308755 Rbm25 "RNA binding motif protein 25" [Rattus norvegicus (taxid:10116)]

 Score = 288 (106.4 bits), Expect = 1.7e-29, Sum P(3) = 1.7e-29
 Identities = 57/144 (39%), Positives = 90/144 (62%)

Query:   623 DEDNNRTRDEHKEKILDRDRDREHGLD-KVKTPDNKKLLDAKQLIDMIPKTKEELFSYEI 681
             DED++    + K   LD   D ++     V T + +K +  K LI+ IP  K ELF+Y +
Sbjct:   211 DEDSDDVPRKRKLVPLDYGEDDKNAAKGTVNTEEKRKHI--KSLIEKIPTAKPELFAYPL 268

Query:   682 NWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDD 741
             +W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S    H     +L+ +  +LD+
Sbjct:   269 DWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDE 328

Query:   742 EAEMFVLKMWRMLIFEIKKVETGL 765
             EAE+F++KMWR+LI+E +  + GL
Sbjct:   329 EAEVFIVKMWRLLIYETEAKKIGL 352

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

GO:0003729 "mRNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

DICTYBASE|DDB_G0269926 DDB_G0269926 "splicing factor PWI domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 201 (75.8 bits), Expect = 1.2e-26, Sum P(2) = 1.2e-26
 Identities = 61/182 (33%), Positives = 88/182 (48%)

Query:    55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             T  Y+GKI    +  F+ S+L  CG V  W RA   +NG  K FG CEFE AEG + ALR
Sbjct:   246 TTAYIGKIPQFVEDSFIRSLLNQCGKVSKWNRAS-DTNGKLKQFGLCEFEHAEGAVTALR 304

Query:   115 LLNKFNID--GQELMLKVDQATREYLERYVDXXXXXXXXXXXX-QDAGAGKEDESVQS-V 170
             +LN   +D  G +L++KVD+  +++   Y+D             QD       ES+++ V
Sbjct:   305 VLNDLEVDRDGGKLVVKVDKG-QKFFSDYLDKKGGLTDQSSDSPQDIILR---ESIKAMV 360

Query:   171 EKN----EPTKSPENLKDNETGNKESHDPTN---FGVVTEEDRKADQEALEKLTCMVEER 223
             EKN       K  E+ + N+  NK+  D T      ++ +E  K  Q   E+     E  
Sbjct:   361 EKNFINIYEKKKMESNEINDFYNKDRRDLTKEEKIKIIEKEKEKEKQRHKERELKNKERD 420

Query:   224 LK 225
             LK
Sbjct:   421 LK 422

GO:0006397 "mRNA processing" evidence=IEA

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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	771
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	6e-35
smart00311	74	smart00311, PWI, PWI, domain in splicing factors	2e-22
pfam01480	74	pfam01480, PWI, PWI domain	2e-14
smart00360	73	smart00360, RRM, RNA recognition motif	6e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	9e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	8e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	9e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-05
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-05
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-05
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	5e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	9e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-04
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	2e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	3e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	4e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	4e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	4e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	6e-04
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	6e-04
pfam05557	722	pfam05557, MAD, Mitotic checkpoint protein	6e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-04
COG2268	548	COG2268, COG2268, Uncharacterized protein conserve	7e-04
COG1390	194	COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase su	7e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	8e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	0.001
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	0.001
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.001
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.001
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.002
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.002
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.002
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.003
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.003
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	0.003
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	0.003
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.003
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.004
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.004
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	0.004

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score =  127 bits (321), Expect = 6e-35
 Identities = 44/84 (52%), Positives = 55/84 (65%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           T V+VG I      DF+  +L+ CG V SWKR + PS G  K FGFCEFE  EG LRALR
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 115 LLNKFNIDGQELMLKVDQATREYL 138
           LLN   + G++L++KVD  TR+ L
Sbjct: 61  LLNGLELGGKKLLVKVDAKTRKLL 84

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|214609 smart00311, PWI, PWI, domain in splicing factors

 Score = 91.3 bits (227), Expect = 2e-22
 Identities = 30/74 (40%), Positives = 45/74 (60%)

Query: 687 DKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMF 746
                 + ++PWI+KK+ EFLG EE TLV++I+S  + H      L  +     ++AE F
Sbjct: 1   LSKLKLDEIKPWITKKVIEFLGFEEDTLVEFILSQIRQHKGPQAKLLQINLTGFEDAEEF 60

Query: 747 VLKMWRMLIFEIKK 760
           V K+WR+LIFE+K 
Sbjct: 61  VDKLWRLLIFELKN 74

Length = 74

>gnl|CDD|216523 pfam01480, PWI, PWI domain

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 693 ERMRPWISKKITEFLGEEETTLVDYIVS--STQDHVKASQMLELLQTILDDEAEMFVLKM 750
           E ++PWI KK+TE LG E+  ++DYI++    + +    ++   L   LD  AE+FV ++
Sbjct: 2   EVIKPWIEKKVTEILGFEDDIVIDYILNLLEDKHNPDPKKIQIQLTGFLDKNAEVFVKEL 61

Query: 751 WRMLIFEIK 759
           W +LI   +
Sbjct: 62  WELLISAQE 70

Length = 74

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

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 23/71 (32%), Positives = 35/71 (49%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
            ++VG + P    + +  +    G V+S +  +    G  KGF F EFES E   +AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 116 LNKFNIDGQEL 126
           LN   +DG+ L
Sbjct: 61  LNGKELDGRPL 71

Length = 73

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           ++VG + P    + +  +    G ++S  R     +G  KGF F EFES E   +AL  L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESV-RIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 117 NKFNIDGQELMLK 129
           N   +DG++L + 
Sbjct: 60  NGKELDGRKLKVS 72

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

>gnl|CDD|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 = 53.8 bits (130), Expect = 2e-09
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           V+VG I   A  + ++ +    G V S++       G PKG+GFCEFE  E    A+R  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIR-- 58

Query: 117 NKFNIDGQELM---LKVDQA 133
              N++G E     L+VD A
Sbjct: 59  ---NLNGYEFNGRALRVDFA 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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 59.8 bits (144), Expect = 6e-09
 Identities = 62/305 (20%), Positives = 135/305 (44%), Gaps = 32/305 (10%)

Query: 144  KKTENTKKLKETQDAGAGKEDESVQSVE---KNEPTKSPENLKDNETGNKESHDPTNFGV 200
            KK +  KK +E + A   K+ E  +  +   K E  K  E  K  E   K   D      
Sbjct: 1522 KKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALR 1581

Query: 201  VTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVD 260
              EE +KA++  +E++  + EE  K                    +E   KA +     +
Sbjct: 1582 KAEEAKKAEEARIEEVMKLYEEEKKMK------------------AEEAKKAEEAKIKAE 1623

Query: 261  MIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRY 320
             ++    E K  ++             +  + ++ +  + +  ++E  +K  +E +    
Sbjct: 1624 ELKKAEEEKKKVEQL-----------KKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 321  EREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKK 380
            +++   E  + E ++++  E  ++E E   K  E +++E E++++ E+ K+ E E K K 
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKA 1732

Query: 381  EILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQ 440
            E    E E++    +  ++   E+K+   ++++EE  A+E+R+E+E  + +   EE++ +
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKR 1792

Query: 441  QQQRD 445
            + + D
Sbjct: 1793 RMEVD 1797

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 58.2 bits (140), Expect = 2e-08
 Identities = 41/184 (22%), Positives = 92/184 (50%), Gaps = 6/184 (3%)

Query: 304  DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEE-AEREYERCLKDWEYREREREK 362
            ++E+ +K E+ ++ +  E + + E ++K  E+++K+E+  ++E E   K  E ++ E E 
Sbjct: 1602 EEEKKMKAEEAKKAE--EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEN 1659

Query: 363  ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED---LAD 419
            + +  +E +K  E K+K E     EEDE  + +  ++   E K+ + +++KE +    A+
Sbjct: 1660 KIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAE 1719

Query: 420  EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDD 479
            E+++ EE    K    +++ ++ ++ A +   D      +A     E K  +      + 
Sbjct: 1720 ELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEA 1779

Query: 480  SIRE 483
             I E
Sbjct: 1780 VIEE 1783

Length = 2084

>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 = 49.8 bits (119), Expect = 8e-08
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E  L A+R L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 117 NKFNIDGQELMLKVDQA 133
           N + ++G++  L+VD A
Sbjct: 61  NGYELNGRQ--LRVDNA 75

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

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

 Score = 49.6 bits (119), Expect = 9e-08
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            ++YV  + P    D + SV +  G +KS   A  P  G  KG+GF E+E+ +    A+ 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 115 LLNKFNIDGQELMLKVDQA 133
            +N F++ GQ   L+V +A
Sbjct: 61  SMNLFDLGGQ--QLRVGKA 77

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

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

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 21/63 (33%), Positives = 30/63 (47%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           VYV  +   A  +++ +V    GTV      +Y   G  KGF F EFE+ E   +A + L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 117 NKF 119
           N  
Sbjct: 62  NNP 64

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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 53.6 bits (128), Expect = 5e-07
 Identities = 63/313 (20%), Positives = 140/313 (44%), Gaps = 28/313 (8%)

Query: 144  KKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTE 203
            +K +  KK +E + A   K+ E  +  +  E  K  E  K  +   K++          E
Sbjct: 1278 RKADELKKAEEKKKADEAKKAEEKKKAD--EAKKKAEEAKKADEAKKKA----------E 1325

Query: 204  EDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIR 263
            E +K    A +K     EE  K         +  AD      +E  A+A +   +    +
Sbjct: 1326 EAKKKADAAKKK----AEEAKKAAEAAKAEAEAAADE--AEAAEEKAEAAEKKKEEAKKK 1379

Query: 264  NDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYERE 323
             D A+ K +++  +D      +  +  + +  +    + +  E   K E++++ D  +++
Sbjct: 1380 ADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKK 1439

Query: 324  AERER----VRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRK 379
            AE  +     +K+ E+ +K EEA+++ E   K  E +++  E ++  E +K+ E  +K+ 
Sbjct: 1440 AEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKA 1499

Query: 380  KEILYDEEEDE--DDSRKRWRRSVLEEKRRKRIREKEEDL--ADEVREEEEIAVAK--RR 433
             E     E  +  D+++K       +E ++    +K ++   A+E ++ +E+  A+  ++
Sbjct: 1500 DEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKK 1559

Query: 434  AEEEQLQQQQRDA 446
            AEE++  ++ + A
Sbjct: 1560 AEEKKKAEEAKKA 1572

Length = 2084

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 51.3 bits (124), Expect = 1e-06
 Identities = 42/179 (23%), Positives = 80/179 (44%), Gaps = 31/179 (17%)

Query: 297 VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE-- 354
           V  +    K ++ + E +R ++  ++EAE  +       +  + EA+ E  +   ++E  
Sbjct: 24  VRKKIAEAKIKEAEEEAKRILEEAKKEAEAIK-------KEALLEAKEEIHKLRNEFEKE 76

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRW---------RRSVLEEK 405
            RER  E ++  ++  +KE    RK E+L   EE+ +   K           +   LEE 
Sbjct: 77  LRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEEL 136

Query: 406 RRKRIREKE-----------EDLADEVREE--EEIAVAKRRAEEEQLQQQQRDALKLLS 451
             ++++E E           E L ++V EE   E AV  +  EEE  ++  + A ++L+
Sbjct: 137 IEEQLQELERISGLTAEEAKEILLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKEILA 195

Length = 520

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

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           ++VG + P    + +  +    G ++S +       G  KGF F EFE  E   +AL  L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIV-RDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 117 NKFNIDGQELM 127
           N   + G+EL 
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 49.9 bits (119), Expect = 3e-06
 Identities = 28/115 (24%), Positives = 46/115 (40%), Gaps = 11/115 (9%)

Query: 301 RGRDKERDLKREKEREIDRYEREAERERVR-KEREQRRKIEEAEREYERCLKDWEYRERE 359
           R RD+ER   R   R       +  RER R + R + R     +R+Y R       R R 
Sbjct: 1   RYRDRERGRLRNDTRR-----SDKGRERSRRRSRSRDRSRRRRDRDYYR---GRRGRSRS 52

Query: 360 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 414
           R   R Y    ++   R  ++     +E   +   +R  R+V   +   + RE++
Sbjct: 53  RSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEA--ERDDRTVFVLQLALKARERD 105

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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.5 bits (120), Expect = 4e-06
 Identities = 67/315 (21%), Positives = 128/315 (40%), Gaps = 18/315 (5%)

Query: 144  KKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTE 203
            KK E  KK  E +      + ++ ++ +  E  K  +  K  E   K            E
Sbjct: 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKK-----AE 1531

Query: 204  EDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIR 263
            E +KAD+    +     +E  K   L     +  A+ +  +  +     R  +       
Sbjct: 1532 EAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEE 1591

Query: 264  NDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVH-DRRGRDKERDLKREKEREIDRYE- 321
              I E     E     KA +  + E +      +      + K   LK+++  E  + E 
Sbjct: 1592 ARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEE 1651

Query: 322  -REAERERVRKEREQRRKIEEAEREYERCLKDWEYR-------EREREKERQYEKEKEKE 373
             ++AE E   K  E+ +K EE +++ E   K  E         ++E E+ ++ E+ K+KE
Sbjct: 1652 LKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKE 1711

Query: 374  RERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRK---RIREKEEDLADEVREEEEIAVA 430
             E K+K E L   EE+     +  ++   E+K++    +  E+E+     +++EEE    
Sbjct: 1712 AEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAE 1771

Query: 431  KRRAEEEQLQQQQRD 445
            + R E+E + +++ D
Sbjct: 1772 EIRKEKEAVIEEELD 1786

Length = 2084

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 48.4 bits (116), Expect = 8e-06
 Identities = 38/142 (26%), Positives = 77/142 (54%), Gaps = 2/142 (1%)

Query: 305 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW-EYREREREKE 363
           +ER+ +R++E E    ERE   E + + +E+     + +RE ++ L++  +    ER + 
Sbjct: 81  EEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIER 140

Query: 364 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVRE 423
           ++ EKE+E+E E K  +      E +E+   +R  R   +E+   R+R ++E+  DE  E
Sbjct: 141 KEEEKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREE 200

Query: 424 EEEIAVAKRRAEEEQLQQQQRD 445
            +E+  A    EE + +++Q++
Sbjct: 201 LDEL-RADLYQEEYERKERQKE 221

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

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

 Score = 43.7 bits (104), Expect = 8e-06
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 4/71 (5%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT-PKGFGFCEFESAEGVLRALRL 115
           +YV  + P+   + +       G V+     +   N   P+GF F EF S E    AL+ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEG---VRLVRNKDRPRGFAFVEFASPEDAEAALKK 57

Query: 116 LNKFNIDGQEL 126
           LN   +DG+ L
Sbjct: 58  LNGLVLDGRTL 68

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

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

 Score = 48.9 bits (116), Expect = 9e-06
 Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 1/95 (1%)

Query: 32  RPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS 91
           RP   P  +P+ +  V    K   ++YV  + P      + SV +  G +   + A+ P+
Sbjct: 183 RPSNMPQAQPI-IDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT 241

Query: 92  NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 126
               KG+GF E+ + +    A+  +N F++ GQ L
Sbjct: 242 GRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYL 276

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 55  TKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 113
           T VY+  + P T D D    + +  G + S K          KG+GF +F+S E  L+A+
Sbjct: 1   TNVYIRGLPPNTTDEDLEK-LCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAI 59

Query: 114 RLLNKFNIDGQ 124
             LN   +  Q
Sbjct: 60  EGLNGRGVQAQ 70

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

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

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 20/60 (33%), Positives = 30/60 (50%)

Query: 58  YVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN 117
           ++G + P  D  ++ S    CG V S K  +    G   G+GF EF + E   +AL+ LN
Sbjct: 3   WMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLN 62

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

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

 Score = 48.4 bits (116), Expect = 1e-05
 Identities = 37/241 (15%), Positives = 67/241 (27%), Gaps = 18/241 (7%)

Query: 185 NETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGIS 244
             T    +             R+A+Q A E      E             +  +      
Sbjct: 67  AATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQ 126

Query: 245 NSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRD 304
             E   +                E   +   T     +     E    +R R  DR  R 
Sbjct: 127 ARERRERGEAARRGA---ARKAGEGG-EQPATEARADAAERTEEEERDERRRRGDREDRQ 182

Query: 305 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 364
            E +      RE    ER  + +   +   + +      RE        + R R R ++R
Sbjct: 183 AEAERGERGRRE----ERGRDGDDRDRRDRREQ---GDRREERGRRDGGDRRGRRRRRDR 235

Query: 365 QYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREE 424
           +  +  +   +R  +     D ++ E    +R RR    ++ R+  R  +     E    
Sbjct: 236 RDARGDDNREDRGDR-----DGDDGEGRGGRRGRRF--RDRDRRGRRGGDGGNEREPELR 288

Query: 425 E 425
           E
Sbjct: 289 E 289

Length = 672

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 48.0 bits (115), Expect = 2e-05
 Identities = 32/131 (24%), Positives = 57/131 (43%), Gaps = 11/131 (8%)

Query: 297 VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYR 356
           +  R    K    +   +R I+  ++EAE  +     E + ++ +   E ER     E +
Sbjct: 18  LRKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELER-----ELK 72

Query: 357 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 416
           ER  E +R   +  ++E    RK E L  +EE+ +   K          + K + EKEE+
Sbjct: 73  ERRNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKEL------SNKEKNLDEKEEE 126

Query: 417 LADEVREEEEI 427
           L + + E+ E 
Sbjct: 127 LEELIAEQREE 137

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

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

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 23/72 (31%), Positives = 36/72 (50%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           ++VG ++  AD D +       G + S +    P +G PKGFG+ EF S E    AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 117 NKFNIDGQELML 128
              ++ G+ + L
Sbjct: 61  GGTDLLGRPVRL 72

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

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

 Score = 42.9 bits (102), Expect = 2e-05
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           ++VGK+    + D +  +    GTVK            P+G+ + EFES E   +A++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 117 NKFNIDGQELM 127
           +   IDGQE+ 
Sbjct: 61  DGGQIDGQEVT 71

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

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 47.7 bits (113), Expect = 2e-05
 Identities = 24/153 (15%), Positives = 61/153 (39%), Gaps = 6/153 (3%)

Query: 306 ERDLKREKEREIDRYEREAERERVRKEREQRRKI------EEAEREYERCLKDWEYRERE 359
           +    + KE+     E    +E++  E E    +      EE     +  L+D +     
Sbjct: 197 KLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIES 256

Query: 360 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 419
            ++E + E+E   +  ++ K+E    + ++E+          L+ +  K  R K +D   
Sbjct: 257 SKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEK 316

Query: 420 EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
               E+E+   ++  ++E+ + ++ +      +
Sbjct: 317 LKESEKELKKLEKELKKEKEEIEELEKELKELE 349

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 47.4 bits (113), Expect = 2e-05
 Identities = 37/170 (21%), Positives = 79/170 (46%), Gaps = 11/170 (6%)

Query: 299 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER 358
           +R  ++ +++ + + E  +   +    RER ++ +E RR+ EE +RE ER ++      +
Sbjct: 36  ERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQ------K 89

Query: 359 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 418
           E + + + EK    E + + +++ L   E  E +  ++   + L         +  + L 
Sbjct: 90  EEQLDARAEKLDNLENQLEEREKALSAREL-ELEELEKQLDNELYRVAGLTPEQARKLLL 148

Query: 419 DEVREE--EEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVE 466
             +  E  EE A   ++ EEE   + +R A  +L+  A+    A E+A +
Sbjct: 149 KLLDAELEEEKAQRVKKIEEEADLEAERKAQNILA-QAMQRI-ASETASD 196

Length = 508

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.4 bits (113), Expect = 3e-05
 Identities = 31/155 (20%), Positives = 67/155 (43%), Gaps = 12/155 (7%)

Query: 308 DLKREKEREIDRYEREAERERVRKEREQRR----------KIEEAEREYERCLKDWEYRE 357
           DL  E E+++++ ER+AE+    +E +             K++E  +E E   ++    E
Sbjct: 193 DLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLE 252

Query: 358 REREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDL 417
            E E+ ++  +E EKE E  + +     EE +E        +  +EE   +    +E   
Sbjct: 253 EELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRER-- 310

Query: 418 ADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
            +E+  E E    +    +E+++  + +  +  + 
Sbjct: 311 LEELENELEELEERLEELKEKIEALKEELEERETL 345

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 29/161 (18%), Positives = 60/161 (37%), Gaps = 1/161 (0%)

Query: 293 DRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKD 352
                       +E + +     E+++   E E  +   E +    +EE E  +E   ++
Sbjct: 325 LEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREE 384

Query: 353 WEYREREREK-ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR 411
               E E  +   + E+ K +    + + E L +  ED  +  K     + E +      
Sbjct: 385 LAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEEL 444

Query: 412 EKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
            +E +  +E  EE    + +   E  +LQ++ +   K LS 
Sbjct: 445 NEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSS 485

Length = 1163

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

 Score = 46.8 bits (111), Expect = 3e-05
 Identities = 29/134 (21%), Positives = 45/134 (33%), Gaps = 30/134 (22%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 362
           RD+E D +REK R  DR   +   ER R+    R                  +R+R R  
Sbjct: 1   RDEEPDREREKSRGRDR---DRSSERPRRRSRDR----------------SRFRDRHRRS 41

Query: 363 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 422
             +  +E  + R+R+R     YD            RRS      R R R +   +    +
Sbjct: 42  RERSYREDSRPRDRRR-----YDSRSPRSLRYSSVRRS------RDRPRRRSRSVRSIEQ 90

Query: 423 EEEEIAVAKRRAEE 436
               +       + 
Sbjct: 91  HRRRLRDRSPSNQW 104

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           +YVG +  T   D +  +    G +KS K  +   N     + F E+        AL+ +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP---YAFVEYYDHRSAAAALQTM 57

Query: 117 NKFNIDGQELMLKVDQA 133
           N   I GQE  +KV+ A
Sbjct: 58  NGRLILGQE--IKVNWA 72

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

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 45.7 bits (109), Expect = 5e-05
 Identities = 47/159 (29%), Positives = 79/159 (49%), Gaps = 15/159 (9%)

Query: 294 RSRVHDRRGRDKERDLKREKERE---IDRYEREAERERVRKEREQRRKIEEAEREYERCL 350
           + R   R    +E      +E +    D Y+ E ER+  +KE+E+  K    ++E     
Sbjct: 180 KEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQKQE---LQ 236

Query: 351 KDWEYREREREKERQYEK-EKEKERERKRKKEILYDEEEDEDDSRKRWRR--------SV 401
           +  E +  E+E+  Q E+ E+E ERER  +K+   +E E E+  ++R +R          
Sbjct: 237 RAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQ 296

Query: 402 LEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQ 440
           +EEK  +R  E+EE+L +  R  EE A  + R EEE+ +
Sbjct: 297 IEEKEERRAAEREEELEEGERLREEEAERQARIEEERQR 335

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

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

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           ++VG ++ +A+ D +    K CG V    R     +G  KGFG  EF + EG  +AL   
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVD-VRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 117 NKFNIDGQELMLKVDQAT 134
               + G+E  ++VD AT
Sbjct: 61  G-EELLGRE--IRVDLAT 75

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 43.9 bits (104), Expect = 9e-05
 Identities = 23/85 (27%), Positives = 50/85 (58%), Gaps = 3/85 (3%)

Query: 321 EREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKK 380
            ++  +   ++ R Q+R+ EE ERE  + L++    ER+ E+E + E+EK+KE E ++++
Sbjct: 5   AKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKER 64

Query: 381 EILYDEEEDEDDSRKRWRRSVLEEK 405
           E   ++   E +  ++ + S + E+
Sbjct: 65  E---EQARKEQEEYEKLKSSFVVEE 86

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 45.9 bits (108), Expect = 1e-04
 Identities = 35/172 (20%), Positives = 82/172 (47%), Gaps = 2/172 (1%)

Query: 268  EDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERE 327
            E K D E     +   ++       +    H  R +   +  +  K  E+ + E + + +
Sbjct: 1234 EAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKAD 1293

Query: 328  RVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEE 387
              +K  E+++K +EA+++ E   K  E +++  E +++ +  K+K  E K+  E    E 
Sbjct: 1294 EAKKA-EEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEA 1352

Query: 388  E-DEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQ 438
            E   D++     ++   EK+++  ++K +    +  E+++   AK++AEE++
Sbjct: 1353 EAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDK 1404

Length = 2084

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.0 bits (106), Expect = 1e-04
 Identities = 29/156 (18%), Positives = 61/156 (39%), Gaps = 16/156 (10%)

Query: 298 HDRRGRDKERDLKREKER----------EIDRYEREAERERVRKEREQRRKIEEAEREYE 347
             R+ +++ + L  E E              +  +  E+ +   E  Q ++  E E E  
Sbjct: 168 EKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENL 227

Query: 348 RCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRR 407
               D+     ER    Q     E  R+ + + E    E E E++   +  +   EE++ 
Sbjct: 228 L-YLDYLKLNEERIDLLQ-----ELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKE 281

Query: 408 KRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQ 443
           K+++E+E  L  +  EE +  + K    +   +++ 
Sbjct: 282 KKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKL 317

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 38/153 (24%), Positives = 70/153 (45%), Gaps = 8/153 (5%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 362
           + K  +L+ +    ++  E   E   + +E ++ +K+EE + E E    +   +E E  +
Sbjct: 184 KAKIEELEGQLSELLEDIEDLLEA--LEEELKELKKLEEIQEEQEEEELE---QEIEALE 238

Query: 363 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRR-KRIREKEEDLADEV 421
           ER  E E+EKER  + K  +L  E   E ++ K     + E +R  + + EK E L +  
Sbjct: 239 ERLAELEEEKERLEELKARLLEIESL-ELEALKIREEELRELERLLEELEEKIERLEELE 297

Query: 422 RE-EEEIAVAKRRAEEEQLQQQQRDALKLLSDN 453
           RE EE     +      +  ++  + LK L + 
Sbjct: 298 REIEELEEELEGLRALLEELEELLEKLKSLEER 330

Length = 908

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

 Score = 44.5 bits (105), Expect = 2e-04
 Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 13/120 (10%)

Query: 292 PDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLK 351
           PDR R    RGRD++R  +R + R  DR      R R R  R + R   E  R  +R   
Sbjct: 5   PDRER-EKSRGRDRDRSSERPRRRSRDR-----SRFRDRHRRSRERSYREDSRPRDR--- 55

Query: 352 DWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR 411
              Y  R     R     + ++R R+R + +   E+      R R R    + ++  + R
Sbjct: 56  -RRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRR---RLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 45/198 (22%), Positives = 92/198 (46%), Gaps = 8/198 (4%)

Query: 253 RDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKRE 312
            D   +     +D+ E   D E++S++  S       SS   S  + R    KE  L+R+
Sbjct: 27  EDCSEESTDSWSDMYEGLKDSESSSNSVPSLSLSSTASSLSDSSTYSRS--LKEVKLERQ 84

Query: 313 KEREID---RYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKE 369
            +   +     ++   +++++K  E+++K E  +   E  L+    +E+  E  RQ  ++
Sbjct: 85  AQEAYENWLSAKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQ 144

Query: 370 KEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIRE--KEEDLADEVREEEEI 427
             K+R  K KKE           S K  R  V +E+ +KR++E   ++    + + EEE 
Sbjct: 145 AAKQRTPKHKKEAAESASSSLSGSAKPERN-VSQEEAKKRLQEWELKKLKQQQQKREEER 203

Query: 428 AVAKRRAEEEQLQQQQRD 445
              +++ +EE+ ++Q+ +
Sbjct: 204 RKQRKKQQEEEERKQKAE 221

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 31/156 (19%), Positives = 68/156 (43%), Gaps = 19/156 (12%)

Query: 294 RSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW 353
           +S+    +  +++R  K E+  E  + ++ AE+ER+++  ++R K +E +++ E      
Sbjct: 68  QSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAE------ 121

Query: 354 EYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREK 413
                E EK+ Q E+++++E+ RK   E     E          +     E  + +   +
Sbjct: 122 -----EAEKQAQLEQKQQEEQARKAAAEQKKKAEAA--------KAKAAAEAAKLKAAAE 168

Query: 414 EEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKL 449
            +  A+E  +  E A AK  A   + + +       
Sbjct: 169 AKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAA 204

Length = 387

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 34/157 (21%), Positives = 72/157 (45%), Gaps = 13/157 (8%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 363
           + E DL + +E  ++  E      R+ + + +  K+EE     E  L++ E +      E
Sbjct: 769 ELEEDLHKLEE-ALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLE 827

Query: 364 RQYEKEKEKERERK------RKKEILYDEEEDEDDSRKRWRRSVLEEKRR--KRIREKEE 415
           ++Y +++ +E + +      + K I  ++E +  + +K      LEE     + +  +  
Sbjct: 828 KEYLEKEIQELQEQRIDLKEQIKSI--EKEIENLNGKKEELEEELEELEAALRDLESRLG 885

Query: 416 DLADEVRE-EEEIAVAKRRAEEEQLQ-QQQRDALKLL 450
           DL  E  E E ++   +R+ EE + Q +++R  L  L
Sbjct: 886 DLKKERDELEAQLRELERKIEELEAQIEKKRKRLSEL 922

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 40/222 (18%), Positives = 83/222 (37%), Gaps = 12/222 (5%)

Query: 246 SELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDK 305
           SEL  +  +   ++  + N+I+  +   +   +  A+   + E        +  +     
Sbjct: 277 SELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELA 336

Query: 306 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 365
           E   + E++ E  + E E+    + +   +  ++E    E E      E  E  R K  Q
Sbjct: 337 EELAELEEKLEELKEELESLEAELEELEAELEELESRLEELE------EQLETLRSKVAQ 390

Query: 366 YEKEKEKERERKRKKEILYDEEEDEDDSRKRWR---RSVLEEKRRKRIREKEEDLADEVR 422
            E +           E L    E  +D R+R +     +L++     ++E + +L +   
Sbjct: 391 LELQIASLNNEI---ERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEE 447

Query: 423 EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESA 464
           E EE+     R EE   + ++       + +A    LA+  A
Sbjct: 448 ELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQA 489

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 44.2 bits (104), Expect = 3e-04
 Identities = 39/170 (22%), Positives = 76/170 (44%), Gaps = 5/170 (2%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 362
             +E   K+ +E E+    +E E E   +  +  R+  + E + +   K+ +  E+E +K
Sbjct: 275 NKEEEKEKKLQEEELKLLAKE-EEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKK 333

Query: 363 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 422
           E++  +E EKE +    K    +EEE++ +  +     + EE   K+  E E   +    
Sbjct: 334 EKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

Query: 423 EEEEIAVA----KRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 468
           +EEE+ +     K      +L +Q+ D LK      +      E ++E+K
Sbjct: 394 KEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETK 443

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.8 bits (103), Expect = 3e-04
 Identities = 26/158 (16%), Positives = 64/158 (40%), Gaps = 15/158 (9%)

Query: 300 RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCL------KDW 353
               +   +L  + E    +  +  E+ +   E  Q ++  E E E    L      ++ 
Sbjct: 180 IEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEER 239

Query: 354 EYREREREKERQYEKEKEKERERKRKKEI-----LYDEEEDEDDSRKRWRRSVLEEKRRK 408
               +E  ++ Q E E  K+   K ++ +        EEE E   ++     +L ++  +
Sbjct: 240 IDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEEL-KLLAKEEEE 298

Query: 409 RIREKEEDLADEVREEEEIAVAK---RRAEEEQLQQQQ 443
              E  +    +V +EE++  ++   ++ E+E  ++++
Sbjct: 299 LKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKE 336

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 38/161 (23%), Positives = 72/161 (44%), Gaps = 9/161 (5%)

Query: 299 DRRGRDKERDLKREKEREIDRYEREAE-RERVRKEREQRRKIEEAEREYERCLKDWEYR- 356
             R  + E +L+  +E      E   E  E+ +  +E+  ++EE   E ER L   E   
Sbjct: 757 QERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALEREL 816

Query: 357 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLE--EKRRKRIREKE 414
           E   ++  + E+E E+  E   + E   DE E+E +  ++    + E  E+      E E
Sbjct: 817 ESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELE 876

Query: 415 EDLADEVREEEEI-----AVAKRRAEEEQLQQQQRDALKLL 450
           ++L +   E+EE+      +    AE ++  ++ R+ L+ L
Sbjct: 877 DELKELEEEKEELEEELRELESELAELKEEIEKLRERLEEL 917

Length = 1163

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 44.2 bits (104), Expect = 3e-04
 Identities = 89/460 (19%), Positives = 164/460 (35%), Gaps = 87/460 (18%)

Query: 143  DKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVT 202
            +   E+  + ++  +  +   +ES   V K +  K+ E+ KD +    E     + G+  
Sbjct: 3910 EPNEEDLLETEQKSNEQSAANNES-DLVSKEDDNKALED-KDRQEKEDEEEMSDDVGI-D 3966

Query: 203  EEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMI 262
            +E +   QE   +               PPP     D     + +L  K  D   D D+ 
Sbjct: 3967 DEIQPDIQENNSQ---------------PPPENEDLDLP--EDLKLDEKEGDVSKDSDLE 4009

Query: 263  RNDIA---EDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDR 319
              D+    E+K + +   D    D D  E ++     + +   +D   DL  + E+    
Sbjct: 4010 DMDMEAADENKEEADAEKDEPMQDEDPLEENNT----LDEDIQQDDFSDLAEDDEKM--- 4062

Query: 320  YEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRK 379
                                EE  +E E   +D    + E E+    E +      +   
Sbjct: 4063 ---------------NEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDNHPKMDA 4107

Query: 380  KEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR-------EKEEDLADEVREEEEIAVAKR 432
            K      E DE+++ K       E      +R       E E+   D    +E ++ A R
Sbjct: 4108 KSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQEDTSTPKEAMSEADR 4167

Query: 433  RAEE--EQLQQ-QQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDD---------- 479
            + +   + L++ QQ + +    D   + S A +   +S+ M V+ D  +D          
Sbjct: 4168 QYQSLGDHLREWQQANRIHEWEDLTESQSQAFD---DSEFMHVKEDEEEDLQALGNAEKD 4224

Query: 480  ---SIRENHMAG-DPSSQNGN----------GDESTNVPIAASDMRQSG--NVPARKLGF 523
               SI  +  A  +P S N            GD+        SD++Q+G   +P     F
Sbjct: 4225 QIKSIDRDESANQNPDSMNSTNIAEDEADEVGDKQLQDGQDISDIKQTGEDTLPTE---F 4281

Query: 524  GLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTE 563
            G +   ++    S     +D+  D + K+ P +PID + +
Sbjct: 4282 GSINQSEKVFELSEDEDIEDELPDYNVKITPAMPIDEARD 4321

Length = 4600

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.0 bits (102), Expect = 4e-04
 Identities = 39/152 (25%), Positives = 67/152 (44%), Gaps = 17/152 (11%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVR----KEREQRRKIEEAEREYERCLKDWEYRER 358
            ++ + L  E+ERE  R E   E   V     +ERE+RR+ E  ER  ER        + 
Sbjct: 49  EERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQER-------EQM 101

Query: 359 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR------IRE 412
           +   ER  E+++ + +E++ K++ L +E ++ ++ R   +    E +R +        RE
Sbjct: 102 DEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEYQRE 161

Query: 413 KEEDLADEVREEEEIAVAKRRAEEEQLQQQQR 444
           K E   +   E  E    K R       QQ+ 
Sbjct: 162 KAEREEEREAERRERKEEKEREVARLRAQQEE 193

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 45/223 (20%), Positives = 100/223 (44%), Gaps = 12/223 (5%)

Query: 246 SELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDK 305
            EL  +  + + +++ ++  + E + + E+  +  A   +  E     R  + +    ++
Sbjct: 740 EELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEEL--EE 797

Query: 306 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 365
             +   E ER +D  ERE E    R+ER ++  IEE E E E   +  +  E E E+  +
Sbjct: 798 LEEELEEAERRLDALERELESLEQRRERLEQE-IEELEEEIEELEEKLDELEEELEELEK 856

Query: 366 YEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEE 425
             +E ++E E    ++   + E++  +  +       +E+  + +RE E +L  E++EE 
Sbjct: 857 ELEELKEELEELEAEKE--ELEDELKELEEE------KEELEEELRELESEL-AELKEEI 907

Query: 426 EIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 468
           E    +    E +L++ + +  +L  +         E+ +E +
Sbjct: 908 EKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELERE 950

Length = 1163

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 41/185 (22%), Positives = 73/185 (39%), Gaps = 25/185 (13%)

Query: 300 RRGRDKERDLKREKEREIDRYEREAERERVRKEREQ-RRKIEEAEREYERCLKDWEYRER 358
           +R R++   LKRE            E  R+    ++  +++ +A R+     K+ E  E+
Sbjct: 677 QRLRERLEGLKRELSSLQS------ELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQ 730

Query: 359 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 418
           E       EK KE+  E +     L  E E+     K             RI E EEDL 
Sbjct: 731 EE------EKLKERLEELEEDLSSLEQEIENVKSELKEL---------EARIEELEEDLH 775

Query: 419 DEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHD 478
              + EE +   + R    ++ + Q +  KL  + +   +   E   +   + +E +Y +
Sbjct: 776 ---KLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLE 832

Query: 479 DSIRE 483
             I+E
Sbjct: 833 KEIQE 837

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.9 bits (104), Expect = 4e-04
 Identities = 34/178 (19%), Positives = 72/178 (40%), Gaps = 21/178 (11%)

Query: 283 DHDRPETSSPDRSRVHDRRGRDKERDLKREKEREI--DRYEREAERERVRKEREQRRKIE 340
           D +    +  +R+R   R  R++ R  +R+ +++    R  ++AE     + ++++++  
Sbjct: 616 DRNERRDTRDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAP 675

Query: 341 EAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRK---RW 397
             ER+          R R  EK +  ++ K    E +        E E E+  ++   R 
Sbjct: 676 RRERQ----------RRRNDEKRQAQQEAKALNVEEQSV-----QETEQEERVQQVQPRR 720

Query: 398 RRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAV 455
           ++  L +K R      EE +A  V EE   A    +       +  +  L +++  A 
Sbjct: 721 KQRQLNQKVRIEQSVAEEAVAPVV-EETVAAEPVVQEVPAPRTELVKVPLPVVAQTAP 777

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 38/169 (22%), Positives = 69/169 (40%), Gaps = 17/169 (10%)

Query: 310 KREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKE 369
            + + +   + +R   R+  R++R +RR      R         E RE  R   RQ +++
Sbjct: 594 PKAEAKPERQQDRRKPRQNNRRDRNERRD-TRDNRTRRE---GRENREENRRNRRQAQQQ 649

Query: 370 KEKERERKRKKEILYDEEEDEDDSRKRW----RRSVLEEKRRKRIREK----EEDLADEV 421
             + RE ++ +       +DE     R     RR+  +EKR+ +   K    EE    E 
Sbjct: 650 TAETRESQQAEVTEKARTQDEQQQAPRRERQRRRN--DEKRQAQQEAKALNVEEQSVQET 707

Query: 422 REEEEIAVAKRRAEEEQLQQQQR---DALKLLSDNAVNGSLAEESAVES 467
            +EE +   + R ++ QL Q+ R      +      V  ++A E  V+ 
Sbjct: 708 EQEERVQQVQPRRKQRQLNQKVRIEQSVAEEAVAPVVEETVAAEPVVQE 756

Length = 1068

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

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
            +YVG +      + +  +    G V S +       G  +GFGF E E+AE    A+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 116 LNKFNIDGQELMLKVDQA 133
           LN  +  G+   L V++A
Sbjct: 61  LNGTDFGGRT--LTVNEA 76

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

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

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN---GTPKGFGFCEFESAEGVLRAL 113
           ++VG +      + +    K CGT+    R     +   G PKGF + EF     V  AL
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTIN---RITILCDKFTGQPKGFAYIEFLDKSSVENAL 58

Query: 114 RLLNKFNIDGQEL 126
            LLN+    G+++
Sbjct: 59  -LLNESEFRGRQI 70

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

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN---GTPKGFGFCEFESAEGVLR 111
           TK++VG +      D +       G ++    A   ++   G  +G+GF  F+  E   R
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIE---EAVVITDRQTGKSRGYGFVTFKDKESAER 57

Query: 112 ALRLLNKFNIDGQELMLK 129
           A +  N   IDG++  + 
Sbjct: 58  ACKDPNP-IIDGRKANVN 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|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 34/146 (23%), Positives = 71/146 (48%), Gaps = 7/146 (4%)

Query: 301 RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERER 360
             +++ER  K E++ E    +R AE+ R +KE EQR   E+A ++ E      +  ++  
Sbjct: 63  AKKEQERQKKLEQQAEEAEKQRAAEQAR-QKELEQRAAAEKAAKQAE------QAAKQAE 115

Query: 361 EKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADE 420
           EK++Q E+ K K+    + K     E++ +++++K+       +   +  ++  E     
Sbjct: 116 EKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKA 175

Query: 421 VREEEEIAVAKRRAEEEQLQQQQRDA 446
             E +  A AK +A+ E+ + +   A
Sbjct: 176 EAEAKAKAEAKAKAKAEEAKAKAEAA 201

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 42.2 bits (100), Expect = 6e-04
 Identities = 36/152 (23%), Positives = 73/152 (48%), Gaps = 10/152 (6%)

Query: 305 KERDLKREKEREIDRYEREAERERVRKERE----QRRKIEEAEREY-ERCLKDWEYRERE 359
           + R+ K EKERE+ R   + E     +E           EE ER+  ++  ++ E R R+
Sbjct: 172 ERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQ 231

Query: 360 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 419
           +++ ++  +E+ +E+E + ++E   +E E E    K+     LE++  ++ R K  +   
Sbjct: 232 KQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRR 291

Query: 420 EVRE-----EEEIAVAKRRAEEEQLQQQQRDA 446
           E+ +     EE  A  +    EE  + ++ +A
Sbjct: 292 ELEQQIEEKEERRAAEREEELEEGERLREEEA 323

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.8 bits (101), Expect = 6e-04
 Identities = 39/168 (23%), Positives = 70/168 (41%), Gaps = 4/168 (2%)

Query: 305 KERDLKREKEREIDRYERE-AERERVRKEREQRRKIEEAEREYERCL--KDWEYRERERE 361
            E++L    E E++  E E +  +   + RE+  ++E+  RE E  L          + E
Sbjct: 471 HEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEE 530

Query: 362 KERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIR-EKEEDLADE 420
            E + EK +    E +  KE L  ++  E+  +   R   L+E   +       ++  +E
Sbjct: 531 LEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEE 590

Query: 421 VREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 468
           +RE  +    K +  EE+L Q +     L    A N     E  +ES+
Sbjct: 591 LRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESE 638

Length = 908

>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 43.2 bits (101), Expect = 6e-04
 Identities = 30/102 (29%), Positives = 52/102 (50%), Gaps = 4/102 (3%)

Query: 286 RPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERV---RKEREQRRKIEEA 342
           R +    +R+R+       K  ++K  +++ I+R ERE ERER+   R ER +R ++E  
Sbjct: 429 RVDKDHAERARIEKENAHRKALEMKILEKKRIERLERE-ERERLERERMERIERERLERE 487

Query: 343 EREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILY 384
             E ER  +D   R+R    ER+     E++R  K ++   +
Sbjct: 488 RLERERLERDRLERDRLDRLERERVDRLERDRLEKARRNSYF 529

Length = 1021

>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein

 Score = 43.0 bits (101), Expect = 6e-04
 Identities = 36/165 (21%), Positives = 66/165 (40%), Gaps = 16/165 (9%)

Query: 314 EREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKE 373
           E E+ + E E +R ++  ER+     E  ERE +R L+     +   E E++ E E  + 
Sbjct: 74  ENELMQKELEHKRAQIELERKASTLAENYERELDRNLELEVRLKALEELEKKAENEAAEA 133

Query: 374 RERKRKKEILYDEEE------------DEDDSRKRWRRSVLEEKRRKRIREKE----EDL 417
            E  +  +   D E             +  +S  R +  + E + R +  + E    E  
Sbjct: 134 EEEAKLLKDKLDAESLKLQNEKEDQLKEAKESISRIKNDLSEMQCRAQNADTELKLLESE 193

Query: 418 ADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEE 462
            +E+RE+ E    +    E++LQ    +      ++     L EE
Sbjct: 194 LEELREQLEECQKELAEAEKKLQSLTSEQASSADNSVKIKHLEEE 238

This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated. Length = 722

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

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 79  GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 130
           G VK+ K  +    G   GFGF +++SAE   RA+R LN   +  Q   +KV
Sbjct: 25  GPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL--QNKRIKV 74

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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.0 bits (101), Expect = 7e-04
 Identities = 29/169 (17%), Positives = 70/169 (41%), Gaps = 4/169 (2%)

Query: 302 GRDKERDLKREKEREIDRYEREAERE--RVRKEREQRRKIEEAEREYERCLKDWEYRERE 359
              +E+  K+E+ +++             + + + Q  K++E  ++     +  E  E E
Sbjct: 164 AGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELE 223

Query: 360 REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 419
            E     +  K  E      +E+L DE+E+ + S++   +      +  +  ++EE    
Sbjct: 224 EENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKK 283

Query: 420 EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESK 468
              +EEE+ +  +  EE + +  + +  K+  +  +  S  E   +E +
Sbjct: 284 L--QEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKE 330

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

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

 Score = 38.8 bits (91), Expect = 7e-04
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKR---AQYPSNGTPKGFGFCEFESAEGVLRA 112
           ++++G +        +L +    G +K +        P  G P+G+ F  FE+ E   +A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 113 LRLLNKFNIDGQELMLK 129
           L+ LN     G++L+++
Sbjct: 61  LKSLNGKTALGKKLVVR 77

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

>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 42.5 bits (100), Expect = 7e-04
 Identities = 28/164 (17%), Positives = 60/164 (36%), Gaps = 14/164 (8%)

Query: 312 EKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK----ERQYE 367
           E E E+  ++ E  RE  + E    + I+E + + E+ ++  +  E    +    ERQ E
Sbjct: 273 ETEAEVAAWKAETRREAEQAEILAEQAIQEEKAQAEQEVQHAKALEAREMRVGLIERQKE 332

Query: 368 -----KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 422
                +E+       +++     +           +     E  R+    +  + A  V 
Sbjct: 333 TELEPQERSYFINAAQRQAQEEAKAAANIAEAIGAQAEAAVETARETEEAERAEQAALVA 392

Query: 423 -----EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAE 461
                E+E++ +A R    +   + Q   +K  ++       AE
Sbjct: 393 AAEAAEQEQVEIAVRAEAAKAEAEAQAAEIKAEAEAIREKGKAE 436

Length = 548

>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]

 Score = 41.2 bits (97), Expect = 7e-04
 Identities = 39/182 (21%), Positives = 74/182 (40%), Gaps = 8/182 (4%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 362
               + + RE E E +    EA  E  + + E +R+ EEA  E  R  +    RER+R  
Sbjct: 5   EKLIKKILREAEEEAEEILEEAREEAEKIKEEAKREAEEAIEEILRKAEKEAERERQRII 64

Query: 363 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 422
                + + K  E   K+EIL    E   ++ +   R++  +   + ++E   +  +++ 
Sbjct: 65  SSALLEARRKLLE--AKEEIL----ESVFEAVEEKLRNIASDPEYESLQELLIEALEKLL 118

Query: 423 EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIR 482
             E +     + +   L +Q    LK+  +      +     VES+   +  D   +SI 
Sbjct: 119 GGELVVYLNEKDKA--LVEQILRELKIGVELGEGIDIIGGVVVESRDGKIRLDNTFESIL 176

Query: 483 EN 484
           E 
Sbjct: 177 ER 178

Length = 194

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 35/155 (22%), Positives = 66/155 (42%), Gaps = 11/155 (7%)

Query: 299 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQ----RRKIEEAEREYERCLKDWE 354
           +   R+ E   +  +       E E   E+++   E+      K+E+ E E E   ++  
Sbjct: 294 EELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKN 353

Query: 355 YR-----EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR 409
                  ER +E E + E E EKE E+  ++    +E   E         S   E+ ++ 
Sbjct: 354 ELAKLLEERLKELEERLE-ELEKELEKALERLKQLEEAIQELKEELA-ELSAALEEIQEE 411

Query: 410 IREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQR 444
           + E E++L +  RE EE+    ++ EE+  Q + +
Sbjct: 412 LEELEKELEELERELEELEEEIKKLEEQINQLESK 446

Length = 908

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

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 21/71 (29%), Positives = 31/71 (43%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           +VYVG I+     D +       G +KS   +  P     KGF F E+E  E    AL  
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 116 LNKFNIDGQEL 126
           +N   + G+ +
Sbjct: 62  MNGVMLGGRNI 72

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 41.8 bits (99), Expect = 0.001
 Identities = 37/154 (24%), Positives = 72/154 (46%), Gaps = 23/154 (14%)

Query: 306 ERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQ 365
           ER+ +RE ER   + E+E E  R+R ++E   + E+   E +    D    E ER++ ++
Sbjct: 164 EREEEREAERRERKEEKEREVARLRAQQE---EAEDEREELDELRADLYQEEYERKERQK 220

Query: 366 YEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA------D 419
            ++E EK   R+R+K+ L           +R R   +EEK  +   E+ E+ A      +
Sbjct: 221 EKEEAEK---RRRQKQEL-----------QRAREEQIEEKEERLQEERAEEEAERERMLE 266

Query: 420 EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDN 453
           +  E+EE+          +  + +R+  + + + 
Sbjct: 267 KQAEDEELEQENAEKRRMKRLEHRRELEQQIEEK 300

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 34/170 (20%), Positives = 64/170 (37%), Gaps = 4/170 (2%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 363
             E     +   E+ R   E ER+    +RE     EE E+   R  +  E  E   E+ 
Sbjct: 694 KNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEEL 753

Query: 364 RQYEKEKEKERERKR---KKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADE 420
            + ++  E+  E      +      EE +E + +++  +  LEE   +    +    A E
Sbjct: 754 EELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALE 813

Query: 421 VREEEEIAVAKRRAEE-EQLQQQQRDALKLLSDNAVNGSLAEESAVESKG 469
              E      +R  +E E+L+++  +  + L +        E+   E K 
Sbjct: 814 RELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKE 863

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 31/149 (20%), Positives = 57/149 (38%), Gaps = 1/149 (0%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 363
           + ER+L+  +E      E+  + E       +     E      + L +   +E     E
Sbjct: 421 ELERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYE 480

Query: 364 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWR-RSVLEEKRRKRIREKEEDLADEVR 422
            + E+ +E+    K + E+  + EE E + R+       L E       E EE L     
Sbjct: 481 LELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLEN 540

Query: 423 EEEEIAVAKRRAEEEQLQQQQRDALKLLS 451
             EE+   K + + +QL+++ R     L 
Sbjct: 541 LLEELEELKEKLQLQQLKEELRQLEDRLQ 569

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 41/154 (26%), Positives = 67/154 (43%), Gaps = 3/154 (1%)

Query: 305 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 364
           +ER  + E+E+E     +    E    E E  +  EE  RE ER L++ E  + ER +E 
Sbjct: 238 EERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELE-EKIERLEEL 296

Query: 365 QYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEE--DLADEVR 422
           + E E+ +E     +  +   EE  E       R   LEEK  K   E EE  +  +E+ 
Sbjct: 297 EREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELA 356

Query: 423 EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVN 456
           +  E  + +     E+L+++   AL+ L      
Sbjct: 357 KLLEERLKELEERLEELEKELEKALERLKQLEEA 390

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 29/171 (16%), Positives = 65/171 (38%), Gaps = 12/171 (7%)

Query: 301 RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEE-AEREYERCLKDWEYRERE 359
           +  +  +++ +E + +I+  E +        E       EE  E +    +++ +  E  
Sbjct: 171 KLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEEL 230

Query: 360 REKERQYE---KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 416
            ++    E    E E+E+ER  + +    E E  +    +         R + +RE E  
Sbjct: 231 EQEIEALEERLAELEEEKERLEELKARLLEIESLELEALK--------IREEELRELERL 282

Query: 417 LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVES 467
           L +   + E +   +R  EE + + +   AL    +  +    + E  +E 
Sbjct: 283 LEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEK 333

Length = 908

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 42/178 (23%), Positives = 69/178 (38%), Gaps = 19/178 (10%)

Query: 308 DLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYE 367
           D+  E ER++   ER+AE+       E+ ++++   RE E  L      E   E E   E
Sbjct: 193 DILNELERQLKSLERQAEKA------ERYKELKAELRELELALLVLRLEELREELEELQE 246

Query: 368 KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKR----------RKRIREKEEDL 417
           + KE E E +     L  +E +E     R   S LEE+              I   E+  
Sbjct: 247 ELKEAEEELEELTAEL--QELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQK 304

Query: 418 ADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHD 475
              +RE       +    E QL++ +    +L  + A      EE   E + ++ E +
Sbjct: 305 Q-ILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELE 361

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter subunit G; Reviewed

 Score = 40.8 bits (95), Expect = 0.001
 Identities = 31/108 (28%), Positives = 58/108 (53%), Gaps = 4/108 (3%)

Query: 288 ETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYE 347
           +T  P   R+ D+    K+ D+K++K   I    R+ + E+ R+ERE+  +  E ER  E
Sbjct: 94  DTGVPLAIRIRDQLRSVKKDDIKKKKSLII----RQEQIEKARQEREELEERMEWERREE 149

Query: 348 RCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRK 395
           +  +  +  E+ERE+E Q  +E+  + E +  ++   + E D+D + K
Sbjct: 150 KIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQDESETESDDDKTEK 197

Length = 197

>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 32/133 (24%), Positives = 61/133 (45%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 363
           D E+DL+  K+    R + EA +  V K   +  K+EE  RE E+ L   +    E  K 
Sbjct: 2   DPEKDLEDLKKEAARRAKEEARKRLVAKHGAEISKLEEENREKEKALPKNDDMTIEEAKR 61

Query: 364 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVRE 423
           R     K K     ++K    +E  +E+ ++ + + +   + +   + +++ +  +EV E
Sbjct: 62  RAAAAAKAKAAALAKQKREGTEEVTEEEKAKAKAKAAAAAKAKAAALAKQKREGTEEVTE 121

Query: 424 EEEIAVAKRRAEE 436
           EE+ A   + A  
Sbjct: 122 EEKAAAKAKAAAA 134

Length = 430

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

 Score = 41.9 bits (97), Expect = 0.001
 Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 2/133 (1%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
            +++    ++VG +      + +  + K  G VK  +  +    G  +GF F EFES E 
Sbjct: 110 KSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEES 169

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQ 168
             +A+  LN   ++G+   L+V +A      R       +    K+     A   ++S  
Sbjct: 170 AEKAIEELNGKELEGRP--LRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDN 227

Query: 169 SVEKNEPTKSPEN 181
               N P K+ E 
Sbjct: 228 LYVGNLPLKTAEE 240

Length = 306

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 5/58 (8%)

Query: 78  CGTVKSWKRAQYPSNGTPK-----GFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 130
           CG V+S   A+      P      G+GF EF+S E   +AL+ L    +DG  L LK+
Sbjct: 24  CGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLDGHALELKL 81

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

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 7/115 (6%)

Query: 281 ASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIE 340
                R    S  R R   R  R++ R+  R +ER+  R  R     R R+ R  RR   
Sbjct: 2   GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRH-R 60

Query: 341 EAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRK 395
              R   R       R+R+RE+++   + K++ER++  K+E L  + ++E +  K
Sbjct: 61  SRSRSPSR------RRDRKRERDKDAREPKKRERQKLIKEEDLEGKSDEEVEMMK 109

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.1 bits (98), Expect = 0.002
 Identities = 33/143 (23%), Positives = 65/143 (45%), Gaps = 4/143 (2%)

Query: 300  RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAER-EYERCLKDWEYRER 358
            R+     +  +  K  E  + E   + E V+K  E ++  EEA++ E ER  ++    E 
Sbjct: 1200 RKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEE 1259

Query: 359  EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRW--RRSVLEEKRRKRIREKEED 416
             R       +   K  E ++  E+   EE+ + D  K+   ++   E K++    +K ++
Sbjct: 1260 ARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADE 1319

Query: 417  LADEVREEEEIA-VAKRRAEEEQ 438
               +  E ++ A  AK++AEE +
Sbjct: 1320 AKKKAEEAKKKADAAKKKAEEAK 1342

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.7 bits (97), Expect = 0.002
 Identities = 57/295 (19%), Positives = 115/295 (38%), Gaps = 17/295 (5%)

Query: 144  KKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTE 203
            +K E  +K +E + A   K+ E+V+  E        E  KD E   K   +  N  +   
Sbjct: 1206 RKAEEERKAEEARKAEDAKKAEAVKKAE--------EAKKDAEEAKKAEEERNNEEIRKF 1257

Query: 204  EDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIR 263
            E+ +    A  +     EE  K + L     +  AD      +E   KA +     +  +
Sbjct: 1258 EEARMAHFARRQAAIKAEEARKADELKKAEEKKKADE--AKKAEEKKKADEAKKKAEEAK 1315

Query: 264  NDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYERE 323
                  K  +E      A+     E      +   +      E +   E++ E    ++E
Sbjct: 1316 KADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAE-AAEEKAEAAEKKKE 1374

Query: 324  AERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEIL 383
              +   +K    ++K EE ++  E   K  E +++  E ++    +K+ +  +K+ +E  
Sbjct: 1375 EAK---KKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEK- 1430

Query: 384  YDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQ 438
              ++ DE   +    +   E K++    +K E+   +  E ++   AK++AEE +
Sbjct: 1431 --KKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAK 1483

Length = 2084

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 30/145 (20%), Positives = 64/145 (44%), Gaps = 2/145 (1%)

Query: 299 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER 358
           ++R    ++   +E E E+   E + E +   + +  + ++   E   E   +  E  ER
Sbjct: 658 NKRSSLAQKRELKELEEELAELEAQLE-KLEEELKSLKNELRSLEDLLEELRRQLEELER 716

Query: 359 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLA 418
           + E+ ++     E+E E+ + +    +EE +E +      +  LEE     +   EE LA
Sbjct: 717 QLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEE-ELESLEEALA 775

Query: 419 DEVREEEEIAVAKRRAEEEQLQQQQ 443
               E EE+   ++  +EE  + ++
Sbjct: 776 KLKEEIEELEEKRQALQEELEELEE 800

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.7 bits (98), Expect = 0.002
 Identities = 40/165 (24%), Positives = 75/165 (45%), Gaps = 5/165 (3%)

Query: 293 DRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKD 352
           +  R  +R   + E  ++R +E E +  E E E E +R   E+  ++ E  +  E  L+ 
Sbjct: 274 EELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEK 333

Query: 353 WE--YREREREKERQYEKEKEKERE-RKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR 409
            E    + E E E   E++ E  +   +R KE+    EE E +  K   R    E+  + 
Sbjct: 334 LEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQE 393

Query: 410 IREKEEDLADEVRE--EEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
           ++E+  +L+  + E  EE   + K   E E+  ++  + +K L +
Sbjct: 394 LKEELAELSAALEEIQEELEELEKELEELERELEELEEEIKKLEE 438

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 37/173 (21%), Positives = 73/173 (42%), Gaps = 25/173 (14%)

Query: 305 KERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 364
            E  LK E E ++++ E   E     KE+ Q ++++E  R+ E  L++ +    E    R
Sbjct: 523 LEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLR 582

Query: 365 QYEKEKEKERERKR----------KKEILYDEEEDEDDSRKRWR-----RSVLEEKRRKR 409
             ++E E+ RER +          ++    +E     +  +           LE +  K 
Sbjct: 583 TRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKL 642

Query: 410 ---------IREKEEDLADEVRE-EEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
                    ++   E+L ++V E E EI    +R E E+  +++ + L+ L +
Sbjct: 643 NLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEE 695

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 36/160 (22%), Positives = 73/160 (45%), Gaps = 13/160 (8%)

Query: 296 RVHDRRGRDKERDLKREKEREIDRYER-EAERERVRKEREQRRKIEEAEREYERCLKDWE 354
            + ++    + ++  R+ E  +   +    E   +R  +E+  ++ E  +E ++ LK+ E
Sbjct: 547 ELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLKELE 606

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEE--DEDDSRKRWRRSVLEEKRRKRIRE 412
            R  + E+  Q  +  E E E +  +E L  E E  +     +   ++ LEE     + E
Sbjct: 607 ERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAALEE-----LEE 661

Query: 413 KEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
           K E+L  E+R E +     R   EEQL+++  +  +L  +
Sbjct: 662 KVEELEAEIRRELQ-----RIENEEQLEEKLEELEQLEEE 696

Length = 908

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 33/152 (21%), Positives = 65/152 (42%), Gaps = 7/152 (4%)

Query: 299 DRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRER 358
           +R+    E +L++  E   +  +R  E E++ +E  ++ K +  E E  R  +     E 
Sbjct: 243 ERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIK-DLGEEEQLRVKEKIGELEA 301

Query: 359 EREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR------IRE 412
           E     +   EKE+E E   ++    + E D+  +        +EE+R++R        E
Sbjct: 302 EIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAE 361

Query: 413 KEEDLADEVREEEEIAVAKRRAEEEQLQQQQR 444
            +E+L D   E EE+        +E    +++
Sbjct: 362 LKEELEDLRAELEEVDKEFAETRDELKDYREK 393

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 41.4 bits (97), Expect = 0.002
 Identities = 29/126 (23%), Positives = 45/126 (35%), Gaps = 20/126 (15%)

Query: 354 EYREREREKERQYEKEKEKERERKRKKEI--------LYDEEEDEDDSRKRWRRSVLEEK 405
           +YRE+++EK     K       R R + I        L+ E  +   +R   +    E K
Sbjct: 293 QYREKQKEK-----KAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKN---EAK 344

Query: 406 -RRKRIREKE---EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAE 461
            R+K I +K    E   +    +E  A   R        + ++  L   S N    S  E
Sbjct: 345 ARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENE 404

Query: 462 ESAVES 467
           ES    
Sbjct: 405 ESKGSP 410

Length = 429

>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 = 37.6 bits (88), Expect = 0.002
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            K++V  ++       + ++    G V+     + P  G  +GFGF  FES E    A+R
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 115 LLNKFNIDGQELMLKVDQATR 135
            LN   ++G+  ++KV++A R
Sbjct: 62  DLNGKELEGR--VIKVEKAKR 80

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

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 91  SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK 129
            NG PK F F  F+    V  A++LLN   + G+EL +K
Sbjct: 37  PNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 28/171 (16%), Positives = 64/171 (37%), Gaps = 22/171 (12%)

Query: 299 DRRGRDKERDLKR-EKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRE 357
           D++ +  ++++   EK+    + +R    ++++    +   +E    E    LK  + R+
Sbjct: 37  DKQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLK--KLRK 94

Query: 358 REREKERQYEKEKEKERERKRKKEILYD------------EEEDEDDSRKRWRRSVLEEK 405
           +  +   +    + +ERE++R+                       +D+++  R ++    
Sbjct: 95  QIADLNARLNALEVQEREQRRRLAEQLAALQRSGRNPPPALLVSPEDAQRSVRLAIYYGA 154

Query: 406 ----RRKRIREKEEDLADEVREEEEIAVAK---RRAEEEQLQQQQRDALKL 449
               R +RI   +  L        EIA  +        EQ  QQ + A  L
Sbjct: 155 LNPARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLL 205

Length = 420

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 24/52 (46%), Positives = 38/52 (73%), Gaps = 4/52 (7%)

Query: 328 RVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRK 379
           ++ K+RE+   +E+A+RE E+  K  E RERE+EKE++ E+E+E+E ER  K
Sbjct: 576 KLAKKREE--AVEKAKREAEQ--KAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           VYVG I   +  D + S    CG ++      +P  G  +G  F  F++ E   RAL  L
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 117 NKFNIDGQEL 126
           +  ++ G+ L
Sbjct: 60  DGEDMGGRFL 69

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           VY G    +     V  + + CG V+         + T +   F  FE+ E    A+  L
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57

Query: 117 NKFNIDGQEL 126
           N  ++DG  +
Sbjct: 58  NGASVDGNCI 67

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|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 37/127 (29%), Positives = 63/127 (49%), Gaps = 7/127 (5%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 363
              +D++R K   I  Y       +V++E   R K E  E E  R +    Y +R ++ E
Sbjct: 372 GIWKDVERIKALVIRGYPLAEALSKVKEEERPREK-EGTEEEERREITV--YEKRIKKLE 428

Query: 364 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKR-IREKE---EDLAD 419
              E+ +E+  E KR+ E L  E E  +   +R+RR V ++ R+ R IR ++   E L  
Sbjct: 429 ETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEK 488

Query: 420 EVREEEE 426
           E+ E+++
Sbjct: 489 ELEEKKK 495

Length = 652

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

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 58  YVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           +V ++  T  D   +  +    G     + A  P NG P+GF F E+ +AE    A + L
Sbjct: 6   FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 117 NKFNIDGQEL 126
           N  ++ G  +
Sbjct: 65  NGHSLQGSPI 74

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

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           +YVG ++     + +  +   CG +K           TP GF F E+ + E    A++ L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 117 NKFNIDGQELMLKVD 131
           N   +D +   ++VD
Sbjct: 61  NGTKLDDRI--IRVD 73

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

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

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 23/97 (23%), Positives = 36/97 (37%), Gaps = 6/97 (6%)

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 414
           YR+RER + R   +  +K RER R++         +   R+R R      + R R R   
Sbjct: 2   YRDRERGRLRNDTRRSDKGRERSRRR-----SRSRDRSRRRRDRDYYRGRRGRSRSRSPN 56

Query: 415 E-DLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLL 450
                   R          R  +E L + +RD   + 
Sbjct: 57  RYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVF 93

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|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 37/166 (22%), Positives = 71/166 (42%), Gaps = 17/166 (10%)

Query: 319 RYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKR 378
           R  +EAER     ++E   K+E A  E +  L     ++R+  +  + E ++E+ER   +
Sbjct: 30  RLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEER-LVQ 88

Query: 379 KKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQ 438
           K+E L    E  D+   +       E+R K +  +E +L +  ++ +           EQ
Sbjct: 89  KEEQLDARAEKLDNLENQ------LEEREKALSARELELEELEKQLDNELYRVAGLTPEQ 142

Query: 439 LQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIREN 484
            ++       LL    ++  L EE A   K +  E +   ++ R+ 
Sbjct: 143 ARKL------LLKL--LDAELEEEKAQRVKKI--EEEADLEAERKA 178

Length = 508

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 31/172 (18%), Positives = 64/172 (37%), Gaps = 17/172 (9%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE--YRERERE 361
           ++ ++   E + EI+  E E    R     E+  ++E    E E  L++ +      + E
Sbjct: 284 EELQEELLELKEEIEELEGEISLLR-----ERLEELENELEELEERLEELKEKIEALKEE 338

Query: 362 KERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEV 421
            E +    +E E+     +E   + EE         + S L E+  +      E+LA+  
Sbjct: 339 LEERETLLEELEQLLAELEEAKEELEE---------KLSALLEELEELFEALREELAELE 389

Query: 422 REEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVE 473
            E  EI   +    + +++  +    +L           +E   E + +  E
Sbjct: 390 AELAEIR-NELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTE 440

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 30/143 (20%), Positives = 61/143 (42%), Gaps = 3/143 (2%)

Query: 306 ERDLKREKEREIDRYEREAERE-RVRKEREQRRKIEEAEREYERCLKDWEYREREREKER 364
           E +L R +E   +  E   E E  + + + +  ++ E   E +  L   E +E   E E 
Sbjct: 245 EEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELL--ELKEEIEELEG 302

Query: 365 QYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREE 424
           +    +E+  E + + E L +  E+  +  +  +  + E +      E+     +E +EE
Sbjct: 303 EISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEE 362

Query: 425 EEIAVAKRRAEEEQLQQQQRDAL 447
            E  ++    E E+L +  R+ L
Sbjct: 363 LEEKLSALLEELEELFEALREEL 385

Length = 1163

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

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
            ++VG ++ + D +++ +  +  GTV   +       G  +GFG+ +FES E   +A+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 116 LNKFNIDGQELMLKVDQA 133
           ++   +DG+   + VD +
Sbjct: 61  MDGKELDGR--PINVDFS 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|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584)

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 33/173 (19%), Positives = 66/173 (38%), Gaps = 19/173 (10%)

Query: 283 DHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRR-KIEE 341
             D       D  R ++R     ++ +K + ER++++         +R+E+++++  IEE
Sbjct: 367 RLDALTGKHQDVQRKYERL----KQKIKEQLERDLEK--NNERLAAIREEKDRQKAAIEE 420

Query: 342 AEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDED----DSRKRW 397
             +  E  L+      +    E +YE E    R ++R        EE E     D     
Sbjct: 421 DLQALESQLRQQLEAGKLEFNEEEYELELRLGRLKQRLDSATATPEELEQLEINDEALEK 480

Query: 398 RRSVLEEKRRKRIREKEE--------DLADEVREEEEIAVAKRRAEEEQLQQQ 442
            +   E+      + + E        D A E  +  E  + + R   ++L+ Q
Sbjct: 481 AQEEQEQAEANVEQLQSELRQLRKRRDEALEALQRAERRLLQLRQALDELELQ 533

This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Length = 1198

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	771
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	100.0
PF01480	77	PWI: PWI domain; InterPro: IPR002483 The PWI domai	99.75
smart00311	74	PWI PWI, domain in splicing factors.	99.71
KOG2146	354	consensus Splicing coactivator SRm160/300, subunit	99.67
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.52
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.48
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.47
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.42
KOG0122	270	consensus Translation initiation factor 3, subunit	99.36
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.35
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.35
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.34
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.26
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.24
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.21
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.21
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.2
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.18
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.18
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.17
PLN03120	260	nucleic acid binding protein; Provisional	99.17
PLN03213	759	repressor of silencing 3; Provisional	99.16
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.16
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.16
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.12
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.12
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.12
smart00362	72	RRM_2 RNA recognition motif.	99.12
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.12
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.11
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.07
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.06
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.06
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.05
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.05
PLN03121	243	nucleic acid binding protein; Provisional	99.05
smart00360	71	RRM RNA recognition motif.	99.04
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.04
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.04
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.04
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.03
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.01
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.97
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.96
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.95
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.95
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.94
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.91
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.89
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.87
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.87
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.77
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.77
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.76
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.76
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.75
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.75
smart00361	70	RRM_1 RNA recognition motif.	98.71
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.71
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.66
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.63
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.59
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.57
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.52
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.49
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.47
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.46
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.43
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.42
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.39
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.34
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.31
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.28
KOG0226	290	consensus RNA-binding proteins [General function p	98.28
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.26
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.24
KOG0151	877	consensus Predicted splicing regulator, contains R	98.22
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.2
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.18
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	98.17
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.16
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.15
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.1
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.09
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	97.95
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.93
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	97.87
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.85
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.81
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.66
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.66
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.44
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.27
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.25
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.16
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.01
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	96.89
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.88
KOG3152	278	consensus TBP-binding protein, activator of basal	96.77
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.75
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	96.73
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.71
KOG4210	285	consensus Nuclear localization sequence binding pr	96.6
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.56
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	96.4
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	96.38
KOG2314	698	consensus Translation initiation factor 3, subunit	96.23
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.21
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	95.97
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	95.92
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.9
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.72
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.54
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	95.36
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	95.03
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	94.54
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.51
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	94.43
KOG1548	382	consensus Transcription elongation factor TAT-SF1	94.03
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	94.02
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	93.96
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	93.39
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	93.24
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	92.89
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	92.89
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	92.71
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	92.47
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	92.41
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	92.31
PTZ00266	1021	NIMA-related protein kinase; Provisional	91.93
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	91.17
KOG1996	378	consensus mRNA splicing factor [RNA processing and	90.97
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	90.49
PTZ00266	1021	NIMA-related protein kinase; Provisional	90.43
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	89.45
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	89.42
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	87.93
KOG2068	327	consensus MOT2 transcription factor [Transcription	87.25
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	85.89
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	84.74
KOG2891	445	consensus Surface glycoprotein [General function p	83.45
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	83.11
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	82.02

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=100.00  E-value=4.3e-69  Score=600.43  Aligned_cols=613  Identities=31%  Similarity=0.472  Sum_probs=367.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      -++..+||||||.+.+....+..++..||.|.+|+++.         ||||.|.++....+|++.|+-..++|..|.+++
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            44578999999999999999999999999999998754         999999999999999999999999999999987


Q ss_pred             ehhhHHHHHHHHHhhhhhhhhhhhhccccCCcccccccccccCCCCCCCc---------ccccCCCCCCCCCCCcccccc
Q 004150          131 DQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPE---------NLKDNETGNKESHDPTNFGVV  201 (771)
Q Consensus       131 a~~~kk~le~~k~kk~e~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~gd~~~~~~~ev~~~~~~  201 (771)
                      +..+-..-+.++  .                     .....+-.|.++.+         ....++..+++++.+++-..+
T Consensus       108 d~q~~~n~~k~~--~---------------------~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is~s~~s  164 (668)
T KOG2253|consen  108 DEQTIENADKEK--S---------------------IANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQISSSAAS  164 (668)
T ss_pred             hhhhhcCccccc--c---------------------chhhhhcccCCchhHHHHHhhccccchhHHHHHHHHhccchhhh
Confidence            722111100000  0                     00111111222111         011111112222333333333


Q ss_pred             chhhhhhhHHHHHHHHHHHHHhhhCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCchhhhccccccccccccccccccc
Q 004150          202 TEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKA  281 (771)
Q Consensus       202 ~~ed~~~d~~~~Eki~~~~eer~~~~~~~~~~~~~~~~~~~~~~~e~p~~~rd~~~~~d~~k~~~~~~~~~~~~~~d~~~  281 (771)
                      +.....+|.-.++.+...+++......++.++.++...     .  .+++  .+.+..+             .+.  .  
T Consensus       165 ~~~~~e~d~h~~e~~~~~~~s~~~~~~~~~~~~~~~e~-----~--~~s~--~~~s~td-------------s~~--~--  218 (668)
T KOG2253|consen  165 RRQIAEADDHCLELEKTETESNSALSKEAESKKSPFED-----T--KDSK--RSFSSTD-------------SGS--E--  218 (668)
T ss_pred             hhhhHHHHHHHHHHHHhhcccccccCcccccccCchhh-----h--chhh--hhhcccC-------------ccc--c--
Confidence            33333444444454444444332221111111100000     0  0000  0000000             000  0  


Q ss_pred             CCCCCCCCCCCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 004150          282 SDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERERE  361 (771)
Q Consensus       282 ~e~er~~~~~~~rsr~r~rr~r~r~r~~ere~ere~~r~~r~rerer~r~~r~~~~~~re~E~~y~er~r~we~RER~r~  361 (771)
                       +.++. ..+.++++.++   +.+...+.|...+.+++.+.....+..++.|...++..++|.||+.||+.|+.||+.++
T Consensus       219 -~d~~~-~~s~~~n~~rd---~sr~~~r~R~~~r~Re~~e~~ed~~~~re~r~~~~~~~~~E~Ayq~rl~~we~Rer~~~  293 (668)
T KOG2253|consen  219 -SDSAE-VNSSSLNYCRD---RSRFDRRSRNDRRIRERLEKNEDSDEYREDRAATIKSVDPEKAYQTRLVFWEIREQTKE  293 (668)
T ss_pred             -chhhh-hcccccccchh---hccchhhhHHHHHHHHHhhhccchHHHHHhhhhhhhccChhHHHHHHHHHHHHHHHHHH
Confidence             00000 00111111111   11111111111111111111112244566788888999999999999999999999985


Q ss_pred             HHHHHHHHHHHHHH------HHHHHHHhhhcccchhhhhhhhhhHHHHHHHHHHHhhhhhcHHHHHHHHHHHHHHHHHHH
Q 004150          362 KERQYEKEKEKERE------RKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAE  435 (771)
Q Consensus       362 ~~r~~ekerere~e------r~r~~e~l~d~dddrdd~rk~~r~~~~~~R~r~r~rE~e~D~~DR~rE~eE~~e~~~~~~  435 (771)
                      +.+++|+.+|+++.      ++++++|++||||++|+ .+||++++|..|++++.+|+|+|.+||.+|++|++|+|++..
T Consensus       294 Ke~eke~~ke~~r~~~~~ke~kr~k~~~ed~DD~rdd-~~y~r~s~l~~r~r~~~re~Ead~~dR~qeqee~~E~Kr~~~  372 (668)
T KOG2253|consen  294 KEREKERLKEKSRQYKREKEAKRLKEFLEDYDDERDD-PKYYRGSALQERLRDREREAEADRRDRHQEQEELEEIKRRHS  372 (668)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhcchhhhh-HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHh
Confidence            55444444444332      36899999999999997 699999999999999999999999999999999999999988


Q ss_pred             HHHHHHHHHHHhhhhhhhccCCCc----cchhhhcccCCcccCCCCCCcccccCCCCCCCCCCCCCCCCCCccccccccc
Q 004150          436 EEQLQQQQRDALKLLSDNAVNGSL----AEESAVESKGMDVEHDYHDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMR  511 (771)
Q Consensus       436 ee~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~  511 (771)
                      ++..+.....+...+.........    .+...++.........+.+.+++..|+...  -.+..+-+    ...+-...
T Consensus       373 ~~~~~~~~~e~~r~~~~~~~~~~~~~~~a~~ke~e~~~~~~~~q~~~e~a~~~~~~~e--ee~~s~r~----~~~~d~~~  446 (668)
T KOG2253|consen  373 EEEAEDPSAEEERNMEEEEALDEEEDDEAVRKEPEERDLEESHQRLGESANQEHSNDE--EEIKSQRD----DYKPDEND  446 (668)
T ss_pred             hhcccccchHHHHHHhhhhhhcchhhHHHHhhCcccccCccccchHHhhhhhccccch--hhcccchh----hhhhhhhh
Confidence            766443322222222222111111    012222233332333333344433321100  00000000    00000011


Q ss_pred             cCCCCccccccCcccCCCCccccCccCCCCCCcchhcccCCCCcccCCCChHHHhhhcCCCCCCCCCchHHHHHHHHHhh
Q 004150          512 QSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRIS  591 (771)
Q Consensus       512 ~~~~~~~~k~~~~~~~~~kr~~v~~vf~~~ddee~~~~~~kr~LvPl~y~~ee~~~~~~~~~~~~~~~~~~~~~~~~~~~  591 (771)
                      .-..+|...+.+++++++.+...+.+|-.-+...++....+..++||.|+.....+     .|+.++++..++.   -+-
T Consensus       447 ~i~~~ps~~~~s~~~~~n~~~~~~~~~~~~~e~~~~es~n~~~n~p~~~~~~~q~~-----~g~sa~~~~i~~k---k~~  518 (668)
T KOG2253|consen  447 HISHAPSASLASGLVDANDRDSSPRGFKERHEREDDESLNKKINRPILASIQNQDE-----IGPSASPIPIAKK---KLP  518 (668)
T ss_pred             hhhcCchhhhhhhccCCCCCCcccccccccccCcchhhhccccccccccccccccc-----ccCCCCccccccc---cCC
Confidence            23457777888899999888899988886555444566667889999987633222     2222222111111   000


Q ss_pred             cccchhhhchHHHHhhhhhccccchhhhccccccccchhhhhhhhhhccccccccccccccCchhhhhhhHHhhhhcCCC
Q 004150          592 NVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPK  671 (771)
Q Consensus       592 ~t~~kee~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ip~  671 (771)
                      .|+.                      .+...++|.+-...+ ++++.+.+++..- ..++.+.+ .|.+++++||.+||+
T Consensus       519 ~~~v----------------------~~~~~d~Dk~v~~~k-k~vp~dyd~n~~~-~~~~~~nd-eK~~~~ksLI~tIP~  573 (668)
T KOG2253|consen  519 ETGV----------------------FREDDDEDKNVHEKK-KLVPLDYDRNQAR-AHSGESND-EKRKRIKSLIETIPT  573 (668)
T ss_pred             Cccc----------------------ccccCCcccccchhh-hcccccCChhhcc-cccCCcch-hHHHHHHhhcccCCc
Confidence            1100                      011112322222333 7777776664211 11222222 345689999999999


Q ss_pred             CchhhhcccccccccchhhHhhhhhhhHHHHHHhhcCcchhHHHHHHHHhhhccCCHHHHHHHHHHhhhHHHHHHHHHHH
Q 004150          672 TKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMW  751 (771)
Q Consensus       672 ~k~~lf~~~i~w~~~d~~~~~~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~~~~p~~l~~~l~~~lde~a~~fv~klW  751 (771)
                      +|++||+|+|+|+.||.-+|+.+|+|||+|||+||||++|++||||||++|..|.+||+||++|.++||++|++||+|||
T Consensus       574 ~keeLf~~pidw~~ld~~lm~~rirpwV~KKIiEflGeeE~tLVdFI~s~i~~h~~~q~iL~dl~~ilDEdAE~FV~KmW  653 (668)
T KOG2253|consen  574 EKEELFAYPIDWDELDSILMNERIRPWVNKKIIEFLGEEEDTLVDFICSNIRQHSSPQQILDDLAMILDEDAEVFVVKMW  653 (668)
T ss_pred             chHHHhhCcccHHHHhhHHHHHHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCHHHHHHHHHHHHhcchHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhhccc
Q 004150          752 RMLIFEIKKVETGLA  766 (771)
Q Consensus       752 rllife~~~~~~gl~  766 (771)
                      ||||||+.+++.||+
T Consensus       654 RlLiyel~ar~~g~~  668 (668)
T KOG2253|consen  654 RLLIYELGARKLGLT  668 (668)
T ss_pred             HHHHHHhhhhhccCC
Confidence            999999999999985

>PF01480 PWI: PWI domain; InterPro: IPR002483 The PWI domain, named after a highly conserved PWI tri-peptide located within its N-terminal region, is a ~80 amino acid module, which is found either at the N terminus or at the C terminus of eukaryotic proteins involved in pre-mRNA processing []

Probab=99.75  E-value=6.9e-19  Score=153.09  Aligned_cols=68  Identities=46%  Similarity=0.808  Sum_probs=61.2

Q ss_pred             hhhhhhHHHHHHhhcCcchhHHHHHHHHhhhccC-----CHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHh
Q 004150          693 ERMRPWISKKITEFLGEEETTLVDYIVSSTQDHV-----KASQMLELLQTILDDEAEMFVLKMWRMLIFEIKK  760 (771)
Q Consensus       693 ~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~~~-----~p~~l~~~l~~~lde~a~~fv~klWrllife~~~  760 (771)
                      ++|||||.+||++|||++|++||+||+++|..+.     +|+.|+++|++||+++|..||.+||++||+.+..
T Consensus         2 ~~lk~WI~~kl~e~lG~edd~lvdyI~~~l~~~~~~~~~~~~~l~~~L~~fL~~~a~~Fv~~Lw~~l~~~q~~   74 (77)
T PF01480_consen    2 EKLKPWISKKLEEILGFEDDVLVDYIVALLKSHKSSNEPDPKELQEQLEDFLDEEAEEFVDELWRLLISAQSS   74 (77)
T ss_dssp             HHHHHHHHHHHHHHHSS--CHHHHHHHHHCCTT--SSS--HHHHHHHHTTTTGHHCHHHHHHHHHHHHHHTTS
T ss_pred             hHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccccccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhcC
Confidence            5799999999999999999999999999999887     9999999999999999999999999999998754

It is generally found in association with other domains such as RRM and RS. The PWI domain is a RNA/DNA-binding domain that has an equal preference for single- and double-stranded nucleic acids and is likely to have multiple important functions in pre-mRNA processing []. Proteins containing this domain include the SR-related nuclear matrix protein of 160kDa (SRm160) splicing and 3'-end cleavage-stimulatory factor, and the mammalian splicing factor PRP3. The PWI domain is a soluble, globular and independently folded domain which consists of a four-helix bundle, with structured N- and C-terminal elements [].; GO: 0006397 mRNA processing; PDB: 1MP1_A 1X4Q_A.

>smart00311 PWI PWI, domain in splicing factors

Probab=99.71  E-value=1.6e-17  Score=143.50  Aligned_cols=70  Identities=43%  Similarity=0.726  Sum_probs=66.9

Q ss_pred             hHhhhhhhhHHHHHHhhcCcchhHHHHHHHHhhhccCCHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Q 004150          690 ELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIK  759 (771)
Q Consensus       690 ~~~~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~~~~p~~l~~~l~~~lde~a~~fv~klWrllife~~  759 (771)
                      +..++|+|||+++|++|||++|++||+||+++|+.|.+|+.++..|..+++.+|+.||.+||+||||++.
T Consensus         4 v~~~~lk~WI~~kv~e~LG~~d~~vvd~i~~~l~~~~~~~~l~~~L~~~~f~da~~Fv~~Lw~~l~~~~~   73 (74)
T smart00311        4 LKLDEIKPWITKKVIEFLGFEEDTLVEFILSQIRQHKGPQAKLLQINLTGFEDAEEFVDKLWRLLIFELK   73 (74)
T ss_pred             hHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCChHHHHHHHHhhcchhHHHHHHHHHHHHHHhhc
Confidence            3458899999999999999999999999999999999999999999999999999999999999999875

>KOG2146 consensus Splicing coactivator SRm160/300, subunit SRm160 (contains PWI domain) [RNA processing and modification; General function prediction only]

Probab=99.67  E-value=1.6e-17  Score=171.12  Aligned_cols=81  Identities=25%  Similarity=0.591  Sum_probs=70.2

Q ss_pred             cchhhHh-hhhhhhHHHHHHhhcCcchhHHHHHHHHhhhc--cCCHHHHHHHHHHhhh-HHHHHHHHHHHHHHHHHHHhh
Q 004150          686 YDKHELH-ERMRPWISKKITEFLGEEETTLVDYIVSSTQD--HVKASQMLELLQTILD-DEAEMFVLKMWRMLIFEIKKV  761 (771)
Q Consensus       686 ~d~~~~~-~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~--~~~p~~l~~~l~~~ld-e~a~~fv~klWrllife~~~~  761 (771)
                      ||++.|+ +.|+|||+++|+|+||+||++||+||+++|.+  ..+|+.||++|+|||. .+|..||.+||-|||-+.-+-
T Consensus        35 VDmsKvnleVlkPWItkrvneilgfEDdVViefvynqLee~k~ldpkkmQiNlTGFLngrnAreFmgeLW~LliS~a~~s  114 (354)
T KOG2146|consen   35 VDMSKVNLEVLKPWITKRVNEILGFEDDVVIEFVYNQLEEAKNLDPKKMQINLTGFLNGRNAREFMGELWSLLISEASQS  114 (354)
T ss_pred             cchhhcchhhhhHHHHHHHHHhhccccchhHHHHHHHHhhhcCCCchheeeeeehhcccccHHHHHHHHHHHHHhhcccc
Confidence            4444443 67899999999999999999999999999976  6799999999999999 899999999999999865555


Q ss_pred             hhccc
Q 004150          762 ETGLA  766 (771)
Q Consensus       762 ~~gl~  766 (771)
                      +.||.
T Consensus       115 ~~giP  119 (354)
T KOG2146|consen  115 QYGIP  119 (354)
T ss_pred             ccCCc
Confidence            55553

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.52  E-value=1.9e-12  Score=143.54  Aligned_cols=82  Identities=11%  Similarity=0.253  Sum_probs=75.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..-.++|||.+|+..+...+|+.||++||.|+..+||++..+...+|||||++.+..+|.+||.+||.++|+|+.|.|.-
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34468999999999999999999999999999999999977778889999999999999999999999999999999975


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +.
T Consensus       482 aK  483 (940)
T KOG4661|consen  482 AK  483 (940)
T ss_pred             cc
Confidence            43

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.48  E-value=3.5e-13  Score=130.95  Aligned_cols=83  Identities=18%  Similarity=0.327  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|+.+|..||.|.++.++.++.+|+++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34577999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       111 a~~  113 (144)
T PLN03134        111 AND  113 (144)
T ss_pred             CCc
Confidence            764

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.47  E-value=4.3e-13  Score=147.00  Aligned_cols=82  Identities=17%  Similarity=0.310  Sum_probs=77.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..+.+|||+|||+.+++++|..+|++||.|.+++++.++.||.++|||||.|.+.++|..||..|||..|+|+.|.|.|.
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            33557999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       347 ~~  348 (352)
T TIGR01661       347 TN  348 (352)
T ss_pred             cC
Confidence            64

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.42  E-value=3.2e-13  Score=125.62  Aligned_cols=82  Identities=22%  Similarity=0.404  Sum_probs=79.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..++|||||||++.++++.|.+||+.||.|..+.+-.|+.+..++|||||+|.+.++|..||+.|+|+.|+.+.|.|+|+
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            56899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       114 ~G  115 (153)
T KOG0121|consen  114 AG  115 (153)
T ss_pred             cc
Confidence            75

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.36  E-value=5.9e-12  Score=128.58  Aligned_cols=85  Identities=22%  Similarity=0.326  Sum_probs=80.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           49 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        49 ~~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ..-...++|-|.|||.++++.+|..||.+||.|.++.++.|+.||.++|||||+|.+.++|.+||..|||+-++.-.|.|
T Consensus       184 R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrv  263 (270)
T KOG0122|consen  184 RERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRV  263 (270)
T ss_pred             ccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEE
Confidence            34456889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+.+
T Consensus       264 EwskP  268 (270)
T KOG0122|consen  264 EWSKP  268 (270)
T ss_pred             EecCC
Confidence            99875

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.35  E-value=1.1e-11  Score=136.58  Aligned_cols=83  Identities=16%  Similarity=0.316  Sum_probs=78.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|+.+|..||.|.+|+|+.+..+|+++|||||+|.+.++|..||..||+..|.++.|.|.+
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            45678999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       184 a~p  186 (346)
T TIGR01659       184 ARP  186 (346)
T ss_pred             ccc
Confidence            754

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.35  E-value=4.8e-12  Score=105.50  Aligned_cols=70  Identities=33%  Similarity=0.571  Sum_probs=67.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           57 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        57 VfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      |||+|||..+++.+|..+|+.||.|..+.+..+ .++.+++||||.|.+.++|..|+..|+|..|+|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 6899999999999999999999999999999999885

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.34  E-value=4.5e-12  Score=138.94  Aligned_cols=81  Identities=19%  Similarity=0.355  Sum_probs=77.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.++|||+|||+.+++.+|+.+|+.||.|.+|+++.++.+|+++|||||+|.+.++|..||..|||..|.|+.|.|.|+.
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            46899999999999999999999999999999999998899999999999999999999999999999999999999875


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        82 ~   82 (352)
T TIGR01661        82 P   82 (352)
T ss_pred             c
Confidence            4

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=2.3e-11  Score=127.24  Aligned_cols=84  Identities=18%  Similarity=0.398  Sum_probs=80.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.+||||+-|++.+++..|+..|..||.|..+.||.+..||+++|||||+|...-+...|....+|..|+|+.|.|+
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            35778999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      |...
T Consensus       177 vERg  180 (335)
T KOG0113|consen  177 VERG  180 (335)
T ss_pred             eccc
Confidence            8654

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.24  E-value=4.7e-11  Score=126.23  Aligned_cols=82  Identities=18%  Similarity=0.229  Sum_probs=76.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...+..|||+|||+.+.+.+|+.+|.+||.|+++.|+.+  ...++|||||+|+++.+|.+|-..|||..|.|++|.|+.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            344688999999999999999999999999999999997  567899999999999999999999999999999999988


Q ss_pred             ehhh
Q 004150          131 DQAT  134 (771)
Q Consensus       131 a~~~  134 (771)
                      +.+.
T Consensus       171 ATar  174 (376)
T KOG0125|consen  171 ATAR  174 (376)
T ss_pred             cchh
Confidence            7664

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.21  E-value=1.2e-10  Score=134.14  Aligned_cols=82  Identities=20%  Similarity=0.399  Sum_probs=77.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||||||+.+++++|..+|..||.|..+.++.+..+|.++|||||+|.+...|..||..|||+.|+|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            54

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.21  E-value=6.9e-11  Score=137.57  Aligned_cols=82  Identities=24%  Similarity=0.428  Sum_probs=77.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+||++.+++++|+.+|+.||.|.+|+++.++.+|+++|||||.|.+.++|..||..||++.|+|+.|.|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            34679999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       282 i~  283 (612)
T TIGR01645       282 VT  283 (612)
T ss_pred             CC
Confidence            64

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.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.20  E-value=8.6e-11  Score=120.67  Aligned_cols=81  Identities=20%  Similarity=0.315  Sum_probs=77.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .....|||-||++.+.+..|.++|+.||.|..+++++|..|.+++|||||++.+.++|..||..|||+.++++.|.|.|-
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            34778999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             h
Q 004150          132 Q  132 (771)
Q Consensus       132 ~  132 (771)
                      .
T Consensus       356 t  356 (360)
T KOG0145|consen  356 T  356 (360)
T ss_pred             c
Confidence            4

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.18  E-value=3.6e-11  Score=122.55  Aligned_cols=81  Identities=23%  Similarity=0.345  Sum_probs=73.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      +...++||||+|++.+..+.|+.+|.+||.|+...|+.|+.+|+++|||||+|.+.++|.+|+. -..-.|+|++-.|++
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~-dp~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACK-DPNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhc-CCCCcccccccccch
Confidence            4457899999999999999999999999999999999999999999999999999999999998 445678999988876


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +-
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            54

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.18  E-value=6.2e-11  Score=137.92  Aligned_cols=79  Identities=28%  Similarity=0.422  Sum_probs=75.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...++|||||||+.+++++|+.+|..||.|.+|.++.++.+|+++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            4568999999999999999999999999999999999999999999999999999999999999999999999999974

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.17  E-value=1.2e-10  Score=98.02  Aligned_cols=70  Identities=33%  Similarity=0.575  Sum_probs=64.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           57 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        57 VfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      |||+|||++++..+|..+|+.||.|..+.+..+.. |.++++|||+|.+.++|..|+..+++..|+|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999855 99999999999999999999999999999999874

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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.17  E-value=1.1e-10  Score=122.35  Aligned_cols=76  Identities=14%  Similarity=0.189  Sum_probs=70.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||||||+.+++.+|+.+|+.||.|.++.|+.+.   .++|||||+|.+..+|..||. |+|..|+|+.|.|.++..
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 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            5799999999999999999999999999999998874   356899999999999999996 999999999999988653

>PLN03213 repressor of silencing 3; Provisional

Probab=99.16  E-value=1.5e-10  Score=127.29  Aligned_cols=89  Identities=19%  Similarity=0.355  Sum_probs=78.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCH--HHHHHHHHHhCCceeCCeEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA--EGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~--esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ....+||||||++.+++++|..+|..||.|..+.|++  .+|  +|||||+|.+.  .++.+||..|||..++|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            4467899999999999999999999999999999994  577  89999999987  68999999999999999999997


Q ss_pred             EehhhHHHHHHHHHhhh
Q 004150          130 VDQATREYLERYVDKKT  146 (771)
Q Consensus       130 ~a~~~kk~le~~k~kk~  146 (771)
                      .+.  ..||+..+..++
T Consensus        84 KAK--P~YLeRLkrERe   98 (759)
T PLN03213         84 KAK--EHYLARLKREWE   98 (759)
T ss_pred             ecc--HHHHHHHHHHHH
Confidence            664  578877765443

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.16  E-value=2e-11  Score=125.66  Aligned_cols=87  Identities=15%  Similarity=0.257  Sum_probs=80.4

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 004150           46 TVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  125 (771)
Q Consensus        46 ~~~~~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~  125 (771)
                      ......+..|+|||-.||..+++.+|.++|-.||.|++.++..|+.|..++|||||.|.++.++..||..|||+.|+.++
T Consensus       277 qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKR  356 (371)
T KOG0146|consen  277 QQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKR  356 (371)
T ss_pred             hhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhh
Confidence            33445778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEeh
Q 004150          126 LMLKVDQ  132 (771)
Q Consensus       126 L~V~~a~  132 (771)
                      |+|.+-.
T Consensus       357 LKVQLKR  363 (371)
T KOG0146|consen  357 LKVQLKR  363 (371)
T ss_pred             hhhhhcC
Confidence            9986543

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.16  E-value=5.6e-12  Score=123.69  Aligned_cols=82  Identities=21%  Similarity=0.325  Sum_probs=77.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      -..+.-|||||||+.+|+.+|.-+|+.||.|+.+.+++|..||+++||||+.|++..++.-|+..|||+.|.|+.|+|+-
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            35577899999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      ..
T Consensus       112 v~  113 (219)
T KOG0126|consen  112 VS  113 (219)
T ss_pred             cc
Confidence            44

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.12  E-value=2.4e-10  Score=130.03  Aligned_cols=80  Identities=26%  Similarity=0.486  Sum_probs=77.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.+++.+|..+|..||.|..|.++.+..+|+++|||||+|.+.++|..||..|||+.|+|+.|.|.|+.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            36899999999999999999999999999999999998889999999999999999999999999999999999999976

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.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.12  E-value=2.3e-10  Score=125.03  Aligned_cols=87  Identities=25%  Similarity=0.419  Sum_probs=80.2

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-CeEE
Q 004150           48 TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQEL  126 (771)
Q Consensus        48 ~~~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr~L  126 (771)
                      .+..+..|-||||.||.++.+++|.-||.+.|.|..++++.|+.+|.++||+||+|++.+.|..||..||+++|. |+.|
T Consensus        77 g~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~i  156 (506)
T KOG0117|consen   77 GPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLL  156 (506)
T ss_pred             CCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEe
Confidence            333456899999999999999999999999999999999999999999999999999999999999999999996 9999


Q ss_pred             EEEEehhh
Q 004150          127 MLKVDQAT  134 (771)
Q Consensus       127 ~V~~a~~~  134 (771)
                      .|.++...
T Consensus       157 gvc~Svan  164 (506)
T KOG0117|consen  157 GVCVSVAN  164 (506)
T ss_pred             EEEEeeec
Confidence            99887653

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.12  E-value=2.3e-10  Score=126.29  Aligned_cols=81  Identities=23%  Similarity=0.393  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  130 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G--r~L~V~~  130 (771)
                      ..++|||+|||..+++++|+.+|+.||.|..|.|+.+..+|+++|||||+|.+.++|..||..||+..|.+  +.|.|.|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            35789999999999999999999999999999999998899999999999999999999999999998875  6888888


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       272 a~~  274 (346)
T TIGR01659       272 AEE  274 (346)
T ss_pred             CCc
Confidence            765

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).

>smart00362 RRM_2 RNA recognition motif

Probab=99.12  E-value=4.5e-10  Score=92.17  Aligned_cols=71  Identities=30%  Similarity=0.539  Sum_probs=67.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      +|||+|||..++..+|..+|..||.|..+.+..+.  +.+.|||||+|.+...|..|+..|++..+.|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            58999999999999999999999999999998874  888999999999999999999999999999999887

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.12  E-value=3.4e-10  Score=116.38  Aligned_cols=89  Identities=16%  Similarity=0.344  Sum_probs=84.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      .....++|.|.-||.++|.++|+.||+..|.|.+|++++|+.+|.+.|||||.|.++.+|++||..|||..|..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34557889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EehhhHHHH
Q 004150          130 VDQATREYL  138 (771)
Q Consensus       130 ~a~~~kk~l  138 (771)
                      ++.++...+
T Consensus       117 yARPSs~~I  125 (360)
T KOG0145|consen  117 YARPSSDSI  125 (360)
T ss_pred             eccCChhhh
Confidence            999876666

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.11  E-value=1.3e-10  Score=130.50  Aligned_cols=82  Identities=33%  Similarity=0.594  Sum_probs=79.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehhh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  134 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~~  134 (771)
                      +.|||||||+.++++.|..+|+.+|.|.+++++.|+.||+++|||||+|.+.+.|..|++.|||..+.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             HH
Q 004150          135 RE  136 (771)
Q Consensus       135 kk  136 (771)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.07  E-value=4.8e-10  Score=130.33  Aligned_cols=81  Identities=23%  Similarity=0.401  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr~L~V~  129 (771)
                      ....++|||+|||.++++++|..+|..||.|..++|+.| .+|+++|||||+|.+.++|..||..||+..|. |+.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            334699999999999999999999999999999999999 79999999999999999999999999999985 7777776


Q ss_pred             Eeh
Q 004150          130 VDQ  132 (771)
Q Consensus       130 ~a~  132 (771)
                      ++.
T Consensus       134 ~S~  136 (578)
T TIGR01648       134 ISV  136 (578)
T ss_pred             ccc
Confidence            543

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.

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

Probab=99.06  E-value=7.3e-10  Score=129.63  Aligned_cols=84  Identities=23%  Similarity=0.406  Sum_probs=78.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+||+..+++++|+.+|+.||.|.+|+++.+ .+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.++
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            34678999999999999999999999999999999999 79999999999999999999999999999999999999998


Q ss_pred             hhhHH
Q 004150          132 QATRE  136 (771)
Q Consensus       132 ~~~kk  136 (771)
                      .....
T Consensus       362 ~~k~~  366 (562)
T TIGR01628       362 QRKEQ  366 (562)
T ss_pred             cCcHH
Confidence            86543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.06  E-value=6.7e-10  Score=113.43  Aligned_cols=80  Identities=26%  Similarity=0.457  Sum_probs=76.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||||||..+++.+|..+|..||.|..+.++.+..+|.++|||||.|.+.+++..|+..|+|..|+|+.|.|.+...
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            59999999999999999999999999999999999988999999999999999999999999999999999999998653

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.05  E-value=2.9e-10  Score=113.69  Aligned_cols=82  Identities=20%  Similarity=0.278  Sum_probs=78.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|.|-||.+.++.++|..+|.+||.|..|.|.+|+.|+.++||+||-|.+..+|+.|+..|+|..|+|+.|.|.+|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        91 ry   92 (256)
T KOG4207|consen   91 RY   92 (256)
T ss_pred             hc
Confidence            64

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

Probab=99.05  E-value=6.3e-10  Score=130.18  Aligned_cols=78  Identities=22%  Similarity=0.400  Sum_probs=75.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      +|||||||+++++.+|..+|+.||.|.+|+++++..|++++|||||+|.+.++|.+||..||+..|.|+.|.|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            799999999999999999999999999999999988999999999999999999999999999999999999998753

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.05  E-value=7.9e-10  Score=114.37  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=69.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..+||||+||++.+++.+|+.+|+.||.|..|.|+.+   +...+||||+|.++..+..||. |+|..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            4689999999999999999999999999999999987   4556899999999999999996 99999999999986543

>smart00360 RRM RNA recognition motif

Probab=99.04  E-value=1.1e-09  Score=89.41  Aligned_cols=70  Identities=31%  Similarity=0.539  Sum_probs=66.5

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           59 VGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        59 VgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      |+|||..++..+|+.+|..||.|..+.+..++.++.++|||||.|.+.++|..|+..|++..++|+.|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            6899999999999999999999999999988778999999999999999999999999999999999887

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.04  E-value=4.7e-10  Score=109.87  Aligned_cols=76  Identities=29%  Similarity=0.455  Sum_probs=69.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..+.||||||+..++..+|..+|..||.|.++-|...     +.||+||+|+++.+|..|+..|+|..|+|..|.|.++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3789999999999999999999999999988766553     56999999999999999999999999999999998766


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        84 G   84 (195)
T KOG0107|consen   84 G   84 (195)
T ss_pred             C
Confidence            4

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.04  E-value=9.9e-10  Score=125.02  Aligned_cols=82  Identities=23%  Similarity=0.356  Sum_probs=76.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|..+|+.||.|..+.++.+..+|+++|||||+|.+.++|..||. |+|..|.|+.|.|.+
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            4557899999999999999999999999999999999998999999999999999999999997 999999999999986


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            543

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.04  E-value=2.4e-09  Score=123.30  Aligned_cols=78  Identities=19%  Similarity=0.216  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      .++.++|||+||++ .++++.|..+|+.||.|.+++++.++     +|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            45678999999998 69999999999999999999998862     5899999999999999999999999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus       347 ~s~~  350 (481)
T TIGR01649       347 PSKQ  350 (481)
T ss_pred             Eccc
Confidence            8754

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.03  E-value=4.4e-10  Score=116.34  Aligned_cols=85  Identities=20%  Similarity=0.343  Sum_probs=79.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ......||||-|+..++.+.|+..|.+||.|..++|++|..|+|++|||||.|.+.++|++||..|||.-|+++.|+.+|
T Consensus        59 ~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNW  138 (321)
T KOG0148|consen   59 SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNW  138 (321)
T ss_pred             cccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccc
Confidence            34467899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ehhhH
Q 004150          131 DQATR  135 (771)
Q Consensus       131 a~~~k  135 (771)
                      +....
T Consensus       139 ATRKp  143 (321)
T KOG0148|consen  139 ATRKP  143 (321)
T ss_pred             cccCc
Confidence            87543

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.01  E-value=3.9e-10  Score=111.04  Aligned_cols=81  Identities=19%  Similarity=0.415  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ....|||||||+..+++..|.++|-++|+|+.+++..|+.+..++|||||+|.+.++|.=|+.+||.+.|-|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            44689999999999999999999999999999999999999999999999999999999999999999999999999754


Q ss_pred             h
Q 004150          132 Q  132 (771)
Q Consensus       132 ~  132 (771)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            4

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.97  E-value=1.6e-09  Score=112.20  Aligned_cols=78  Identities=24%  Similarity=0.397  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ..+..|+||||||+..++++.|++.|+.||.|..+++..+.      ||+||.|++.++|..||..+|+.+|+|..+++.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            45678999999999999999999999999999999998874      999999999999999999999999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      |-..
T Consensus       234 WGKe  237 (321)
T KOG0148|consen  234 WGKE  237 (321)
T ss_pred             cccc
Confidence            8764

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.96  E-value=4.1e-10  Score=120.03  Aligned_cols=77  Identities=29%  Similarity=0.446  Sum_probs=75.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      -|.||||.|++.+.++.|+..|..||.|+++.+.+|+.||+++||+||+|+-++.|.-|+..|||..++|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999975

>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=98.95  E-value=6.1e-09  Score=85.82  Aligned_cols=74  Identities=27%  Similarity=0.486  Sum_probs=68.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      +|||+|||..++..+|..+|..||.|..+.+..++ .+.+.|+|||.|.+.++|..|+..+++..++|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999875 447889999999999999999999999999999998864

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).

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.95  E-value=4.3e-10  Score=113.21  Aligned_cols=83  Identities=22%  Similarity=0.389  Sum_probs=79.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...+|||||+|...+++.-|...|-+||.|..+.++.|-.+++++|||||+|...++|.+||..||+.+|.|+.|+|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      .+.
T Consensus        88 kP~   90 (298)
T KOG0111|consen   88 KPE   90 (298)
T ss_pred             CCc
Confidence            763

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.94  E-value=1.6e-09  Score=102.02  Aligned_cols=83  Identities=17%  Similarity=0.203  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      +.....|||.++...+++++|...|.-||.|+.+.+-.|+.||..+||++|+|++...|..|+..|||..|.|.+|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            34478999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      |--
T Consensus       149 ~Fv  151 (170)
T KOG0130|consen  149 CFV  151 (170)
T ss_pred             EEe
Confidence            853

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.92  E-value=3.9e-09  Score=115.20  Aligned_cols=88  Identities=20%  Similarity=0.297  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee---CCeEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI---DGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I---~Gr~L~  127 (771)
                      +....++|||.||..+++.+|+.+|.+||.|.+|.|++|+.||.++|||||.|.+.++|..|+.+||....   +...|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            45577899999999999999999999999999999999999999999999999999999999999988643   357899


Q ss_pred             EEEehhhHHHH
Q 004150          128 LKVDQATREYL  138 (771)
Q Consensus       128 V~~a~~~kk~l  138 (771)
                      |++++.-+..+
T Consensus       111 vk~Ad~E~er~  121 (510)
T KOG0144|consen  111 VKYADGERERI  121 (510)
T ss_pred             ecccchhhhcc
Confidence            99988755443

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.91  E-value=7.1e-09  Score=119.56  Aligned_cols=73  Identities=25%  Similarity=0.339  Sum_probs=61.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcC------------CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCG------------TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  117 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G------------~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln  117 (771)
                      .....++|||||||+.+++.+|..+|..|+            .|..+.      .++.+|||||+|.+.++|..||. |+
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~------~~~~kg~afVeF~~~e~A~~Al~-l~  243 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN------INKEKNFAFLEFRTVEEATFAMA-LD  243 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE------ECCCCCEEEEEeCCHHHHhhhhc-CC
Confidence            456678999999999999999999999752            223332      24557999999999999999995 99


Q ss_pred             CceeCCeEEEEE
Q 004150          118 KFNIDGQELMLK  129 (771)
Q Consensus       118 g~~I~Gr~L~V~  129 (771)
                      |+.|.|+.|.|.
T Consensus       244 g~~~~g~~l~v~  255 (509)
T TIGR01642       244 SIIYSNVFLKIR  255 (509)
T ss_pred             CeEeeCceeEec
Confidence            999999999985

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.89  E-value=2.3e-08  Score=90.54  Aligned_cols=82  Identities=16%  Similarity=0.290  Sum_probs=73.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ....|||.|||+.+|.+++..||+.||.|..+++.-   +...+|-+||.|++..+|.+|+..|+|+.++++.|.|-+-.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~---~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN---TKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecC---ccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            367899999999999999999999999999998864   45667999999999999999999999999999999998877


Q ss_pred             hhHHH
Q 004150          133 ATREY  137 (771)
Q Consensus       133 ~~kk~  137 (771)
                      +...+
T Consensus        94 ~~~~~   98 (124)
T KOG0114|consen   94 PEDAF   98 (124)
T ss_pred             HHHHH
Confidence            65443

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.87  E-value=4.9e-09  Score=117.05  Aligned_cols=86  Identities=19%  Similarity=0.322  Sum_probs=79.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +-..|.|.|||+.|...+|+.+|+.||.|..+.|++. ..|+.+|||||.|.....|..||..|||..|+|++|.|+|+-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k-~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRK-KDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccC-CCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            3678999999999999999999999999999999976 588888999999999999999999999999999999999998


Q ss_pred             hhHHHHH
Q 004150          133 ATREYLE  139 (771)
Q Consensus       133 ~~kk~le  139 (771)
                      ....|-.
T Consensus       195 ~Kd~ye~  201 (678)
T KOG0127|consen  195 DKDTYED  201 (678)
T ss_pred             ccccccc
Confidence            7655543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.87  E-value=3.3e-09  Score=113.09  Aligned_cols=86  Identities=19%  Similarity=0.342  Sum_probs=81.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .+|-.-|||..|++.+++++|.-||+.||.|.+|.+++|..||.+..|+||+|.+.+++..|...|+++.|+.+.|.|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ehhhHH
Q 004150          131 DQATRE  136 (771)
Q Consensus       131 a~~~kk  136 (771)
                      +++..+
T Consensus       316 SQSVsk  321 (479)
T KOG0415|consen  316 SQSVSK  321 (479)
T ss_pred             hhhhhh
Confidence            998765

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=98.77  E-value=2.3e-08  Score=115.26  Aligned_cols=75  Identities=19%  Similarity=0.185  Sum_probs=68.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELMLKV  130 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L--ng~~I~Gr~L~V~~  130 (771)
                      ++.+|||+|||+.+++.+|..+|+.||.|.+|.++.+      ++||||+|.+.++|..||..|  ++..|+|+.|.|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4679999999999999999999999999999998864      479999999999999999864  78999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        75 s~~   77 (481)
T TIGR01649        75 STS   77 (481)
T ss_pred             cCC
Confidence            864

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).

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.77  E-value=7.8e-09  Score=116.02  Aligned_cols=78  Identities=26%  Similarity=0.502  Sum_probs=73.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..||||||.+++++.+|+.+|..||.|..+.+..|..||.++||||++|.+.+.|..|+..|||++|.|+.|+|.+..
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            339999999999999999999999999999999997799999999999999999999999999999999999987644

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.76  E-value=9.1e-09  Score=107.67  Aligned_cols=71  Identities=18%  Similarity=0.407  Sum_probs=66.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ..|||||||..++...|+.||.+||+|++|.|+.+        ||||..++...+..||+.|||..|+|..|.|.-+.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccc
Confidence            46999999999999999999999999999999986        999999999999999999999999999999975443

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.76  E-value=1.1e-08  Score=109.31  Aligned_cols=95  Identities=26%  Similarity=0.467  Sum_probs=85.5

Q ss_pred             CCCCCCCCCCCC-------CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHH
Q 004150           38 VVRPVPLPTVTP-------AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL  110 (771)
Q Consensus        38 ~~~p~~~p~~~~-------~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~  110 (771)
                      +++|+++|++.+       .......|||..+.++.++.+|+.+|..||.|++|.+.+++..+.++||||++|.+..+..
T Consensus       187 VgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~  266 (544)
T KOG0124|consen  187 VGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  266 (544)
T ss_pred             ccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchH
Confidence            456777777666       2456789999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCceeCCeEEEEEEeh
Q 004150          111 RALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus       111 ~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .||..||-+.|+|..|+|.-+-
T Consensus       267 eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  267 EAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             HHhhhcchhhcccceEeccccc
Confidence            9999999999999999997554

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=98.75  E-value=3e-08  Score=115.51  Aligned_cols=73  Identities=21%  Similarity=0.421  Sum_probs=68.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVC--GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~--G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...+|||+||+..+++++|+.+|+.|  |.|..+.++.        +||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35789999999999999999999999  9999998764        5999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +.+
T Consensus       304 Akp  306 (578)
T TIGR01648       304 AKP  306 (578)
T ss_pred             ccC
Confidence            965

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.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.75  E-value=1.6e-08  Score=99.94  Aligned_cols=80  Identities=18%  Similarity=0.340  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||||||.++.+.+|+.||.+||.|..+.+-..   ..+.+||||+|+++-+|..||..-+|+.++|..|.|.+
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            345789999999999999999999999999999987443   34458999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      ...
T Consensus        80 prg   82 (241)
T KOG0105|consen   80 PRG   82 (241)
T ss_pred             ccC
Confidence            775

>smart00361 RRM_1 RNA recognition motif

Probab=98.71  E-value=6.4e-08  Score=82.44  Aligned_cols=61  Identities=20%  Similarity=0.169  Sum_probs=54.2

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EeecCCC--CCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           68 SDFVLSVLK----VCGTVKSWK-RAQYPSN--GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        68 e~~L~~lF~----~~G~V~s~k-iv~d~~t--Gk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      +.+|..+|.    .||.|.++. ++.++.+  |.++|||||.|.+.++|..|+..|||..++|+.|.+
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            357788888    999999995 6666555  999999999999999999999999999999999976

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.71  E-value=4.3e-08  Score=109.71  Aligned_cols=84  Identities=15%  Similarity=0.233  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh-----CC-ceeCCeE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-----NK-FNIDGQE  125 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L-----ng-~~I~Gr~  125 (771)
                      .-..||||.|||+++++..|...|++||.|.++.++.++.||.++|+|||.|.+...+..||.+.     .| +.|+|+.
T Consensus       290 ~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~  369 (678)
T KOG0127|consen  290 TEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRL  369 (678)
T ss_pred             cccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccE
Confidence            34689999999999999999999999999999999999999999999999999999999999866     33 7899999


Q ss_pred             EEEEEehhhH
Q 004150          126 LMLKVDQATR  135 (771)
Q Consensus       126 L~V~~a~~~k  135 (771)
                      |.|..+-..+
T Consensus       370 Lkv~~Av~Rk  379 (678)
T KOG0127|consen  370 LKVTLAVTRK  379 (678)
T ss_pred             EeeeeccchH
Confidence            9998876643

>PF13893 RRM_5: RNA recognition motif

Probab=98.66  E-value=1.2e-07  Score=76.91  Aligned_cols=56  Identities=29%  Similarity=0.452  Sum_probs=50.5

Q ss_pred             HHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           71 VLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        71 L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      |..+|++||.|..+.+....     .+++||+|.+.++|..|+..|||..++|++|.|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999987652     689999999999999999999999999999999985

(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 ....

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.63  E-value=3.9e-08  Score=107.55  Aligned_cols=81  Identities=19%  Similarity=0.305  Sum_probs=76.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .+...++||++||....+.+|...|..||.|++.++..|+.||.++|||||.|++..+|..||..|||+.|++++|+|.+
T Consensus       421 GpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQl  500 (510)
T KOG0144|consen  421 GPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQL  500 (510)
T ss_pred             CCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEe
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             e
Q 004150          131 D  131 (771)
Q Consensus       131 a  131 (771)
                      .
T Consensus       501 k  501 (510)
T KOG0144|consen  501 K  501 (510)
T ss_pred             e
Confidence            4

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=98.59  E-value=9.7e-08  Score=104.94  Aligned_cols=75  Identities=16%  Similarity=0.359  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .....|||.||+.++|++.|+.+|+.||.|..++.++|        ||||.|.+.++|.+||..+||..|+|..|.|.++
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLA  328 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLA  328 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEec
Confidence            34577999999999999999999999999999998876        9999999999999999999999999999999999


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      .+.
T Consensus       329 KP~  331 (506)
T KOG0117|consen  329 KPV  331 (506)
T ss_pred             CCh
Confidence            874

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.57  E-value=1.5e-07  Score=94.79  Aligned_cols=84  Identities=25%  Similarity=0.334  Sum_probs=76.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhc-CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVC-GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~-G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      .....-+||+.||..+.+..|..+|..| |.|..+++.+++.||.++|||||+|++.+-|..|-..||++.|+|+.|.|.
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            3445679999999999999999999988 678888888999999999999999999999999999999999999999999


Q ss_pred             Eehhh
Q 004150          130 VDQAT  134 (771)
Q Consensus       130 ~a~~~  134 (771)
                      |=.+-
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            87664

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.52  E-value=1.6e-07  Score=92.86  Aligned_cols=83  Identities=23%  Similarity=0.398  Sum_probs=75.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS-WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s-~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||||.+.+.+..|..+|+.||.+.. -++++++.||.++||||+.|.+.+.+.+|+..+||..++.+++.|.
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~  172 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS  172 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence            344688999999999999999999999998765 4678888899999999999999999999999999999999999998


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++-.
T Consensus       173 ya~k  176 (203)
T KOG0131|consen  173 YAFK  176 (203)
T ss_pred             EEEe
Confidence            7753

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.49  E-value=1.1e-07  Score=99.64  Aligned_cols=75  Identities=24%  Similarity=0.438  Sum_probs=71.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++||||||++.++..+|+..|.+||.|..|+|+.+        |+||.|.-.++|..|++.|++.++.|+.|+|.+
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            557889999999999999999999999999999999986        999999999999999999999999999999988


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +.+
T Consensus       147 sts  149 (346)
T KOG0109|consen  147 STS  149 (346)
T ss_pred             ecc
Confidence            765

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.47  E-value=4.4e-07  Score=99.31  Aligned_cols=79  Identities=25%  Similarity=0.416  Sum_probs=73.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLK-VCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~-~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..+.+||.|||+++.+.+|+.||. +.|.|..|.+..| .+||++||+.|+|.+++.+.+|++.||.+.+.|+.|.|+-+
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            355699999999999999999997 7899999999999 79999999999999999999999999999999999999755


Q ss_pred             h
Q 004150          132 Q  132 (771)
Q Consensus       132 ~  132 (771)
                      .
T Consensus       122 ~  122 (608)
T KOG4212|consen  122 H  122 (608)
T ss_pred             C
Confidence            4

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.46  E-value=4.4e-07  Score=101.13  Aligned_cols=79  Identities=24%  Similarity=0.453  Sum_probs=72.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..+..|||-||++.++...|..+|+.||.|++|++..+ .+| ++|| ||.|.+.++|..||..|||..+.|++|.|...
T Consensus        74 rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~-~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   74 RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATD-ENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEc-CCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence            33444999999999999999999999999999999998 577 9999 99999999999999999999999999999766


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       151 ~~  152 (369)
T KOG0123|consen  151 ER  152 (369)
T ss_pred             cc
Confidence            54

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.43  E-value=6.5e-07  Score=95.99  Aligned_cols=83  Identities=24%  Similarity=0.365  Sum_probs=75.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--------WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  121 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s--------~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I  121 (771)
                      .....+.|||.|||.++|.+++..+|++||.|.+        |++..+ ..|+++|=|.|.|...+++.-|+.+|++..|
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd-~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD-NQGKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec-CCCCccCceEEEeecccHHHHHHHHhCcccc
Confidence            3445677999999999999999999999998864        788888 5799999999999999999999999999999


Q ss_pred             CCeEEEEEEehh
Q 004150          122 DGQELMLKVDQA  133 (771)
Q Consensus       122 ~Gr~L~V~~a~~  133 (771)
                      .|+.|+|..|..
T Consensus       209 rg~~~rVerAkf  220 (382)
T KOG1548|consen  209 RGKKLRVERAKF  220 (382)
T ss_pred             cCcEEEEehhhh
Confidence            999999987764

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.42  E-value=2.1e-06  Score=87.40  Aligned_cols=84  Identities=14%  Similarity=0.203  Sum_probs=69.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee-cCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC---CeEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQ-YPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQEL  126 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~-d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~---Gr~L  126 (771)
                      ....+||||.+||.++.--+|..||..|-....+.+-. ++...-++-+|||+|.+...|..|+..|||+.++   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            34578999999999999999999999997666665433 3222234579999999999999999999999997   7899


Q ss_pred             EEEEehhh
Q 004150          127 MLKVDQAT  134 (771)
Q Consensus       127 ~V~~a~~~  134 (771)
                      .|.++.+.
T Consensus       111 hiElAKSN  118 (284)
T KOG1457|consen  111 HIELAKSN  118 (284)
T ss_pred             EeeehhcC
Confidence            99988764

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.39  E-value=7.5e-07  Score=91.06  Aligned_cols=84  Identities=15%  Similarity=0.313  Sum_probs=75.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           54 QTKVYVGKIAPTADSDFVLS----VLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~----lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ..||||.||+..+..++|+.    ||+.||.|+.+...   .+.+.+|-|||.|.+...|..|+..|+|+.+-|+.+.|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            44999999999999998887    99999999988765   378999999999999999999999999999999999999


Q ss_pred             EehhhHHHHHH
Q 004150          130 VDQATREYLER  140 (771)
Q Consensus       130 ~a~~~kk~le~  140 (771)
                      ++....+++..
T Consensus        86 yA~s~sdii~~   96 (221)
T KOG4206|consen   86 YAKSDSDIIAQ   96 (221)
T ss_pred             cccCccchhhc
Confidence            99887777744

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.34  E-value=6.2e-07  Score=103.46  Aligned_cols=90  Identities=24%  Similarity=0.367  Sum_probs=78.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...+.|+|.|||+..+...++.||+.||.|.+|+++.-...+.++|||||+|-++.+|.+|+.+|.++.|-|+.|++.|+
T Consensus       611 k~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA  690 (725)
T KOG0110|consen  611 KKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWA  690 (725)
T ss_pred             cccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehh
Confidence            34689999999999999999999999999999998775456778999999999999999999999999999999999998


Q ss_pred             hhhHHHHHHHH
Q 004150          132 QATREYLERYV  142 (771)
Q Consensus       132 ~~~kk~le~~k  142 (771)
                      ...-. ++...
T Consensus       691 ~~d~~-~e~~r  700 (725)
T KOG0110|consen  691 KSDNT-MEALR  700 (725)
T ss_pred             ccchH-HHHHH
Confidence            76433 44433

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.31  E-value=9e-07  Score=91.85  Aligned_cols=83  Identities=20%  Similarity=0.344  Sum_probs=75.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQELMLK  129 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~---Gr~L~V~  129 (771)
                      ..++||||-|...-++++++.+|..||.|.+|.+.+. .+|.++||+||.|.+.-+|..||..|||...+   ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg-~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG-PDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC-CCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            5789999999999999999999999999999999998 59999999999999999999999999997654   4679999


Q ss_pred             EehhhHH
Q 004150          130 VDQATRE  136 (771)
Q Consensus       130 ~a~~~kk  136 (771)
                      +++..++
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            9886533

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.28  E-value=1.4e-06  Score=101.26  Aligned_cols=74  Identities=14%  Similarity=0.254  Sum_probs=70.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ++|||||+|+.++++.+|..+|..||.|.++.++..      +|||||.+....+|.+||..|+.+.+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            589999999999999999999999999999998765      49999999999999999999999999999999999875

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.28  E-value=1e-06  Score=91.11  Aligned_cols=91  Identities=18%  Similarity=0.351  Sum_probs=79.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .....||+|-|.-.++++.|-..|.+|-.....+++++.-||+++|||||.|.++.++.+|+..|+|..++.+.|.+.-.
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999988655


Q ss_pred             hhhHHHHHHHH
Q 004150          132 QATREYLERYV  142 (771)
Q Consensus       132 ~~~kk~le~~k  142 (771)
                      ......++..+
T Consensus       268 ~wkeRn~dvv~  278 (290)
T KOG0226|consen  268 EWKERNLDVVK  278 (290)
T ss_pred             hHHhhhhHHHh
Confidence            54444444433

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.26  E-value=2.2e-06  Score=92.04  Aligned_cols=79  Identities=20%  Similarity=0.349  Sum_probs=70.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHH-HHhCCceeCCeEEE
Q 004150           49 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL-RLLNKFNIDGQELM  127 (771)
Q Consensus        49 ~~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al-~~Lng~~I~Gr~L~  127 (771)
                      +.+....|||||+|...+++.+|+.+|.+||.|.++.++...      +|+||+|.+..+|..|. ..++.+.|+|..|.
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~  296 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLK  296 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEE
Confidence            345668899999999999999999999999999999887753      69999999999999666 67788899999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.|...
T Consensus       297 i~Wg~~  302 (377)
T KOG0153|consen  297 IKWGRP  302 (377)
T ss_pred             EEeCCC
Confidence            999887

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.24  E-value=2.4e-06  Score=98.83  Aligned_cols=78  Identities=28%  Similarity=0.420  Sum_probs=69.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC----CCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG----TPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tG----k~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      .++|||.||++.++...|..+|..+|.|.++.|..-+ .+    .+.|||||+|.++++|.+|+..|+|+.|+|+.|.|.
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkk-d~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKK-DPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccc-cccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEE
Confidence            3449999999999999999999999999999887653 22    345999999999999999999999999999999999


Q ss_pred             Eeh
Q 004150          130 VDQ  132 (771)
Q Consensus       130 ~a~  132 (771)
                      ++.
T Consensus       594 ~S~  596 (725)
T KOG0110|consen  594 ISE  596 (725)
T ss_pred             ecc
Confidence            887

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.22  E-value=3.5e-06  Score=97.06  Aligned_cols=83  Identities=25%  Similarity=0.378  Sum_probs=74.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC---CCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP---SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~---~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      .+..++||||||++.+++.+|...|+.||+|.+++|++.+   .......||||.|-+..+|.+|+..|+|..|.+..|+
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            4557889999999999999999999999999999999865   2345567999999999999999999999999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      +.|..+
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999854

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.20  E-value=1.1e-06  Score=95.39  Aligned_cols=80  Identities=24%  Similarity=0.426  Sum_probs=71.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++||||+|++.++++.|+.+|.+||.|..|.++.++.++.++|||||+|.++..+.++|. ..-+.|+|+.|.++.+-
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            57899999999999999999999999999999999999999999999999999999888876 44567788888776655


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      +
T Consensus        84 ~   84 (311)
T KOG4205|consen   84 S   84 (311)
T ss_pred             C
Confidence            4

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.18  E-value=3.4e-06  Score=94.07  Aligned_cols=77  Identities=19%  Similarity=0.364  Sum_probs=70.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehhh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  134 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~~  134 (771)
                      ..||||   +.+++..|..+|+.+|.|+++++++|. |  +.|||||.|.++.+|.+||..||...|.|+.|.|.|....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            358999   999999999999999999999999995 4  9999999999999999999999999999999999998754


Q ss_pred             HHH
Q 004150          135 REY  137 (771)
Q Consensus       135 kk~  137 (771)
                      ..+
T Consensus        76 ~~~   78 (369)
T KOG0123|consen   76 PSL   78 (369)
T ss_pred             Cce
Confidence            333

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=98.17  E-value=6.8e-06  Score=93.26  Aligned_cols=78  Identities=13%  Similarity=0.185  Sum_probs=66.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee---CCeE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLK-VCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI---DGQE  125 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~-~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I---~Gr~  125 (771)
                      ....++.|||.||...+|...|+.||+ .||.|...  +.|    +.+.+|||.|.+.++|...+.+|||+.+   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmD----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMD----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHH----HhhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            456678899999999999999999999 56666655  455    5667999999999999999999999987   5788


Q ss_pred             EEEEEehh
Q 004150          126 LMLKVDQA  133 (771)
Q Consensus       126 L~V~~a~~  133 (771)
                      |.+.|+..
T Consensus       514 L~adf~~~  521 (718)
T KOG2416|consen  514 LIADFVRA  521 (718)
T ss_pred             eEeeecch
Confidence            99988765

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.16  E-value=9.7e-06  Score=91.23  Aligned_cols=76  Identities=26%  Similarity=0.418  Sum_probs=65.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+|||+|||++++...|..+|..||.|....|..-.-.++..|||||+|.+..++..||. -+-..|++++|.|.
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~-Asp~~ig~~kl~Ve  362 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIE-ASPLEIGGRKLNVE  362 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhh-cCccccCCeeEEEE
Confidence            45669999999999999999999999999988765532235555999999999999999998 45889999999994

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.15  E-value=3.7e-06  Score=92.24  Aligned_cols=76  Identities=20%  Similarity=0.263  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....|+|||.|||+++|+..|+.-|..||.|.++.|+.   +|+++|  .|.|.+++.|++|+.+|+|..|+|+.|.|.+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            45689999999999999999999999999999999853   688877  8999999999999999999999999999986


Q ss_pred             e
Q 004150          131 D  131 (771)
Q Consensus       131 a  131 (771)
                      +
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.10  E-value=3.4e-06  Score=96.05  Aligned_cols=84  Identities=23%  Similarity=0.428  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....+.+|||+||..+++..+.+++..||.+....++.+..+|.++||+||+|.++.-+..|+..|||..+++++|.|..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34577899999999999999999999999999999999998899999999999999999999999999999999999976


Q ss_pred             ehhh
Q 004150          131 DQAT  134 (771)
Q Consensus       131 a~~~  134 (771)
                      +-..
T Consensus       366 A~~g  369 (500)
T KOG0120|consen  366 AIVG  369 (500)
T ss_pred             hhcc
Confidence            6543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.09  E-value=1.1e-05  Score=84.72  Aligned_cols=82  Identities=18%  Similarity=0.217  Sum_probs=74.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|+|.||++.|++.+|+++|..||.+..+.+..+ .+|.+.|.|-|.|....+|.+||..|||+.++|+.|.+.+
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            444688999999999999999999999999989888888 5999999999999999999999999999999999998875


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      ...
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=97.95  E-value=9.9e-06  Score=88.07  Aligned_cols=81  Identities=20%  Similarity=0.372  Sum_probs=74.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ....||||+||+++++.+|+.+|.+||.|..+.++.|..+..++|||||+|.+.+++..++. .+.+.|+|+.+.|+.+.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            35689999999999999999999999999999999999999999999999999999998887 78889999999998777


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      +.
T Consensus       175 pk  176 (311)
T KOG4205|consen  175 PK  176 (311)
T ss_pred             ch
Confidence            63

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.93  E-value=1.1e-05  Score=84.41  Aligned_cols=81  Identities=25%  Similarity=0.389  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+...+||||+.+.++-..+...|..||.|..+.+..+...|.++||+||+|.+...+..|+. |+|..|.|..+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            4567889999999999999999999999999999999998888999999999999999999999 999999999999865


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      -.
T Consensus       177 ~r  178 (231)
T KOG4209|consen  177 KR  178 (231)
T ss_pred             ee
Confidence            43

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=97.87  E-value=0.00037  Score=80.79  Aligned_cols=34  Identities=35%  Similarity=0.642  Sum_probs=26.8

Q ss_pred             CCccccCccCCCCCCcchhcccCCCCcccCCCChH
Q 004150          529 GKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTE  563 (771)
Q Consensus       529 ~kr~~v~~vf~~~ddee~~~~~~kr~LvPl~y~~e  563 (771)
                      .+.+.+.+||+.++|.|-+-..++ +||||+|+..
T Consensus       514 ~kk~~~~~v~~~~~d~Dk~v~~~k-k~vp~dyd~n  547 (668)
T KOG2253|consen  514 KKKLPETGVFREDDDEDKNVHEKK-KLVPLDYDRN  547 (668)
T ss_pred             cccCCCcccccccCCcccccchhh-hcccccCChh
Confidence            356789999999998875545544 9999999884

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.85  E-value=7.3e-06  Score=83.32  Aligned_cols=79  Identities=14%  Similarity=0.141  Sum_probs=71.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ...||||+|+...++++.|.++|-..|.|..+.|..+ ..++.+ |+||.|.+..++.-|+.++||..+.+..|.|.+--
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~-~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSG-QDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCC-ccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            3679999999999999999999999999999999887 577777 99999999999999999999999999999887644


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        86 G   86 (267)
T KOG4454|consen   86 G   86 (267)
T ss_pred             C
Confidence            3

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.81  E-value=1.7e-05  Score=81.71  Aligned_cols=71  Identities=25%  Similarity=0.421  Sum_probs=64.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ..||||+||+.+.+.+|..||..||.+..+.+..        |||||.|.+.-+|.-||..||+..|+|-.+.|.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            4699999999999999999999999999987754        6999999999999999999999999998888877764

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.66  E-value=0.00037  Score=63.61  Aligned_cols=78  Identities=15%  Similarity=0.231  Sum_probs=67.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC----CeEEEE
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVC--GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID----GQELML  128 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~--G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~----Gr~L~V  128 (771)
                      +||.|.|||-..+..+|..++..+  |..--+.++.|..++-+.|||||.|.++..|..-...++|..+.    .+.+.|
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            799999999999999999998743  56666778888889999999999999999999999999999886    566777


Q ss_pred             EEeh
Q 004150          129 KVDQ  132 (771)
Q Consensus       129 ~~a~  132 (771)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=97.66  E-value=5.6e-05  Score=85.82  Aligned_cols=72  Identities=22%  Similarity=0.399  Sum_probs=64.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ..+..+|+|-|||..|+.+.|..+|+.||.|..+..     +-...|.+||+|-+...|.+|+..|++..|.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            455789999999999999999999999999999643     445668999999999999999999999999988877

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.44  E-value=0.0013  Score=72.51  Aligned_cols=78  Identities=14%  Similarity=0.234  Sum_probs=68.6

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           54 QTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .+.|.|.||.. .+|.+.|..+|+.||.|.+++|...+.     --+.|.|.+...|.-|+.+|+|..|.|+.|+|.++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            57788888875 689999999999999999999988631     579999999999999999999999999999998876


Q ss_pred             hhHH
Q 004150          133 ATRE  136 (771)
Q Consensus       133 ~~kk  136 (771)
                      -+-.
T Consensus       372 H~~v  375 (492)
T KOG1190|consen  372 HTNV  375 (492)
T ss_pred             Cccc
Confidence            5433

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.27  E-value=0.00086  Score=73.07  Aligned_cols=84  Identities=14%  Similarity=0.231  Sum_probs=74.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--------WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s--------~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      .....+|||-+||..++...|..+|.+||.|..        +.|.+++.|+++++=|.|+|.++..|+.||..+++..++
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            445678999999999999999999999998853        567788899999999999999999999999999999999


Q ss_pred             CeEEEEEEehhh
Q 004150          123 GQELMLKVDQAT  134 (771)
Q Consensus       123 Gr~L~V~~a~~~  134 (771)
                      +..|.|.++...
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            988888766543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.25  E-value=0.0005  Score=70.43  Aligned_cols=67  Identities=16%  Similarity=0.281  Sum_probs=55.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ..+.||||.||.++|+++.|+.+|+.|......+|..  ..|.  +.+|+.|++.+.|..||..|+|+.|-
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~--~~g~--~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA--RGGM--PVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec--CCCc--ceEeecHHHHHHHHHHHHHhhcceec
Confidence            3467999999999999999999999997766666532  1333  58999999999999999999998763

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.16  E-value=0.00023  Score=80.88  Aligned_cols=84  Identities=18%  Similarity=0.292  Sum_probs=78.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ......|||+..|+..++.-+|..+|+.+|.|..+.++.|..++.++|.|||+|.+..++..||. |.|.-+.|.+|.|.
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            46678999999999999999999999999999999999999999999999999999999999996 99999999999998


Q ss_pred             Eehhh
Q 004150          130 VDQAT  134 (771)
Q Consensus       130 ~a~~~  134 (771)
                      ...+-
T Consensus       254 ~sEae  258 (549)
T KOG0147|consen  254 LSEAE  258 (549)
T ss_pred             ccHHH
Confidence            76653

>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=97.01  E-value=0.0024  Score=56.55  Aligned_cols=73  Identities=21%  Similarity=0.340  Sum_probs=49.1

Q ss_pred             CEEEEcCCCCCCCHH----HHHHHHHhcC-CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           55 TKVYVGKIAPTADSD----FVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        55 ~tVfVgNLp~~vte~----~L~~lF~~~G-~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      +.|||.|||.+....    -|++|+..|| .|.++   .       .+.|++.|.+.+.|.+|..-|+|-.+-|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v---~-------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV---S-------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE---e-------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            469999999988875    5677888897 56665   2       2689999999999999999999999999999999


Q ss_pred             EehhhHHH
Q 004150          130 VDQATREY  137 (771)
Q Consensus       130 ~a~~~kk~  137 (771)
                      +......+
T Consensus        73 ~~~~~r~~   80 (90)
T PF11608_consen   73 FSPKNREF   80 (90)
T ss_dssp             SS--S---
T ss_pred             EcCCcccc
Confidence            87654333

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=96.89  E-value=0.0016  Score=76.48  Aligned_cols=7  Identities=0%  Similarity=-0.197  Sum_probs=3.2

Q ss_pred             CCCCCCC
Q 004150           61 KIAPTAD   67 (771)
Q Consensus        61 NLp~~vt   67 (771)
                      .||+.+.
T Consensus       609 vlP~gLk  615 (1102)
T KOG1924|consen  609 VLPFGLK  615 (1102)
T ss_pred             cCCCCCC
Confidence            4554443

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.88  E-value=0.0024  Score=69.04  Aligned_cols=95  Identities=22%  Similarity=0.294  Sum_probs=76.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G--~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ......+|||||-+.+|+.+|.+.+...|  .+..+++..++.+|.++||++|...+..++...+.+|....|+|..-.|
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            34466799999999999999999998877  5677788888899999999999999999999999999999999976555


Q ss_pred             E-EehhhHHHHHHHHHhh
Q 004150          129 K-VDQATREYLERYVDKK  145 (771)
Q Consensus       129 ~-~a~~~kk~le~~k~kk  145 (771)
                      - +.......++...+|.
T Consensus       157 ~~~NK~~~ak~E~~~~K~  174 (498)
T KOG4849|consen  157 LSYNKTNQAKLEDAQAKN  174 (498)
T ss_pred             eccchhhHHHHHHHHhhh
Confidence            3 3344455555555544

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.77  E-value=0.00081  Score=70.24  Aligned_cols=86  Identities=26%  Similarity=0.279  Sum_probs=65.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC--------CCCce----EEEEEeCCHHHHHHHHHHhCCce
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN--------GTPKG----FGFCEFESAEGVLRALRLLNKFN  120 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~t--------Gk~kG----fGFVeF~~~esA~~Al~~Lng~~  120 (771)
                      ..-.||+++||+.+...-|+.||+.||.|-.+.+.....+        |.+.+    =|+|+|.+...|..+...||+..
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            3457999999999999999999999999999887654323        23322    37899999999999999999999


Q ss_pred             eCCeEEE-EEEehhhHHHH
Q 004150          121 IDGQELM-LKVDQATREYL  138 (771)
Q Consensus       121 I~Gr~L~-V~~a~~~kk~l  138 (771)
                      |+|++-. +..+.-.-+||
T Consensus       153 Iggkk~S~~~~dlWNmKYL  171 (278)
T KOG3152|consen  153 IGGKKKSPFRDDLWNMKYL  171 (278)
T ss_pred             cCCCCCCchHHhhhhhhhc
Confidence            9987533 33333344555

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.75  E-value=0.0076  Score=70.22  Aligned_cols=79  Identities=18%  Similarity=0.203  Sum_probs=66.3

Q ss_pred             CCCC-EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQT-KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~-tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .+.+ -|-|.|+|+.++-++|.++|.-|-.+-...+++....|++.|-|.|.|++.++|.+|..-|++..|..+++.+.+
T Consensus       864 ~pGp~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  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3444 677999999999999999999997655433334336899999999999999999999999999999999988754

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=96.73  E-value=0.0069  Score=62.53  Aligned_cols=78  Identities=17%  Similarity=0.300  Sum_probs=67.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELML  128 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr~L~V  128 (771)
                      ..++..++|+.|||..++...|..+|..|+....++++...     .+.+||+|.+...+..|...|.|+.|- ...+.|
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEe
Confidence            35668899999999999999999999999999999887642     379999999999999999999999887 677777


Q ss_pred             EEeh
Q 004150          129 KVDQ  132 (771)
Q Consensus       129 ~~a~  132 (771)
                      .++.
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            6653

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.71  E-value=0.00059  Score=74.66  Aligned_cols=66  Identities=14%  Similarity=-0.026  Sum_probs=53.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ....||+|++|+..+...++..+|..+|.|....+.    .|-...||.+.|....+...|+. ++|+.+.
T Consensus       149 eirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  149 EIRRTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             HHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            345889999999999999999999999999887653    34455688899999999999988 6666653

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.60  E-value=0.0014  Score=70.94  Aligned_cols=81  Identities=22%  Similarity=0.379  Sum_probs=72.6

Q ss_pred             CCCCEEE-EcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVY-VGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVf-VgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .+..++| |+++++.++.+.|..+|..||.|..+++..++.+|.+.||+|+.|........++.. +...+.++.+.|..
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            3445555 999999999999999999999999999999999999999999999999999999886 78889999999876


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       261 ~~~  263 (285)
T KOG4210|consen  261 DEP  263 (285)
T ss_pred             CCC
Confidence            654

>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=96.56  E-value=0.0066  Score=56.24  Aligned_cols=85  Identities=19%  Similarity=0.333  Sum_probs=51.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC-----CceeCCeEEEEE
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN-----KFNIDGQELMLK  129 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln-----g~~I~Gr~L~V~  129 (771)
                      +.|+|.+++..++-.+|+.+|+.||.|..+.+...-      .-|||-|.+++.|..|+..+.     +..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            678999999999999999999999999998876542      489999999999999997663     346667666666


Q ss_pred             Eeh--hhHHHHHHHHHhh
Q 004150          130 VDQ--ATREYLERYVDKK  145 (771)
Q Consensus       130 ~a~--~~kk~le~~k~kk  145 (771)
                      +-.  .-..|.++..+.+
T Consensus        76 vLeGeeE~~Yw~ki~e~~   93 (105)
T PF08777_consen   76 VLEGEEEEEYWKKIIEDR   93 (105)
T ss_dssp             ---HHHHHHHHHHHHHHH
T ss_pred             ECCCHHHHHHHHHHHHHH
Confidence            543  3456766665543

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=96.40  E-value=0.0052  Score=72.42  Aligned_cols=6  Identities=17%  Similarity=0.363  Sum_probs=2.3

Q ss_pred             EEEcCC
Q 004150           57 VYVGKI   62 (771)
Q Consensus        57 VfVgNL   62 (771)
                      .|.|+-
T Consensus       590 g~~Gg~  595 (1102)
T KOG1924|consen  590 GFLGGP  595 (1102)
T ss_pred             CCCCCC
Confidence            334433

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=96.38  E-value=0.0088  Score=67.61  Aligned_cols=76  Identities=21%  Similarity=0.363  Sum_probs=64.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ...-|-+.+||+++|+.+|..+|+.|+ |..+.+.+  .+|++.|=+||+|.+.+++..||+ .+...++.+.|.|-.+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            355677899999999999999999997 56655544  589999999999999999999998 78888888899886543

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.23  E-value=0.016  Score=66.45  Aligned_cols=77  Identities=18%  Similarity=0.282  Sum_probs=63.7

Q ss_pred             CCCCEEEEcCCCCCCCH------HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-Ce
Q 004150           52 KPQTKVYVGKIAPTADS------DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQ  124 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte------~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr  124 (771)
                      .-...|+|.|+|---..      .-|..+|+++|.+....++.+. .|+++||.|++|.+..+|..|+..|||..|+ ++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e-~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            34567899999864332      3677899999999999998884 5669999999999999999999999999997 56


Q ss_pred             EEEEE
Q 004150          125 ELMLK  129 (771)
Q Consensus       125 ~L~V~  129 (771)
                      .+.|.
T Consensus       135 tf~v~  139 (698)
T KOG2314|consen  135 TFFVR  139 (698)
T ss_pred             eEEee
Confidence            77764

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.21  E-value=0.067  Score=58.81  Aligned_cols=78  Identities=22%  Similarity=0.254  Sum_probs=67.7

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           50 AEKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~-vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ...+.+-+.|-+|... ++.+.|..+|..||.|..++++..+ +    |-|.|++.+.....+|+.+||+..+-|.+|.|
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-~----gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-P----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-c----ceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            3456788999999874 5667999999999999999998862 2    68999999999999999999999999999999


Q ss_pred             EEeh
Q 004150          129 KVDQ  132 (771)
Q Consensus       129 ~~a~  132 (771)
                      .++.
T Consensus       358 ~~Sk  361 (494)
T KOG1456|consen  358 CVSK  361 (494)
T ss_pred             eecc
Confidence            8765

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=95.97  E-value=0.019  Score=65.40  Aligned_cols=64  Identities=20%  Similarity=0.354  Sum_probs=60.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHH
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLK-VCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR  114 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~-~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~  114 (771)
                      -.+..|||||+||.-++..+|-.||. -||.|..+-|=+|+.=+.++|-|-|+|.+..+-.+||.
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            45688999999999999999999999 89999999999998889999999999999999999997

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=95.92  E-value=0.0058  Score=63.35  Aligned_cols=71  Identities=18%  Similarity=0.327  Sum_probs=62.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      +....+.++|-|++..+...+|..+|..+|.+....+        ..+|+||.|....++..|+..|++..+.|+.|.+
T Consensus        95 p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   95 PSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             cccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            3455788999999999999999999999999844333        2379999999999999999999999999999998

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.90  E-value=0.017  Score=62.51  Aligned_cols=87  Identities=20%  Similarity=0.286  Sum_probs=64.3

Q ss_pred             CCEEEEcCCCCCCCHHH------HHHHHHhcCCeeEEEEeecC--CCCCCceEE-EEEeCCHHHHHHHHHHhCCceeCCe
Q 004150           54 QTKVYVGKIAPTADSDF------VLSVLKVCGTVKSWKRAQYP--SNGTPKGFG-FCEFESAEGVLRALRLLNKFNIDGQ  124 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~------L~~lF~~~G~V~s~kiv~d~--~tGk~kGfG-FVeF~~~esA~~Al~~Lng~~I~Gr  124 (771)
                      ..-|||-+||+.+..++      -.++|++||.|..+.+-.--  .+.....+| ||+|.+.++|.+||..++|..++|+
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            35689999999887765      35799999999988765431  111111233 9999999999999999999999999


Q ss_pred             EEEEEEehhhHHHHHHHH
Q 004150          125 ELMLKVDQATREYLERYV  142 (771)
Q Consensus       125 ~L~V~~a~~~kk~le~~k  142 (771)
                      .|+..+..  -+|--.|.
T Consensus       194 ~lkatYGT--TKYCtsYL  209 (480)
T COG5175         194 VLKATYGT--TKYCTSYL  209 (480)
T ss_pred             eEeeecCc--hHHHHHHH
Confidence            99987643  34444444

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.72  E-value=0.043  Score=53.59  Aligned_cols=71  Identities=21%  Similarity=0.319  Sum_probs=52.1

Q ss_pred             CCCCEEEEcCCC------CCCCH---HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           52 KPQTKVYVGKIA------PTADS---DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        52 ~~~~tVfVgNLp------~~vte---~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ++..||.|.-+.      ..+.+   ..|.+.|..||.+.-++++.+        .-+|+|.+..+|++|+. |+|..|+
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~   95 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVN   95 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEET
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEEC
Confidence            345667666555      12333   267788889999888877654        68999999999999999 9999999


Q ss_pred             CeEEEEEEe
Q 004150          123 GQELMLKVD  131 (771)
Q Consensus       123 Gr~L~V~~a  131 (771)
                      |+.|.|..-
T Consensus        96 g~~l~i~LK  104 (146)
T PF08952_consen   96 GRTLKIRLK  104 (146)
T ss_dssp             TEEEEEEE-
T ss_pred             CEEEEEEeC
Confidence            999999653

; PDB: 1UFW_A 2DNR_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.54  E-value=0.013  Score=65.34  Aligned_cols=77  Identities=23%  Similarity=0.393  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec---CCC--CCC--------ceEEEEEeCCHHHHH
Q 004150           44 LPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY---PSN--GTP--------KGFGFCEFESAEGVL  110 (771)
Q Consensus        44 ~p~~~~~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d---~~t--Gk~--------kGfGFVeF~~~esA~  110 (771)
                      +|......-+.+||.+-|||.+-.-.-|..||+.||.|..++|+..   +.+  |.+        +-|+||+|...+.|.
T Consensus       221 lp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~  300 (484)
T KOG1855|consen  221 LPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAAR  300 (484)
T ss_pred             CCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHH
Confidence            4444444567899999999999999999999999999999998875   322  222        458999999999999


Q ss_pred             HHHHHhCCce
Q 004150          111 RALRLLNKFN  120 (771)
Q Consensus       111 ~Al~~Lng~~  120 (771)
                      .|...|+...
T Consensus       301 KA~e~~~~e~  310 (484)
T KOG1855|consen  301 KARELLNPEQ  310 (484)
T ss_pred             HHHHhhchhh
Confidence            9999776543

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=95.36  E-value=0.46  Score=56.70  Aligned_cols=12  Identities=33%  Similarity=0.659  Sum_probs=4.6

Q ss_pred             HHHHhhhCCCCC
Q 004150          219 MVEERLKTNPLP  230 (771)
Q Consensus       219 ~~eer~~~~~~~  230 (771)
                      +|+-...+-++|
T Consensus       257 liema~sGq~lP  268 (1118)
T KOG1029|consen  257 LIEMAKSGQPLP  268 (1118)
T ss_pred             HHHHHhcCCCCC
Confidence            343333344433

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=95.03  E-value=0.069  Score=60.64  Aligned_cols=76  Identities=18%  Similarity=0.168  Sum_probs=61.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS-WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s-~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      .+...|-+.+||+.|++.+|.++|+..-.|.. +.++.+ ..|++.|=+||.|++.+.|..||. -|...|+.+-|.|.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF  177 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVF  177 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEee
Confidence            34567889999999999999999987654444 445555 578899999999999999999997 67778888888774

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=94.54  E-value=0.12  Score=57.66  Aligned_cols=79  Identities=14%  Similarity=0.196  Sum_probs=66.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCe-EEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ-ELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr-~L~V~  129 (771)
                      -+++.++...|||..+++++|+.+|...|.........    ++.+.++++.+.+.++|..|+..+|.+.+++. -|+|.
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            35677999999999999999999999998776654432    45567999999999999999999999999854 89999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      |+..
T Consensus       487 FSks  490 (492)
T KOG1190|consen  487 FSKS  490 (492)
T ss_pred             eecc
Confidence            8765

>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=94.51  E-value=0.19  Score=46.31  Aligned_cols=78  Identities=19%  Similarity=0.141  Sum_probs=52.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-------CCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCe-E
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-------SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ-E  125 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~-------~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr-~  125 (771)
                      .+.|.|-+.|+. ....|...|+.||.|+...-+...       .......+-.|.|.++.+|.+||. -||..|+|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            455778788887 456788899999999887511110       011223588999999999999999 899999875 5


Q ss_pred             EEEEEehh
Q 004150          126 LMLKVDQA  133 (771)
Q Consensus       126 L~V~~a~~  133 (771)
                      +-|.+++.
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            55777754

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.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=94.43  E-value=0.18  Score=50.82  Aligned_cols=66  Identities=18%  Similarity=0.259  Sum_probs=59.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      .-.....|.|.+||++.++.+|+.++...|.|+...+..|       |+|.|+|...++..-||+.|....+.
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            3445678999999999999999999999999999999988       79999999999999999989876553

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=94.03  E-value=0.15  Score=55.70  Aligned_cols=79  Identities=13%  Similarity=0.185  Sum_probs=62.6

Q ss_pred             CCCCEEEEcCCCC----CCCH-------HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce
Q 004150           52 KPQTKVYVGKIAP----TADS-------DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  120 (771)
Q Consensus        52 ~~~~tVfVgNLp~----~vte-------~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~  120 (771)
                      ...+||.|.||=.    ..+.       ++|..-+.+||.|.++.|.-.    -+.|.+-|.|.+.+.|..||..|+|-.
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCee
Confidence            4568899988742    2221       355566889999999987533    456899999999999999999999999


Q ss_pred             eCCeEEEEEEehhh
Q 004150          121 IDGQELMLKVDQAT  134 (771)
Q Consensus       121 I~Gr~L~V~~a~~~  134 (771)
                      ++|++|...+....
T Consensus       339 fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  339 FDGRQLTASIWDGK  352 (382)
T ss_pred             ecceEEEEEEeCCc
Confidence            99999998776654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=94.02  E-value=0.097  Score=57.93  Aligned_cols=77  Identities=14%  Similarity=0.172  Sum_probs=58.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC---CCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE-EEe
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP---SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML-KVD  131 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~---~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V-~~a  131 (771)
                      .|.|.||.+.++.+.|+.||+..|.|..+.|+...   .-......|||.|.+..++..|-. |.++.+-++.|.| -+.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEecC
Confidence            78999999999999999999999999999887643   122334689999999999988877 5555554555444 443


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        88 ~~   89 (479)
T KOG4676|consen   88 DE   89 (479)
T ss_pred             CC
Confidence            33

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=93.96  E-value=0.23  Score=58.56  Aligned_cols=79  Identities=11%  Similarity=0.073  Sum_probs=66.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS-WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s-~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ......|||-.||..++...+..+|...-.|.. +.|... -+++..+-|||.|..+..+..|+..-+.+.++.+.|.|.
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            344678999999999999999999987777766 555555 588999999999999999999988788888888999986


Q ss_pred             E
Q 004150          130 V  130 (771)
Q Consensus       130 ~  130 (771)
                      -
T Consensus       510 s  510 (944)
T KOG4307|consen  510 S  510 (944)
T ss_pred             c
Confidence            3

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=93.39  E-value=0.16  Score=61.27  Aligned_cols=79  Identities=13%  Similarity=0.252  Sum_probs=68.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELM  127 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G--r~L~  127 (771)
                      ...+.+.+|||+|..++....|...|..||.|..+.+-.      ...|+||.|++...+..|+..|.|+.|+|  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            455678899999999999999999999999998876532      23699999999999999999999999984  6789


Q ss_pred             EEEehhh
Q 004150          128 LKVDQAT  134 (771)
Q Consensus       128 V~~a~~~  134 (771)
                      |.|+...
T Consensus       525 vdla~~~  531 (975)
T KOG0112|consen  525 VDLASPP  531 (975)
T ss_pred             cccccCC
Confidence            9887654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=93.24  E-value=0.21  Score=57.86  Aligned_cols=64  Identities=20%  Similarity=0.186  Sum_probs=52.8

Q ss_pred             HHHHHHHhcCCeeEEEEeec-C--CCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           70 FVLSVLKVCGTVKSWKRAQY-P--SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        70 ~L~~lF~~~G~V~s~kiv~d-~--~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      +++.-+++||.|.+|.+.++ .  ...-..|..||+|.+.+++.+|+..|+|..++|+.+...|...
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            44555668999999998876 2  3344567789999999999999999999999999999988765

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=92.89  E-value=0.58  Score=53.76  Aligned_cols=65  Identities=23%  Similarity=0.373  Sum_probs=47.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCe-eEEEEeecC-CCCCCce---EEEEEeCCHHHHHHHHHHh
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTV-KSWKRAQYP-SNGTPKG---FGFCEFESAEGVLRALRLL  116 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V-~s~kiv~d~-~tGk~kG---fGFVeF~~~esA~~Al~~L  116 (771)
                      .-.+.||||+||+++++..|...|..||.+ +.|-.-... .---++|   |.|+.|++..++...|..+
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            447889999999999999999999999975 345320100 0112245   9999999998887766544

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=92.89  E-value=0.25  Score=40.11  Aligned_cols=52  Identities=17%  Similarity=0.287  Sum_probs=40.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHH
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL  113 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al  113 (771)
                      +.|-|.+.++...+. +...|..||.|....+..      ...+.|+.|.+..+|.+||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            567788888777644 455888999999987652      2359999999999999885

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=92.71  E-value=0.46  Score=52.03  Aligned_cols=73  Identities=12%  Similarity=0.131  Sum_probs=54.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHH-HHHHHhCCceeCCeEEEEEEehhhH
Q 004150           57 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL-RALRLLNKFNIDGQELMLKVDQATR  135 (771)
Q Consensus        57 VfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~-~Al~~Lng~~I~Gr~L~V~~a~~~k  135 (771)
                      +.|+.-.+.+++.++..++...-.|.+..|.+. .++.+.|    .|.+..+.. .||.++       +.-+|.-++.|+
T Consensus       348 r~~~p~~~plSeAEFEdiM~RNraiSSSAIsrA-vsdASaG----Dy~~AiETllTAI~lI-------KqSrv~~DdRCr  415 (498)
T KOG4849|consen  348 RHVNPQMFPLSEAEFEDIMTRNRAISSSAISRA-VSDASAG----DYKGAIETLLTAIQLI-------KQSRVGHDDRCR  415 (498)
T ss_pred             ccCCCCCccchHHHHHHHHhhcchhhHHHHHHH-hcccccc----cchhHHHHHHHHHHHH-------HhhccccchHHH
Confidence            556666677899999999999988888777665 5667766    677766654 888876       456677788888


Q ss_pred             HHHHHH
Q 004150          136 EYLERY  141 (771)
Q Consensus       136 k~le~~  141 (771)
                      .++...
T Consensus       416 vLissL  421 (498)
T KOG4849|consen  416 VLISSL  421 (498)
T ss_pred             HHHHHH
Confidence            877443

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=92.47  E-value=0.33  Score=53.78  Aligned_cols=77  Identities=17%  Similarity=0.135  Sum_probs=64.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCC-eeE--EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGT-VKS--WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~-V~s--~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...|-+.+||+..+-++|..+|.-|.. |..  +.++.+ ..|.+.|-+||.|.+.+.|..|....|.....++.|.|--
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            556889999999999999999998863 333  777777 6899999999999999999999988887777777777754


Q ss_pred             e
Q 004150          131 D  131 (771)
Q Consensus       131 a  131 (771)
                      +
T Consensus       359 ~  359 (508)
T KOG1365|consen  359 C  359 (508)
T ss_pred             c
Confidence            4

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=92.41  E-value=0.05  Score=65.24  Aligned_cols=79  Identities=14%  Similarity=0.170  Sum_probs=69.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ...|||.|.|+..|.+.|+.+|..+|.+++..+++. ..|+++|.+||.|.+..++.+++.......+.-..+.|.+..+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            457999999999999999999999999999998887 5999999999999999999999987777777766677766554

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=92.31  E-value=0.014  Score=69.61  Aligned_cols=76  Identities=13%  Similarity=0.192  Sum_probs=62.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ..+++||.||++.+...+|...|..+|.+..+.+......|.++|+||+.|..+..+.+||....+..++...+.|
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i  741 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAI  741 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhhe
Confidence            3578999999999999999999999998877777655578999999999999999999999855555554333333

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=91.93  E-value=0.89  Score=57.26  Aligned_cols=21  Identities=14%  Similarity=0.242  Sum_probs=10.3

Q ss_pred             CCCCchhhhcccccccccchh
Q 004150          669 IPKTKEELFSYEINWAVYDKH  689 (771)
Q Consensus       669 ip~~k~~lf~~~i~w~~~d~~  689 (771)
                      |..-|..++.-.++=..|.+.
T Consensus       874 ~~~~~~~~~~~~~~~~~~~~~  894 (1021)
T PTZ00266        874 INAKKASIYNNTCDEGTLSKK  894 (1021)
T ss_pred             hhhhhhhhhhhcccccccccc
Confidence            344455555545555555443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=91.17  E-value=0.29  Score=54.69  Aligned_cols=74  Identities=15%  Similarity=0.262  Sum_probs=58.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEEEeh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF-NIDGQELMLKVDQ  132 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~-V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~-~I~Gr~L~V~~a~  132 (771)
                      ..+|||||++.++..+|..+|..... +..-.++..       ||+||.+.+...+..|+..|+|. ++.|+.+.|...-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~-------gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKS-------GYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeec-------ceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            46899999999999999999985421 112223333       89999999999999999999885 6889999997765


Q ss_pred             hhH
Q 004150          133 ATR  135 (771)
Q Consensus       133 ~~k  135 (771)
                      ..+
T Consensus        75 ~kk   77 (584)
T KOG2193|consen   75 PKK   77 (584)
T ss_pred             hHH
Confidence            543

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=90.97  E-value=0.66  Score=49.90  Aligned_cols=64  Identities=22%  Similarity=0.134  Sum_probs=51.6

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCC-ceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           69 DFVLSVLKVCGTVKSWKRAQYPSNGTP-KGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        69 ~~L~~lF~~~G~V~s~kiv~d~~tGk~-kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.+..-+.+||.|..|.|.-.+..... ..--||+|+..++|..|+..|||..|+|+.+...|..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            467788889999999988776533222 3457999999999999999999999999998876543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=90.49  E-value=0.73  Score=50.98  Aligned_cols=75  Identities=23%  Similarity=0.164  Sum_probs=62.4

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC--CeEEEEEEehhhHH
Q 004150           59 VGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID--GQELMLKVDQATRE  136 (771)
Q Consensus        59 VgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~--Gr~L~V~~a~~~kk  136 (771)
                      |-|--+.+|.+-|..++..+|.|.++.|..-  +|   --+.|+|++.+.|.+|-..|||..|-  =..|+|.++.+++.
T Consensus       127 IlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  127 ILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             eecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCccee
Confidence            4566678999999999999999999988763  33   46899999999999999999999875  36899999887654


Q ss_pred             HH
Q 004150          137 YL  138 (771)
Q Consensus       137 ~l  138 (771)
                      .+
T Consensus       202 nV  203 (494)
T KOG1456|consen  202 NV  203 (494)
T ss_pred             ee
Confidence            33

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=90.43  E-value=2.7  Score=53.07  Aligned_cols=8  Identities=25%  Similarity=0.289  Sum_probs=3.7

Q ss_pred             HHHHHhCC
Q 004150          111 RALRLLNK  118 (771)
Q Consensus       111 ~Al~~Lng  118 (771)
                      .||..||.
T Consensus       129 ~ALaYLHs  136 (1021)
T PTZ00266        129 HALAYCHN  136 (1021)
T ss_pred             HHHHHHHh
Confidence            44444553

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=89.45  E-value=0.25  Score=59.81  Aligned_cols=80  Identities=9%  Similarity=0.069  Sum_probs=65.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .....|||+|||...+++..|+..|..+|.|..+.|-+. .-+....||||.|.+...+-.|+..+.+..|..-.+.+.+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP-~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTP-HIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccC-CCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            345789999999999999999999999999999887554 2445557999999999999999988888877755555544


Q ss_pred             e
Q 004150          131 D  131 (771)
Q Consensus       131 a  131 (771)
                      .
T Consensus       448 G  448 (975)
T KOG0112|consen  448 G  448 (975)
T ss_pred             c
Confidence            4

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=89.42  E-value=0.38  Score=50.88  Aligned_cols=62  Identities=19%  Similarity=0.304  Sum_probs=56.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  117 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln  117 (771)
                      ..|||.||+..++.+.|..-|+.||.|....++.| ..|++.+=|+|.|...-.+..|++.+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            67999999999999999999999999998887777 689999999999999999999998773

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=87.93  E-value=4.8  Score=43.76  Aligned_cols=62  Identities=24%  Similarity=0.265  Sum_probs=47.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  125 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~  125 (771)
                      =|-|-+.|+.-. ..|..+|.+||.|+....      +....|-+|.|.+...|.+||. .+|..|+|..
T Consensus       199 WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~------~~ngNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  199 WVTVFGFPPGQV-SIVLNLFSRCGEVVKHVT------PSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             eEEEeccCccch-hHHHHHHHhhCeeeeeec------CCCCceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            344556666544 577789999999987643      3444699999999999999998 8999998754

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=87.25  E-value=0.22  Score=54.46  Aligned_cols=86  Identities=21%  Similarity=0.295  Sum_probs=62.2

Q ss_pred             CEEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeecCC--CC-CCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           55 TKVYVGKIAPTADSDFVL---SVLKVCGTVKSWKRAQYPS--NG-TPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~---~lF~~~G~V~s~kiv~d~~--tG-k~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      .-+||-+|+..+....+.   .+|+.||.|..+.+..++.  .+ .+.+-++|+|...++|..||...+|+.++|+.|..
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            568899999877666443   5788999999998877642  11 11233899999999999999999999999988555


Q ss_pred             EEehhhHHHHHHHH
Q 004150          129 KVDQATREYLERYV  142 (771)
Q Consensus       129 ~~a~~~kk~le~~k  142 (771)
                      .+  .+.+|-..|.
T Consensus       158 ~~--gttkycs~~l  169 (327)
T KOG2068|consen  158 SL--GTTKYCSFYL  169 (327)
T ss_pred             hh--CCCcchhHHh
Confidence            43  3334444443

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=85.89  E-value=1.3  Score=49.28  Aligned_cols=80  Identities=24%  Similarity=0.306  Sum_probs=60.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHh-c---CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKV-C---GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~-~---G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ....|-+.+||++++..++..+|.. |   |.+..+-+++. .+|+..|-+||.|...+.|..||. -|...|       
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~-khrq~i-------  230 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALR-KHRQNI-------  230 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHH-HHHHHH-------
Confidence            3556788999999999999999962 1   34455666665 589999999999999999999997 232222       


Q ss_pred             EEehhhHHHHHHHHHhhh
Q 004150          129 KVDQATREYLERYVDKKT  146 (771)
Q Consensus       129 ~~a~~~kk~le~~k~kk~  146 (771)
                           -+.|++-|+....
T Consensus       231 -----GqRYIElFRSTaa  243 (508)
T KOG1365|consen  231 -----GQRYIELFRSTAA  243 (508)
T ss_pred             -----hHHHHHHHHHhHH
Confidence                 2568887776553

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=84.74  E-value=2.1  Score=51.98  Aligned_cols=73  Identities=18%  Similarity=0.155  Sum_probs=58.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC--CeEEEEEEeh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID--GQELMLKVDQ  132 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~--Gr~L~V~~a~  132 (771)
                      .+.++-|.+-+.+...|..+|..||.|.+....++-      ..+.|.|.+.++|..|+.+|+|..+-  |-+.+|.++.
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            445556666678888999999999999887665653      57899999999999999999998653  6677777765


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus       373 ~  373 (1007)
T KOG4574|consen  373 T  373 (1007)
T ss_pred             c
Confidence            4

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=83.45  E-value=52  Score=35.59  Aligned_cols=38  Identities=8%  Similarity=0.131  Sum_probs=29.0

Q ss_pred             CCCCCEEEEcCCCCC------------CCHHHHHHHHHhcCCeeEEEEee
Q 004150           51 EKPQTKVYVGKIAPT------------ADSDFVLSVLKVCGTVKSWKRAQ   88 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~------------vte~~L~~lF~~~G~V~s~kiv~   88 (771)
                      +..+.|||+.+||-.            -++.-|...|..||.|..+.|+.
T Consensus       146 gerpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipi  195 (445)
T KOG2891|consen  146 GERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPI  195 (445)
T ss_pred             CCCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcc
Confidence            444678888888853            34578999999999999887653

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=83.11  E-value=5.1  Score=39.29  Aligned_cols=75  Identities=16%  Similarity=0.217  Sum_probs=56.3

Q ss_pred             CCCCCCEEEEcCCCCCCCH----HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 004150           50 AEKPQTKVYVGKIAPTADS----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  125 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte----~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~  125 (771)
                      .+++-.||.|.=|..++..    ..+..-++.||.|.++.+.-       +.-+.|.|.+..+|-.|+.+++. ..-|..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm  153 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGTM  153 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCce
Confidence            3566778888766665543    35666678999999986532       25789999999999999999977 455778


Q ss_pred             EEEEEeh
Q 004150          126 LMLKVDQ  132 (771)
Q Consensus       126 L~V~~a~  132 (771)
                      +.+.|-.
T Consensus       154 ~qCsWqq  160 (166)
T PF15023_consen  154 FQCSWQQ  160 (166)
T ss_pred             EEeeccc
Confidence            8887754

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=82.02  E-value=6.1  Score=33.40  Aligned_cols=55  Identities=15%  Similarity=0.032  Sum_probs=43.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhc---CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVC---GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL  116 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~---G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L  116 (771)
                      +..|+|.|+. .++..+|+.+|..|   .....+..+-|       .-|-|.|.+...|.+||..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD-------tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD-------TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC-------CcEEEEECCHHHHHHHHHcC
Confidence            4579999984 68889999999988   13456677777       36778999999999999754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	771
3v53_A	119	Crystal Structure Of Human Rbm25 Length = 119		4e-23
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		6e-05

>pdb|3V53|A Chain A, Crystal Structure Of Human Rbm25 Length = 119

Iteration: 1
 Score =  106 bits (265), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 47/104 (45%), Positives = 72/104 (69%)
Query: 663 KQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSST 722
           K LI+ IP  K ELF+Y ++W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S  
Sbjct: 15  KSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKV 74
Query: 723 QDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLA 766
             H     +L+ +  +LD+EAE+F++KMWR+LI+E +  + GL 
Sbjct: 75  MAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGLV 118

>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 = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           ++YV  +      D + SV +  G +KS   A+ P+ G  KG+GF E+E A+    A+  
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 116 LNKFNIDGQEL 126
           +N F++ GQ L
Sbjct: 187 MNLFDLGGQYL 197

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E  L A+R L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 117 NKFNIDGQELMLKVDQATRE 136
           N     G+   L+VD A  E
Sbjct: 71  NGREFSGR--ALRVDNAASE 88

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 38/71 (53%)
Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           ++YV  +      D + SV +  G +KS   A+ P+ G  KG+GF E+E A+    A+  
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 116 LNKFNIDGQEL 126
            N F++ GQ L
Sbjct: 171 XNLFDLGGQYL 181

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           ++YV  +      D + SV +  G +KS   A+ P+ G  KG+GF E+E A+    A+  
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 116 LNKFNIDGQEL 126
           +N F++ GQ L
Sbjct: 172 MNLFDLGGQYL 182

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	771
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-07
1mp1_A	111	Ser/Arg-related nuclear matrix protein; four helix	9e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-10
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-10
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-10
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	2e-10
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	2e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-09
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-09
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	4e-08
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-06
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	3e-09
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	4e-09
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	1e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-09
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	7e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	9e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-04
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-05
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-08
2div_A	99	TRNA selenocysteine associated protein; structural	2e-08
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-07
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	6e-08
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	5e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-04
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	8e-08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-07
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-07
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-07
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-07
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	8e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	9e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-06
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-06
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-06
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-06
1x5o_A	114	RNA binding motif, single-stranded interacting pro	9e-06
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	9e-06
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	9e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-05
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-05
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-05
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-04
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-04
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-04
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-04
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-04
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-04
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	7e-04
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	8e-04

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 17/94 (18%), Positives = 29/94 (30%), Gaps = 10/94 (10%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--------NGTPKGFGF 100
            +      ++V  +      + V    K  G +K+ K+   P          G  KG   
Sbjct: 8   HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 67

Query: 101 CEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT 134
             F+       A+   +     G    +KV  AT
Sbjct: 68  VSFDDPPSAKAAIDWFDGKEFSGNP--IKVSFAT 99

>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 = 67.7 bits (166), Expect = 4e-13
 Identities = 27/115 (23%), Positives = 48/115 (41%), Gaps = 4/115 (3%)

Query: 20  VARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCG 79
           + RP            P V  P  + TV P      K+++G +    + D V  +L   G
Sbjct: 82  IRRPHDYQPLPGMSENPSVYVPGVVSTVVP--DSAHKLFIGGLPNYLNDDQVKELLTSFG 139

Query: 80  TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT 134
            +K++   +  + G  KG+ FCE+       +A+  LN   +  +   L V +A+
Sbjct: 140 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK--KLLVQRAS 192

>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 = 50.8 bits (122), Expect = 3e-07
 Identities = 28/177 (15%), Positives = 53/177 (29%), Gaps = 22/177 (12%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY-----PSNGTPKGFGFCEFESAEGVL 110
           ++YVG I      + ++        +    +A             K F F EF S +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 111 RALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGK-------- 162
           +A+   +     GQ L ++     +       +        +       A K        
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 163 --EDESVQSV-EKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKL 216
              D+ V+ +     P K+   +KD+ TG         +      D     +A+  L
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGL-----SKGYAFCEYVDINVTDQAIAGL 176

>1mp1_A Ser/Arg-related nuclear matrix protein; four helix bundle, RNA binding protein; NMR {Homo sapiens} SCOP: a.188.1.1 Length = 111

 Score = 61.5 bits (149), Expect = 9e-12
 Identities = 19/65 (29%), Positives = 42/65 (64%), Gaps = 2/65 (3%)

Query: 693 ERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLEL-LQTILDDE-AEMFVLKM 750
           E ++PWI+K++TE LG E+  ++++I +  +     S+M+++ L   L+ + A  F+ ++
Sbjct: 23  EVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGEL 82

Query: 751 WRMLI 755
           W +L+
Sbjct: 83  WPLLL 87

>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 = 62.2 bits (152), Expect = 2e-11
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
              K+++G +    + D V  +L   G +K++   +  + G  KG+ FCE+       +A
Sbjct: 93  GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152

Query: 113 LRLLNKFNIDGQELMLKVDQAT 134
           +  LN   +  ++  L V +A+
Sbjct: 153 IAGLNGMQLGDKK--LLVQRAS 172

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 6/79 (7%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY-----PSNGTPKGFGFCEFESAEGVL 110
           ++YVG I      + ++        +    +A             K F F EF S +   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 111 RALRLLNKFNIDGQELMLK 129
           +A+   +     GQ L ++
Sbjct: 66  QAMA-FDGIIFQGQSLKIR 83

>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 = 59.6 bits (145), Expect = 2e-11
 Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 49  PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--NGTPKGFGFCEFES 105
           PA++     V+VG +      + +  +    G +             G PK FGF  F+ 
Sbjct: 10  PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTK---VTICKDREGKPKSFGFVCFKH 66

Query: 106 AEGVLRALRLLNKFNIDGQELMLKVDQAT 134
            E V  A+ LLN   + G+   + V   +
Sbjct: 67  PESVSYAIALLNGIRLYGRP--INVSGPS 93

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 59.3 bits (144), Expect = 6e-11
 Identities = 18/93 (19%), Positives = 29/93 (31%), Gaps = 10/93 (10%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--------NGTPKGFGFCE 102
                 ++V  +      + V    K  G +K+ K+   P          G  KG     
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 103 FESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
           F+       A+   +     G    +KV  ATR
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNP--IKVSFATR 94

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 58.4 bits (142), Expect = 8e-11
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
           P   VY+G I      + +L +    G V + K    P  G  KG+ F EF   E    A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 113 LRLLNKFNIDGQELMLKVDQAT 134
           +R LN + +  +   LK   ++
Sbjct: 61  VRNLNGYQLGSRF--LKCGYSS 80

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 35  MPPVVRPVPLPTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG 93
           +PP V P  +  +  +  P+ T  Y+G I   A    ++ + +  G +  +K        
Sbjct: 7   LPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH------Y 60

Query: 94  TPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 126
             KG  F ++++ E     +  L  F   G+ L
Sbjct: 61  PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 58.2 bits (141), Expect = 1e-10
 Identities = 14/91 (15%), Positives = 36/91 (39%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
           + P  +V   ++       F+  + +  G V+  +   +P      G     F S  G  
Sbjct: 3   QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62

Query: 111 RALRLLNKFNIDGQELMLKVDQATREYLERY 141
             ++ L+  ++ G  +  ++D   ++ ++ Y
Sbjct: 63  ETVKNLHLTSVMGNIIHAQLDIKGQQRMKYY 93

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 60.8 bits (148), Expect = 1e-10
 Identities = 23/114 (20%), Positives = 42/114 (36%), Gaps = 6/114 (5%)

Query: 43  PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 102
                  A    ++VYVG I      D +       G +KS   +        KGF F E
Sbjct: 17  SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76

Query: 103 FESAEGVLRALRLLNKFNIDGQELMLKVDQAT----REYLERYVDKKTENTKKL 152
           +E  E    AL  +N   + G+   +KV + +     + +   + ++     ++
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRN--IKVGRPSNIGQAQPIIDQLAEEARAFNRI 128

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 58.9 bits (143), Expect = 6e-10
 Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 2/96 (2%)

Query: 40  RPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFG 99
               +  +    +   ++YV  +      D + SV +  G +KS   A+ P+ G  KG+G
Sbjct: 111 AQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYG 170

Query: 100 FCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
           F E+E A+    A+  +N F++ GQ   L+V +A  
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLGGQ--YLRVGKAVT 204

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A* Length = 995

 Score = 63.9 bits (156), Expect = 2e-10
 Identities = 19/156 (12%), Positives = 47/156 (30%), Gaps = 7/156 (4%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 362
                  + +          +   E +R E ++++KI    ++Y R LK  E     +  
Sbjct: 840 PAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSV 899

Query: 363 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV------LEEKRRKRIREKEED 416
                +  +     + K + L   + +      +    +      L E     + E  E 
Sbjct: 900 YLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTER 959

Query: 417 LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
                 ++     +     +  L  +  + L+ + D
Sbjct: 960 KDTFFAQQWTGVKSSAETYKNTLLAEL-ERLQKIED 994

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A* Length = 995

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 17/147 (11%), Positives = 51/147 (34%), Gaps = 2/147 (1%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERERE-- 361
           ++ER  ++ K   + R     +    ++   + R   ++    +  +   +  ++  +  
Sbjct: 751 EEERASEQTKSDYLKRANELVQWINDKQASLESRDFGDSIESVQSFMNAHKEYKKTEKPP 810

Query: 362 KERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEV 421
           K ++  + +      + K  ++  E                     K  +E  E L  E+
Sbjct: 811 KGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQEHAEALRIEL 870

Query: 422 REEEEIAVAKRRAEEEQLQQQQRDALK 448
           + +++IAV  ++      + +     K
Sbjct: 871 KRQKKIAVLLQKYNRILKKLENWATTK 897

>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 = 57.0 bits (138), Expect = 3e-10
 Identities = 24/100 (24%), Positives = 36/100 (36%), Gaps = 11/100 (11%)

Query: 45  PTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS--------NGTP 95
            +  P E    + +YV  +  +   D +    K CG VK  KR   P          G P
Sbjct: 5   SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64

Query: 96  KGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
           KG     +E       A+   +  +  G +  LKV  A +
Sbjct: 65  KGDATVSYEDPPTAKAAVEWFDGKDFQGSK--LKVSLARK 102

>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 = 56.0 bits (136), Expect = 4e-10
 Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 9/86 (10%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
           E     +YVG +   A ++ + +    CG+V          +G PKGF + EF   E V 
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 111 RALRLLNKFNIDGQELM---LKVDQA 133
            +L L      D        +KV   
Sbjct: 63  TSLAL------DESLFRGRQIKVIPK 82

>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 = 58.0 bits (141), Expect = 5e-10
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 2/81 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           T + V  +        + ++ +  G + + +  +    G   G+ F +F S     RA++
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 115 LLNKFNIDGQELMLKVDQATR 135
           +LN   +  +   LKV  A  
Sbjct: 64  VLNGITVRNK--RLKVSYARP 82

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 51.4 bits (124), Expect = 1e-07
 Identities = 18/81 (22%), Positives = 30/81 (37%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
             T +YV  +  T   D + ++    G++      +    G P+G  F  +   E    A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 113 LRLLNKFNIDGQELMLKVDQA 133
           +  LN    +G    L V  A
Sbjct: 148 ISALNNVIPEGGSQPLSVRLA 168

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 55.8 bits (135), Expect = 6e-10
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 2/90 (2%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
              +  +   T + V  +  T   D +L        +      +Y   G P G     FE
Sbjct: 6   SGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFE 65

Query: 105 SAEGVLRALRLLNKFNIDGQELMLKVDQAT 134
           S +    A+  LN   I  ++  +K+   +
Sbjct: 66  SRDEATAAVIDLNDRPIGSRK--VKLSGPS 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 55.7 bits (135), Expect = 6e-10
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
                 + K+++  +  +   + +  + K  GTVK   R      G PKG  + E+E+  
Sbjct: 11  YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKD-LRLVTNRAGKPKGLAYVEYENES 69

Query: 108 GVLRALRLLNKFNIDGQELMLKVDQA 133
              +A+  ++   I      +KV  +
Sbjct: 70  QASQAVMKMDGMTIKENI--IKVAIS 93

>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 = 55.4 bits (134), Expect = 1e-09
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 9/97 (9%)

Query: 43  PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 102
           P+  ++P E+    V+  ++A       +       G V+  +     ++   KG  + E
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 103 FESAEGVLRALRLLNKFNIDGQELM---LKVDQATRE 136
           F   + V  A+ L       GQ L+   + V  +  E
Sbjct: 74  FCEIQSVPLAIGL------TGQRLLGVPIIVQASQAE 104

>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 = 54.6 bits (132), Expect = 2e-09
 Identities = 17/93 (18%), Positives = 34/93 (36%), Gaps = 10/93 (10%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
           P           +++G + P      +   +                 GT + FG+ +FE
Sbjct: 8   PVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFE 66

Query: 105 SAEGVLRALRLLNKFNIDGQELM---LKVDQAT 134
           SAE + +AL L       G ++    +K+++  
Sbjct: 67  SAEDLEKALEL------TGLKVFGNEIKLEKPK 93

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 56.7 bits (136), Expect = 2e-09
 Identities = 16/74 (21%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 321 EREAERERVRKEREQRRK-IEEAEREYERCLKDWEYREREREKE--RQYEKEKEKERERK 377
               E E +RK RE++RK ++E +   +   ++W  + ++  +E  ++  ++ EK +   
Sbjct: 79  RLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINN 138

Query: 378 RKKEILYDEEEDED 391
           R  +  + ++ D D
Sbjct: 139 RIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 53.2 bits (127), Expect = 4e-08
 Identities = 16/94 (17%), Positives = 38/94 (40%), Gaps = 15/94 (15%)

Query: 334 EQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDS 393
           +  R  +E E      ++ W    RE +++R  E +      +  ++E     ++D ++ 
Sbjct: 76  QADRLTQEPE-----SIRKW----REEQRKRLQELD---AASKVMEQEWREKAKKDLEEW 123

Query: 394 RKRWRRSVLEEKRRKRIREKEEDLADEVREEEEI 427
            +R    V  EK +   R  ++    +  + + I
Sbjct: 124 NQRQSEQV--EKNKINNRIADKAFYQQ-PDADII 154

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 47.8 bits (113), Expect = 3e-06
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 28/85 (32%)

Query: 384 YDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAK------------ 431
            D    E +S ++WR     E++RKR++E +   A +V E+E    AK            
Sbjct: 77  ADRLTQEPESIRKWR-----EEQRKRLQELDA--ASKVMEQEWREKAKKDLEEWNQRQSE 129

Query: 432 ---------RRAEEEQLQQQQRDAL 447
                    R A++   QQ   D +
Sbjct: 130 QVEKNKINNRIADKAFYQQPDADII 154

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 59.7 bits (145), Expect = 3e-09
 Identities = 15/160 (9%), Positives = 47/160 (29%), Gaps = 4/160 (2%)

Query: 294  RSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQR-RKIEEAEREYERCLKD 352
             + +           L++ ++   +    E +R++      Q+  +I +    +      
Sbjct: 848  PAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSV 907

Query: 353  WEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIRE 412
            +       +     + + +       + + L  +   +  S       +      +    
Sbjct: 908  YLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTER 967

Query: 413  KEEDLADEVREEEEIAVAKR---RAEEEQLQQQQRDALKL 449
            K+   A +    +  A   +    AE E+LQ+ +      
Sbjct: 968  KDTFFAQQWTGVKSSAETYKNTLLAELERLQKIEDLHHHH 1007

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 59.4 bits (143), Expect = 4e-09
 Identities = 31/191 (16%), Positives = 64/191 (33%), Gaps = 3/191 (1%)

Query: 271 LDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVR 330
           +D  T    + S     E ++  +        +  E++ +   ER+    + EAE+ R  
Sbjct: 646 VDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKE 705

Query: 331 KEREQ--RRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEE 388
               +     +E             E    E E      K K +    + + E+   ++ 
Sbjct: 706 LLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKV 765

Query: 389 DEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAE-EEQLQQQQRDAL 447
            E +      +  LE  + +++   E     E+ E       +  A    ++Q +   +L
Sbjct: 766 REMELIYARAQLELEVSKAQQLANVEAKKFKEMTEALGPGTIRDLAVAGPEMQVKLLQSL 825

Query: 448 KLLSDNAVNGS 458
            L S    +GS
Sbjct: 826 GLKSTLITDGS 836

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 51.0 bits (121), Expect = 1e-06
 Identities = 25/143 (17%), Positives = 51/143 (35%), Gaps = 11/143 (7%)

Query: 316 EIDRYEREAERERVRKEREQRRKI-EEAEREYERCLKDWEYREREREKERQYEKEK---E 371
            +D    E   +R R   ++  ++  E     +      E +  E+E   + E++K   +
Sbjct: 637 SVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQ 696

Query: 372 KERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDL-------ADEVREE 424
            E E+ RK+ +  +      +S    +          RI  +   L       A  +  E
Sbjct: 697 SEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETE 756

Query: 425 EEIAVAKRRAEEEQLQQQQRDAL 447
            E+   K+  E E +  + +  L
Sbjct: 757 AELERVKKVREMELIYARAQLEL 779

>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 = 53.8 bits (130), Expect = 4e-09
 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 2/90 (2%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
             +        ++YVG +      D +  + +  G ++S +       G  KG+GF  F 
Sbjct: 17  NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76

Query: 105 SAEGVLRALRLLNKFNIDGQELMLKVDQAT 134
            +E   +AL  LN F + G+   +KV   T
Sbjct: 77  DSECAKKALEQLNGFELAGRP--MKVGHVT 104

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
           +       +++V  +        +      CG V          NG  KG G  +FES E
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPE 59

Query: 108 GVLRALRLLNKFNIDGQELMLKVDQ 132
              RA R++N   + G+E+ +++D+
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDR 84

>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 = 55.3 bits (134), Expect = 5e-09
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 54  QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 113
           +T + V  +      +   S+    G ++S K  +    G   G+GF  +   +   +A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 114 RLLNKFNIDGQELMLKVDQA 133
             LN   +  +   +KV  A
Sbjct: 62  NTLNGLRLQTK--TIKVSYA 79

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 48.7 bits (117), Expect = 7e-07
 Identities = 15/83 (18%), Positives = 27/83 (32%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
                 +YV  +  T     +  +    G + + +       G  +G GF  F+      
Sbjct: 85  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144

Query: 111 RALRLLNKFNIDGQELMLKVDQA 133
            A++ LN     G    + V  A
Sbjct: 145 EAIKGLNGQKPSGATEPITVKFA 167

>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 = 53.0 bits (128), Expect = 5e-09
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 2/85 (2%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
                ++ VYV  +  +  ++ +  +    G V      +       KG  F  F   + 
Sbjct: 11  GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70

Query: 109 VLRALRLLNKFNIDGQELMLKVDQA 133
                R +N   + G+   +K   A
Sbjct: 71  AQNCTRAINNKQLFGRV--IKASIA 93

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 55.2 bits (133), Expect = 6e-09
 Identities = 21/130 (16%), Positives = 39/130 (30%), Gaps = 1/130 (0%)

Query: 7   PPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTA 66
            PR   P        RP     P   P                  +   K+ V  +    
Sbjct: 41  GPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGV 100

Query: 67  DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 126
               +  +    GT+K      Y  +G   G     FE     L+A++      +DG+ +
Sbjct: 101 SDADIQELFAEFGTLKKAA-VDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM 159

Query: 127 MLKVDQATRE 136
            +++  +  +
Sbjct: 160 DIQLVASQID 169

>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 = 53.4 bits (129), Expect = 6e-09
 Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 3/91 (3%)

Query: 50  AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 109
            ++    V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E  
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 110 LRALRLLNKFNIDGQELMLKVDQATREYLER 140
           L A+R LN     G+   L+VD A      +
Sbjct: 64  LSAMRNLNGREFSGRA--LRVDNA-ASEKNK 91

>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 = 54.4 bits (131), Expect = 6e-09
 Identities = 25/111 (22%), Positives = 44/111 (39%), Gaps = 2/111 (1%)

Query: 23  PPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK 82
            P      ++ +     + +P   + P       + V  I  T D   +  + +  G ++
Sbjct: 11  DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIE 70

Query: 83  SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA 133
           S K          +G+GF +F+S     +A+  LN FNI  +   LKV  A
Sbjct: 71  SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR--LKVALA 119

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 53.0 bits (128), Expect = 6e-09
 Identities = 13/90 (14%), Positives = 30/90 (33%), Gaps = 7/90 (7%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
           P  +   +    +    ++     D +  V +    ++   +     +G  KG  + EF+
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFK 61

Query: 105 SAEGVLRALRLLNKFNIDGQELMLKVDQAT 134
           S     + L       IDG+   + +    
Sbjct: 62  SEADAEKNLEEKQGAEIDGRS--VSLYYTG 89

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 56.9 bits (138), Expect = 7e-09
 Identities = 15/82 (18%), Positives = 29/82 (35%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             +++    P+     +  +L+    V    R       T + F + +  S E     + 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 115 LLNKFNIDGQELMLKVDQATRE 136
            LN   I+G  L+ KV     +
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEK 199

>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 = 50.4 bits (121), Expect = 1e-06
 Identities = 22/131 (16%), Positives = 45/131 (34%), Gaps = 7/131 (5%)

Query: 45  PTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEF 103
                    + T V V  +  + + + V    K CG +     A   S      F   EF
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEF 88

Query: 104 ESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKET-QDAGAGK 162
              +G L A+   +K  +   E+++        ++  +    T+  + +++  QD     
Sbjct: 89  ARYDGALAAITKTHKV-VGQNEIIVSHLTECTLWMTNFPPSYTQ--RNIRDLLQDINVVA 145

Query: 163 EDESVQSVEKN 173
               + S+  N
Sbjct: 146 LSIRLPSLRFN 156

>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 = 43.8 bits (104), Expect = 1e-04
 Identities = 12/83 (14%), Positives = 33/83 (39%), Gaps = 5/83 (6%)

Query: 55  TKVYVGKIAPTADSDFVLSVL-KVCGTVKSWKRAQ-YPSNGTPKGFGFCEFESAEGVLRA 112
            ++ +  ++     + +L    +  G+++          +       F  FE+ +   RA
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270

Query: 113 LRLLNKFNIDGQELMLKVDQATR 135
           L+ +N+  +  +E  + V  A +
Sbjct: 271 LQ-MNRSLLGNRE--ISVSLADK 290

>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 = 52.7 bits (127), Expect = 7e-09
 Identities = 17/94 (18%), Positives = 31/94 (32%), Gaps = 2/94 (2%)

Query: 43  PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 102
                +  +   T + V  +  T   D +L        +      +Y   G P G     
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 103 FESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 136
           FES +    A+  LN   I  ++  +K+   +  
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRK--VKLVLGSGP 95

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 52.7 bits (127), Expect = 8e-09
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
                   + +  ++ +A  + +  V +    +K  +      NG  KG+ F EF S E 
Sbjct: 10  TWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQ----NGKSKGYAFIEFASFED 65

Query: 109 VLRALRLLNKFNIDGQELMLKVDQAT 134
              AL   NK  I+G+   ++++   
Sbjct: 66  AKEALNSCNKREIEGRA--IRLELQG 89

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 57.9 bits (140), Expect = 9e-09
 Identities = 24/153 (15%), Positives = 66/153 (43%), Gaps = 9/153 (5%)

Query: 300  RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERE 359
                 +++  +  +E+ + + + +AE E   +  E R ++   ++E E  L +       
Sbjct: 879  ELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHE------M 932

Query: 360  REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 419
              +  + E+  ++ +  K+K +    + E++ +  +  R+ +  EK       K + + D
Sbjct: 933  EARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTA--DGKIKKMED 990

Query: 420  EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
            ++   E+    K   E + L+++  D    L++
Sbjct: 991  DILIMED-QNNKLTKERKLLEERVSDLTTNLAE 1022

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 56.8 bits (137), Expect = 2e-08
 Identities = 27/147 (18%), Positives = 60/147 (40%), Gaps = 8/147 (5%)

Query: 309 LKREKEREIDRYEREAER-ERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYE 367
           +       +  +       +  R+E E + K EE +R  ER  K     +   +K  Q  
Sbjct: 832 MNVXHWPWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLC 891

Query: 368 KEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEI 427
           +EK   +E+ + +  LY E E       R R +  +++  + + E E  + +E    +++
Sbjct: 892 EEKNLLQEKLQAETELYAEAE-----EMRVRLAAKKQELEEILHEMEARIEEEEERSQQL 946

Query: 428 AVAKRRAEEE--QLQQQQRDALKLLSD 452
              K++ +++   L++Q  +       
Sbjct: 947 QAEKKKMQQQMLDLEEQLEEEEAARQK 973

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 53.7 bits (129), Expect = 2e-07
 Identities = 32/169 (18%), Positives = 67/169 (39%), Gaps = 11/169 (6%)

Query: 296  RVHDRRGRDKERDLKREKEREIDRYEREAE-RERVRKEREQRRKIEEAEREYERCLKDWE 354
            +       + E    R   ++ +  E   E   R+ +E E+ ++++  +++ ++ + D E
Sbjct: 902  QAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLE 961

Query: 355  YREREREKERQ-YEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREK 413
             +  E E  RQ  + EK     + +K E      ED+++            K RK + E+
Sbjct: 962  EQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKL---------TKERKLLEER 1012

Query: 414  EEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEE 462
              DL   + EEEE A    + + +         ++L  +      L + 
Sbjct: 1013 VSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKI 1061

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 53.3 bits (128), Expect = 3e-07
 Identities = 46/349 (13%), Positives = 127/349 (36%), Gaps = 22/349 (6%)

Query: 300  RRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERE 359
            +  R +E    +++E +  +  ++     +++  ++  ++ E +   +  L+       E
Sbjct: 851  KVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAE 910

Query: 360  REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRK---RIREKEED 416
             E+ R     K++E E       L++ E   ++  +R ++  L+ +++K   ++ + EE 
Sbjct: 911  AEEMRVRLAAKKQELEEI-----LHEMEARIEEEEERSQQ--LQAEKKKMQQQMLDLEEQ 963

Query: 417  LADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDY 476
            L +E    +++ + K    + ++++ + D L +  ++  N    E   +E +  D+  + 
Sbjct: 964  LEEEEAARQKLQLEK-VTADGKIKKMEDDILIM--EDQNNKLTKERKLLEERVSDLTTNL 1020

Query: 477  HDDSIRENHMAGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPS 536
             ++  +  ++    +       E           RQ      RKL               
Sbjct: 1021 AEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKL-----EGESSDLHEQ 1075

Query: 537  VFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSK 596
            +  ++      K +  +    +  +   L+      + A    L    E    IS++   
Sbjct: 1076 IAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNA----LKKIRELESHISDLQED 1131

Query: 597  EEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDRE 645
             E   A R ++ +     S+  +    E  +       ++ L     ++
Sbjct: 1132 LESEKAARNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKD 1180

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.5 bits (100), Expect = 6e-04
 Identities = 23/161 (14%), Positives = 65/161 (40%), Gaps = 25/161 (15%)

Query: 303  RDKERDLKREK---EREIDRYEREAERERVRKE--REQRRKIEEAEREYERCLKD----- 352
             +K ++L + K   E  I   E   ++E   ++   + +RK+E    +    + +     
Sbjct: 1024 EEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQI 1083

Query: 353  WEYREREREKERQYEKEKEKERERKRKKEIL----------YDEEEDEDDSRKRWRRSVL 402
             E + +  +KE + +    +  +   +K               + +++ +S K  R    
Sbjct: 1084 AELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAE 1143

Query: 403  EEKRR-----KRIREKEEDLADEVREEEEIAVAKRRAEEEQ 438
            ++KR      + ++ + ED  D    ++E+  +  + ++++
Sbjct: 1144 KQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDDDK 1184

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.8 bits (140), Expect = 1e-08
 Identities = 23/159 (14%), Positives = 60/159 (37%), Gaps = 16/159 (10%)

Query: 304  DKERDLKREKEREIDRYER--EAERERVRKEREQRRKIEEAEREYERCLKDWE--YRERE 359
            ++ + L    E +I + +R  + + +  +   E+   +E         L+      R  E
Sbjct: 917  ERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSE 976

Query: 360  REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLE--------EKRRKRIR 411
             E +    +    + E  + ++ L+  + ++    +   +   E        +++   ++
Sbjct: 977  EEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLK 1036

Query: 412  EKEEDL----ADEVREEEEIAVAKRRAEEEQLQQQQRDA 446
             ++E+L     D+ +E  E    K   E +QL+    D 
Sbjct: 1037 TEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLNDE 1075

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.8 bits (140), Expect = 1e-08
 Identities = 35/190 (18%), Positives = 67/190 (35%), Gaps = 20/190 (10%)

Query: 294  RSRVHDRRGRDKERDLKREKEREIDRYER---EAERERVRKEREQRRKIEEAEREYERCL 350
             +RVH  R       L+    R + + E    + E   V + ++    +E    + +R +
Sbjct: 878  LARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKI 937

Query: 351  KDWEYRERE-REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEE----- 404
             +     +   EK    E     E E+ R         E+E  +      S+ EE     
Sbjct: 938  DEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLR 997

Query: 405  -------KRRKRIREKEEDLADEVRE---EEEIAVAKRRAEEEQLQQQQRDALKLLSDNA 454
                     +K I E  +    E  +   E +      + E+E+L ++  D  K +++  
Sbjct: 998  KELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITE-T 1056

Query: 455  VNGSLAEESA 464
            +   L EE+ 
Sbjct: 1057 MEKKLVEETK 1066

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.7 bits (132), Expect = 9e-08
 Identities = 21/153 (13%), Positives = 55/153 (35%), Gaps = 5/153 (3%)

Query: 301  RGRDKERDLKREKEREIDRYEREAERERVRKEREQRR-KIEEAEREYERCLKDWEYRERE 359
            RG        R  +  +     +    R+  +RE ++ KIE    E  + L      +  
Sbjct: 875  RGWLARVHYHRTLKAIV---YLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIM 931

Query: 360  REKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLAD 419
            + + +  E+ KE +   ++   +      + +  R    R  + E+  K    +   L +
Sbjct: 932  QLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQE 991

Query: 420  EVREEEEIAVAKRRAEEEQLQQQQRDALKLLSD 452
            E+ +  +  + + + E++ +++           
Sbjct: 992  EIAKLRK-ELHQTQTEKKTIEEWADKYKHETEQ 1023

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.3 bits (131), Expect = 1e-07
 Identities = 31/189 (16%), Positives = 66/189 (34%), Gaps = 12/189 (6%)

Query: 295  SRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 354
            + +     R+K + + RE +  I +        R        + I   +  Y R +   E
Sbjct: 847  ALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLAR-VHYHRTLKAIVYLQCCYRRMMAKRE 905

Query: 355  YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 414
             ++ + E  R  E+ K+     + K   L  + ++++   K      L EK         
Sbjct: 906  LKKLKIE-ARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKS-----LLEKMNNLEITY- 958

Query: 415  EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEH 474
                +++R + E    + R  EE+ +      L L  + A       ++  E K ++   
Sbjct: 959  STETEKLRSDVE----RLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWA 1014

Query: 475  DYHDDSIRE 483
            D +     +
Sbjct: 1015 DKYKHETEQ 1023

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 52.0 bits (125), Expect = 6e-07
 Identities = 19/181 (10%), Positives = 55/181 (30%), Gaps = 10/181 (5%)

Query: 303  RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 362
            R + + ++               R + +    + + I       ++ ++ W  R      
Sbjct: 832  RKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIII-----QKHVRGWLARVHYHRT 886

Query: 363  ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 422
             +     +   R    K+E+   + E     R +     LE K    I + +  + ++ +
Sbjct: 887  LKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENK----IMQLQRKIDEQNK 942

Query: 423  EEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGMDVEHDYHDDSIR 482
            E + + + K    E     +       +    ++   A+ +      +  E       + 
Sbjct: 943  EYKSL-LEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELH 1001

Query: 483  E 483
            +
Sbjct: 1002 Q 1002

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 42.0 bits (99), Expect = 8e-04
 Identities = 20/115 (17%), Positives = 46/115 (40%), Gaps = 2/115 (1%)

Query: 294  RSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDW 353
            RS V   R  ++E      +   +   E    R+ + + + +++ IEE   +Y+   +  
Sbjct: 966  RSDVERLRMSEEEAKNATNRVLSLQE-EIAKLRKELHQTQTEKKTIEEWADKYKHETEQL 1024

Query: 354  EYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRK 408
                +E+    + EKE E  R    + + + +  E +     +     L ++R +
Sbjct: 1025 VSELKEQNTLLKTEKE-ELNRRIHDQAKEITETMEKKLVEETKQLELDLNDERLR 1078

>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 = 56.1 bits (136), Expect = 1e-08
 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 4/89 (4%)

Query: 48  TPAEKPQTKVYVGKIAPTA-DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 106
           TPA      + V ++ P   D D +   L    +     +     +G  KGF   E+E+A
Sbjct: 178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTF-CQLACGQDGQLKGFAVLEYETA 236

Query: 107 EGVLRALRLLNKFNIDGQELMLKVDQATR 135
           E    A +  +  ++ G    L+V     
Sbjct: 237 EMAEEAQQQADGLSLGGS--HLRVSFCAP 263

>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 = 54.6 bits (132), Expect = 3e-08
 Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
                + V  + P+        +++  G+++          G  KG+GF E+   +   R
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 112 ALRLLNKFNIDGQELMLKVDQATR 135
           A   L    +  +   L V     
Sbjct: 153 AKSDLLGKPLGPRT--LYVHWTDA 174

>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 = 44.6 bits (106), Expect = 6e-05
 Identities = 14/101 (13%), Positives = 29/101 (28%), Gaps = 9/101 (8%)

Query: 35  MPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT 94
           + P      L       + + K+ +  +     +  V  +L     +K            
Sbjct: 3   LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCF------VDK 55

Query: 95  PKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
            KG  F    + E    A+   ++  +  +E  L V     
Sbjct: 56  YKGTAFVTLLNGEQAEAAINAFHQSRLRERE--LSVQLQPT 94

>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 = 53.7 bits (130), Expect = 1e-08
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           +YVG +      D +    +V G + +  +     N     + F E+  +     AL+ L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIAN-IKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 117 NKFNIDGQELMLKVDQATR 135
           N   I+     +K++ A +
Sbjct: 62  NGKQIENNI--VKINWAFQ 78

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 49.4 bits (119), Expect = 5e-07
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 8/86 (9%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               ++VG +    D + + +  K   +  S         G+ +G+GF  F S +    A
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145

Query: 113 LRLLNKFNIDGQELM---LKVDQATR 135
           +  +      GQ+L    L+++ A +
Sbjct: 146 MDSMQ-----GQDLNGRPLRINWAAK 166

>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 = 51.8 bits (125), Expect = 1e-08
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 50  AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 109
                + +YVG +      D +  + +  G + +    +    G  KG+GF  F  +E  
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 110 LRALRLLNKFNIDGQELMLKVDQAT 134
            RAL  LN F + G+   ++V   T
Sbjct: 61  RRALEQLNGFELAGRP--MRVGHVT 83

>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 = 51.9 bits (125), Expect = 2e-08
 Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
             +    K+++G+I    D   +  + +  G +      +    G  KG  F  +   E 
Sbjct: 8   MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67

Query: 109 VLRALRLLN-KFNIDGQELMLKVDQATRE 136
            L+A   L+ +  + G    ++V  A  E
Sbjct: 68  ALKAQSALHEQKTLPGMNRPIQVKPADSE 96

>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 = 51.6 bits (124), Expect = 2e-08
 Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 3/91 (3%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESA 106
           + +      +++G + P  D +F+       G TV S K  +    G P G+ F EF   
Sbjct: 3   SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 107 EGVLRALRLLNKFNIDGQEL--MLKVDQATR 135
               + L  +N   + G       K++ AT 
Sbjct: 63  ATAEKCLHKINGKPLPGATPAKRFKLNYATY 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 = 51.5 bits (124), Expect = 2e-08
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 50  AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWK---RAQYPSNGTPKGFGFCEFESA 106
                + +++  +  +   + +  V    G +KS     +          GFGF E++  
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 107 EGVLRALRLLNKFNIDGQELMLKVDQATR 135
           E   +AL+ L    +DG +  L+V  + R
Sbjct: 61  EQAQKALKQLQGHTVDGHK--LEVRISER 87

>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 = 50.6 bits (122), Expect = 3e-08
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 8/88 (9%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
                +  +YVG +A   D   + +     G +   +          +GF F EFE AE 
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 109 VLRALRLLNKFNIDGQELM---LKVDQA 133
              A+  +N       EL    ++V+ A
Sbjct: 62  AAAAIDNMN-----ESELFGRTIRVNLA 84

>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 = 51.5 bits (124), Expect = 3e-08
 Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               VYVG +        +  +    G V +    +    G  +G+GF EF S E    A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 113 LRLLNKFNIDGQELMLKVDQATRE 136
           +++++   + G+   ++V++A+  
Sbjct: 74  IKIMDMIKLYGKP--IRVNKASAH 95

>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 = 52.9 bits (127), Expect = 3e-08
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 2/84 (2%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
           K    +YVG ++     + +  +    G +K           T  GF F E+ S      
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

Query: 112 ALRLLNKFNIDGQELMLKVDQATR 135
           A+R +N   +D +   ++ D    
Sbjct: 97  AMRYINGTRLDDRI--IRTDWDAG 118

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 52.1 bits (125), Expect = 3e-08
 Identities = 20/94 (21%), Positives = 34/94 (36%), Gaps = 8/94 (8%)

Query: 43  PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 102
                  +   +  +YVG +A   D   + +     G +   +          +GF F E
Sbjct: 52  GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111

Query: 103 FESAEGVLRALRLLNKFNIDGQELM---LKVDQA 133
           FE AE    A+  +N       EL    ++V+ A
Sbjct: 112 FELAEDAAAAIDNMN-----ESELFGRTIRVNLA 140

>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 = 50.2 bits (121), Expect = 5e-08
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 9/83 (10%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN----GTPKGFGFCEFESAEGVL 110
           TKV++G++      D ++ +    G +K       P         KG+ + EFE+ +   
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKM---IDMPVERMHPHLSKGYAYVEFENPDEAE 61

Query: 111 RALRLLNKFNIDGQELMLKVDQA 133
           +AL+ ++   IDGQE  +     
Sbjct: 62  KALKHMDGGQIDGQE--ITATAV 82

>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 = 50.3 bits (121), Expect = 5e-08
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 6/85 (7%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
            P T+++VG + P      +       G++++              F + ++ES +    
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQA 68

Query: 112 ALRLLNKFNIDGQELMLKVDQATRE 136
           A   +  F + G +  L+VD A   
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKSG 93

>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 = 52.2 bits (126), Expect = 5e-08
 Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 50  AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 109
             +    +    ++     D +  V +    ++         +G  KG  + EF+S    
Sbjct: 95  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEADA 149

Query: 110 LRALRLLNKFNIDGQELMLKVDQATR 135
            + L       IDG+   + +     
Sbjct: 150 EKNLEEKQGAEIDGRS--VSLYYTGE 173

>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 = 51.5 bits (124), Expect = 1e-07
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
                 +++G + P      +   +                 GT + FG+ +FESAE + 
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLE 68

Query: 111 RALRLLNKFNIDGQELMLKVDQATRE 136
           +AL  L    + G E+ L+  +    
Sbjct: 69  KALE-LTGLKVFGNEIKLEKPKGRDS 93

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 55.3 bits (132), Expect = 6e-08
 Identities = 24/148 (16%), Positives = 59/148 (39%), Gaps = 6/148 (4%)

Query: 304 DKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKE 363
              R   ++ +    +Y  E  +    +E  Q     +          D    E+E+E E
Sbjct: 431 GGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIE 490

Query: 364 RQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSV------LEEKRRKRIREKEEDL 417
            +  K +  +   K   E+    E+  +   + ++  +      +E  R + ++E+E  L
Sbjct: 491 VERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTL 550

Query: 418 ADEVREEEEIAVAKRRAEEEQLQQQQRD 445
           A +++E+E++     + E   ++ + +D
Sbjct: 551 ALKLQEQEQLLKEGFQKESRIMKNEIQD 578

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 42.6 bits (99), Expect = 5e-04
 Identities = 22/126 (17%), Positives = 51/126 (40%), Gaps = 6/126 (4%)

Query: 301 RGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYRERER 360
           + ++   D   + ++ +   E+E E ERV+ E  Q       E + +      +     +
Sbjct: 466 KSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQ 525

Query: 361 EKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADE 420
           E  +Q  ++ E +R +  K      E+E     + + +  +L+E  +K  R  + ++ D 
Sbjct: 526 EHLKQLTEKMENDRVQLLK------EQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDL 579

Query: 421 VREEEE 426
             +   
Sbjct: 580 QTKMRR 585

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 54.9 bits (131), Expect = 6e-08
 Identities = 42/337 (12%), Positives = 91/337 (27%), Gaps = 7/337 (2%)

Query: 43  PLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCE 102
           P             ++V ++        +    +V G +K         +G P+G+ F E
Sbjct: 91  PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150

Query: 103 FESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGK 162
           +E    +  A +  +   IDG+ +++ V++       R            +   D     
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRH 210

Query: 163 EDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEE 222
                 S     P  SP   +D +   +      +     E +R+  +            
Sbjct: 211 SGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSR-------SRDRR 263

Query: 223 RLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKAS 282
           R   +       ++               +R  +                 +    ++A 
Sbjct: 264 RRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAG 323

Query: 283 DHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEA 342
           D    +    +          +K RD  RE+ R               ++R++  K  E 
Sbjct: 324 DAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGER 383

Query: 343 EREYERCLKDWEYREREREKERQYEKEKEKERERKRK 379
             E  R         ++   E      ++   E +  
Sbjct: 384 GSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGG 420

>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 = 45.6 bits (107), Expect = 5e-05
 Identities = 26/157 (16%), Positives = 53/157 (33%), Gaps = 1/157 (0%)

Query: 269 DKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERER 328
            +       + +    +R +    DR R   R      R+ +R++E      +     E 
Sbjct: 263 RRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEA 322

Query: 329 VRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEE 388
                +     E      +   +    R+RER +  + E+E+ ++R+R R ++  +   E
Sbjct: 323 GDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGE 382

Query: 389 DEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEE 425
              + R R         +   +     D  D   E E
Sbjct: 383 RGSE-RGRDEARGGGGGQDNGLEGLGNDSRDMYMESE 418

>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 = 42.9 bits (100), Expect = 3e-04
 Identities = 23/159 (14%), Positives = 51/159 (32%)

Query: 277 SDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQR 336
                S        S +RS+  DR  + +    +    RE +R E          E  + 
Sbjct: 263 RRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEA 322

Query: 337 RKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKR 396
                 +        D      E+ ++R  E+ +    ER+R+++   D + D +  R  
Sbjct: 323 GDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGE 382

Query: 397 WRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAE 435
                  ++ R     ++  L     +  ++ +     +
Sbjct: 383 RGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGD 421

>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 = 50.4 bits (121), Expect = 7e-08
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 4/87 (4%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
                V++  ++  ++ + +  VL+  G +K  +   +P     KG  F +F + E   +
Sbjct: 13  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 112 ALRLLNKFN-IDGQELM---LKVDQAT 134
            L   +      G +L    LKVD A 
Sbjct: 73  CLAAASLEAEGGGLKLDGRQLKVDLAV 99

>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 = 29/117 (24%), Positives = 47/117 (40%), Gaps = 4/117 (3%)

Query: 21  ARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGT 80
           +  P P +       P    P  L T +     +  VYVG  +       ++ V++  G 
Sbjct: 22  SMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGV 81

Query: 81  --VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
             V   K A+  +NG  KG+      S   V + L LL    ++G++  + V  ATR
Sbjct: 82  YDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK--VDVRPATR 136

>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 = 50.5 bits (121), Expect = 8e-08
 Identities = 21/106 (19%), Positives = 36/106 (33%), Gaps = 9/106 (8%)

Query: 31  VRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP 90
           +         P PL      E  +  VYVG +   + +  + +    CG++         
Sbjct: 13  MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDK 72

Query: 91  SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQA 133
            +G PKG+ + EF     V  A+ +      D        +KV   
Sbjct: 73  FSGHPKGYAYIEFAERNSVDAAVAM------DETVFRGRTIKVLPK 112

>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 = 49.0 bits (118), Expect = 9e-08
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             ++VG +    D + + +  K   +  S         G+ +G+GF  F S +    A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 115 LLNKFNIDGQELMLKVDQATR 135
            +   +++G+   L+++ A +
Sbjct: 62  SMQGQDLNGRP--LRINWAAK 80

>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 = 49.5 bits (119), Expect = 9e-08
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 2/87 (2%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
           +     + K++VG ++   +   +  V    G +      +       +GFGF  FE+ +
Sbjct: 6   SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65

Query: 108 GVLRALRLLNKFNIDGQELMLKVDQAT 134
               A+  +N  ++DG+   ++VDQA 
Sbjct: 66  DAKDAMMAMNGKSVDGR--QIRVDQAG 90

>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 = 50.1 bits (120), Expect = 1e-07
 Identities = 18/112 (16%), Positives = 41/112 (36%), Gaps = 3/112 (2%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
           +    +Y+  +     ++ +  +    G ++     +  +    +G  +  +E       
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 62

Query: 112 ALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKE 163
           A+  L+ FN+  + L++    A R + +    KK E  K LKE         
Sbjct: 63  AVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPP 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 50.1 bits (120), Expect = 1e-07
 Identities = 21/118 (17%), Positives = 37/118 (31%), Gaps = 12/118 (10%)

Query: 26  PGIPGVRPIMPPVVRPV---------PLPTVTPAEKPQ-TKVYVGKIAPTADSDFVLSVL 75
            G+P           P+                 E P+   +++  +        + S  
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61

Query: 76  KVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA 133
              G V S K          K FGF  F++ +    A++ +N F +  +   LKV   
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKR--LKVQLK 117

>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 = 49.5 bits (118), Expect = 1e-07
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 8/87 (9%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGT------VKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
           V+V  ++       VL   +  G       V       Y  +  P    +  +  +E  L
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 111 RALRLLNKFNIDGQELMLKVDQATREY 137
           RA++ +N   +DG+   LK    T +Y
Sbjct: 78  RAIQCVNNVVVDGR--TLKASLGTTKY 102

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEG 108
                 + +  IAP    D +++ L    +  V + +  +       +GF F +  SA  
Sbjct: 6   HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65

Query: 109 VLRALRLLNK----FNIDGQELMLKVDQA 133
             + L++L        IDG+   + VD A
Sbjct: 66  ASQLLQILQSLHPPLKIDGKT--IGVDFA 92

>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 = 49.2 bits (118), Expect = 2e-07
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 51  EKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 109
           E P+   +++  +        +L +    G V S K          K FGF  +++    
Sbjct: 21  EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80

Query: 110 LRALRLLNKFNIDGQELMLKVDQATRE 136
             A++ +N F I  +   LKV     +
Sbjct: 81  QAAIQSMNGFQIGMKR--LKVQLKRSK 105

>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 = 52.0 bits (124), Expect = 2e-07
 Identities = 23/125 (18%), Positives = 37/125 (29%), Gaps = 9/125 (7%)

Query: 18  PSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQ-----TKVYVGKIAPTADSDFVL 72
           PS      P        +PP V         P            +Y+G +      + + 
Sbjct: 27  PSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLT 86

Query: 73  SVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 130
             +   G   +   K  +  +NG  KGF      S     + + LL K  + GQ     V
Sbjct: 87  EAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN--PVV 144

Query: 131 DQATR 135
               +
Sbjct: 145 TPVNK 149

>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 = 51.5 bits (124), Expect = 2e-07
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 4/95 (4%)

Query: 43  PLPTVTPA--EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGF 100
           PL ++ P+    P   +YVG + P      +       G + S +  +        G+ +
Sbjct: 2   PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61

Query: 101 CEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
             F+      RAL  +N   I G+   +++  + R
Sbjct: 62  VNFQQPADAERALDTMNFDVIKGKP--VRIMWSQR 94

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 43.8 bits (104), Expect = 7e-05
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 4/83 (4%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               +++  +  + D+  +       G + S K          KG+GF  FE+ E   RA
Sbjct: 102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 159

Query: 113 LRLLNKFNIDGQELMLKVDQATR 135
           +  +N   ++ ++  + V +   
Sbjct: 160 IEKMNGMLLNDRK--VFVGRFKS 180

>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 = 48.3 bits (116), Expect = 2e-07
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           + +Y+  + P      ++ + +  G + S K     +    KG+GF +F+S     +A+ 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 115 LLNKFNIDGQELMLKVDQA 133
            L    +  Q  M K    
Sbjct: 66  ALKASGVQAQ--MAKQSGP 82

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
                ++V  +   A  + +       G +K+         G  KG+   E+E+ +    
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 112 ALRLLNKFNIDGQELMLKVDQAT 134
           A+  LN  ++ GQ   + VD   
Sbjct: 81  AMEGLNGQDLMGQP--ISVDWCF 101

>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 = 48.9 bits (117), Expect = 2e-07
 Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
           PA     ++YVG + P   +  +  V    G ++        +      F F EFE    
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAFVEFEDPRD 73

Query: 109 VLRALRLLNKFNIDGQELMLKVDQAT 134
              A+   + ++ DG    L+V+   
Sbjct: 74  AEDAVYGRDGYDYDGYR--LRVEFPR 97

>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 = 50.3 bits (121), Expect = 3e-07
 Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 54  QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP--KGFGFCEFESAEGVLR 111
             K++VG++  T     +  + +  G V      +  S   P  KG  F  F + +  L 
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 112 ALRLLNKFNIDGQELM-LKVDQATREYLERYVDKK 145
           A   L+   +       +++  A  E      D+K
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRK 97

>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 = 42.2 bits (100), Expect = 2e-04
 Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            K+++G I+     + +  +    G ++   R     +G  +G  F  F +      A++
Sbjct: 96  RKLFIGMISKKCTENDIRVMFSSFGQIEE-CRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154

Query: 115 LLN 117
            ++
Sbjct: 155 AMH 157

>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 = 48.0 bits (115), Expect = 3e-07
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 2/87 (2%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
               P   + V  ++       +  V    G +          +   +GF F  FE+ + 
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATR 135
              A    N   +DG+   ++V   + 
Sbjct: 70  AKEAKERANGMELDGRR--IRVSGPSS 94

>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 = 48.0 bits (115), Expect = 3e-07
 Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 2/87 (2%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
           P       + V  +      D +  V +  G V      + P    P+GF F  F     
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATR 135
              A   ++   +DG+E  L+V  A  
Sbjct: 68  AQDAEAAMDGAELDGRE--LRVQVARY 92

>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 = 48.9 bits (117), Expect = 3e-07
 Identities = 14/92 (15%), Positives = 32/92 (34%), Gaps = 1/92 (1%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
              +   K+ V  +        +  +    GT+K      Y  +G   G     FE    
Sbjct: 30  EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA-VDYDRSGRSLGTADVHFERRAD 88

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATREYLER 140
            L+A++      +DG+ + +++  +  +    
Sbjct: 89  ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH 120

>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 = 48.0 bits (115), Expect = 4e-07
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 2/85 (2%)

Query: 50  AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 109
               +  +YVG +A   D   + +     G +   +          +GF F EFE AE  
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 110 LRALRLLNKFNIDGQELMLKVDQAT 134
             A+  +N+  + G+   ++V+ A 
Sbjct: 68  AAAIDNMNESELFGRT--IRVNLAK 90

>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 = 48.0 bits (115), Expect = 4e-07
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            K+ V  +        +  +    GT+K      Y  +G   G     FE     L+A++
Sbjct: 30  GKLLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMK 88

Query: 115 LLNKFNIDGQELMLKVDQAT 134
             N   +DG+   + +   T
Sbjct: 89  QYNGVPLDGRP--MNIQLVT 106

>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 = 48.1 bits (115), Expect = 5e-07
 Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 1/85 (1%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
             A +  + V+V  +        +  V  + G V          +G  +G G   FE + 
Sbjct: 9   LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRAD-ILEDKDGKSRGIGTVTFEQSI 67

Query: 108 GVLRALRLLNKFNIDGQELMLKVDQ 132
             ++A+ + N   +  + + +K+D+
Sbjct: 68  EAVQAISMFNGQLLFDRPMHVKMDE 92

>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 = 47.6 bits (114), Expect = 5e-07
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
                  +++V  ++ T+  + +  +    G +             PKGF F  F   E 
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 109 VLRALRLLNKFNIDGQELMLKVDQAT 134
            ++A   ++     G+  ML V  +T
Sbjct: 63  AVKAYAEVDGQVFQGR--MLHVLPST 86

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 47.6 bits (114), Expect = 6e-07
 Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 15/98 (15%)

Query: 40  RPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFG 99
               LPT     +P    YVG +        + ++ K    ++S +  +       KGF 
Sbjct: 6   SGKELPT-----EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59

Query: 100 FCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQAT 134
           + EF+  + +  AL        DG  L    L+VD A 
Sbjct: 60  YVEFDEVDSLKEALTY------DGALLGDRSLRVDIAE 91

>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 = 47.6 bits (114), Expect = 6e-07
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 12/88 (13%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS----WKRAQYPSNGTPKGFGFCEFESA 106
           +     +YVG ++       +L +    G  KS     +        +   + F EF   
Sbjct: 12  DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT------SNDPYCFVEFYEH 65

Query: 107 EGVLRALRLLNKFNIDGQELMLKVDQAT 134
                AL  +N   I G+E  +KV+ AT
Sbjct: 66  RDAAAALAAMNGRKILGKE--VKVNWAT 91

>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 = 7e-07
 Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               V+VG ++P   ++ + +     G +   +  +  + G  KG+GF  F +      A
Sbjct: 14  NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 73

Query: 113 LRLLNKFNIDGQELMLKVDQATR 135
           ++ +    + G++  ++ + ATR
Sbjct: 74  IQQMGGQWLGGRQ--IRTNWATR 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 47.1 bits (112), Expect = 8e-07
 Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 11/77 (14%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTV---KSWKRAQYPSNGTPKGFGFCEFESAEGV 109
               VYVG +   A    +   L+  G+V    +W+         P+   F  +  +   
Sbjct: 18  LAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG--------PRRRAFLHYPDSAAA 69

Query: 110 LRALRLLNKFNIDGQEL 126
            +A+  L    +    L
Sbjct: 70  QQAVSCLQGLRLGTDTL 86

>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 = 9e-07
 Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 14/102 (13%)

Query: 36  PPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP 95
                   LP       P    ++G +      + +    +           +  +    
Sbjct: 2   SSGSSGSRLPK-----SPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERL 56

Query: 96  KGFGFCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQAT 134
           KGFG+ EFE  + +L AL L      + + L    ++VD A 
Sbjct: 57  KGFGYAEFEDLDSLLSALSL------NEESLGNKRIRVDVAD 92

>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 = 46.5 bits (111), Expect = 9e-07
 Identities = 14/83 (16%), Positives = 34/83 (40%), Gaps = 9/83 (10%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
              K+Y+G ++P   +D +  +        + +           G+ F ++      +RA
Sbjct: 7   GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRA 60

Query: 113 LRLLN-KFNIDGQELMLKVDQAT 134
           +  L+ K  + G+   ++VD + 
Sbjct: 61  IETLSGKVELHGKI--MEVDYSV 81

>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 = 46.1 bits (110), Expect = 2e-06
 Identities = 13/91 (14%), Positives = 37/91 (40%), Gaps = 10/91 (10%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
            + +        ++V  +A T   + +       G ++  K+         K + F  F+
Sbjct: 2   SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFD 53

Query: 105 SAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
             +G ++A+  +N  +++G+   +++  A  
Sbjct: 54  ERDGAVKAMEEMNGKDLEGEN--IEIVFAKP 82

>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 = 46.5 bits (111), Expect = 2e-06
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
            ++V  I   A  D +       G +K+         G  KG+   E+E+ +  L A   
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 116 LNKFNIDGQELMLKVDQAT 134
           LN   I GQ   ++VD   
Sbjct: 88  LNGAEIMGQT--IQVDWCF 104

>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 = 46.5 bits (111), Expect = 2e-06
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             +++  +  + D+  +       G + S K          KG+GF  FE+ E   RA+ 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIE 63

Query: 115 LLNKFNIDGQELMLKVDQATR 135
            +N   ++ ++  + V +   
Sbjct: 64  KMNGMLLNDRK--VFVGRFKS 82

>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 = 46.1 bits (110), Expect = 2e-06
 Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               + V  ++       +  + +  G++     A+  + G  KGF F  F   E   RA
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 113 LRLLNKFNIDGQELMLKVDQAT 134
           +  ++ F  D   L+L V+ A 
Sbjct: 74  IAGVSGFGYDH--LILNVEWAK 93

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN-GTPKGFGFCEFESA 106
           + ++    +++V  I        +  +    G +      +   N    KGFGF  FE++
Sbjct: 9   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILD---VEIIFNERGSKGFGFVTFENS 65

Query: 107 EGVLRALRLLNKFNIDGQELMLKVDQAT 134
               RA   L+   ++G++  ++V+ AT
Sbjct: 66  ADADRAREKLHGTVVEGRK--IEVNNAT 91

>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 = 45.4 bits (108), Expect = 3e-06
 Identities = 18/89 (20%), Positives = 40/89 (44%), Gaps = 4/89 (4%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQ-YPSNGTPKGFGFCEFESA 106
            P ++  +K+ V  I   A+   +  +    G +K+ +  +     G  +GFGF +F + 
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68

Query: 107 EGVLRALR-LLNKFNIDGQELMLKVDQAT 134
           +   +A   L +  ++ G+   L ++ A 
Sbjct: 69  QDAKKAFNALCHSTHLYGRR--LVLEWAD 95

>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 = 44.9 bits (107), Expect = 3e-06
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               V+VG ++P   +  + +     G +   +  +  + G  KG+GF  F +      A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 113 LRLLNKFNIDGQELMLKVDQATR 135
           ++ +    + G++  ++ + ATR
Sbjct: 65  IQQMGGQWLGGRQ--IRTNWATR 85

>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 = 45.3 bits (108), Expect = 3e-06
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 9/87 (10%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKR-AQYPSNGTPKGFGFCEFESAEGVLR 111
             + +++G + P  D   +       G +    +  + P  G  KG+ F  F S +    
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 112 ALRLLNKFNIDGQELM---LKVDQATR 135
           A+  +N     GQ L    + V  A +
Sbjct: 64  AIEAMN-----GQYLCNRPITVSYAFK 85

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 3/84 (3%)

Query: 58  YVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN 117
            +           + S+    G V + +     + G  KGF F E  S     + ++  +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 118 KFNIDGQELMLKVDQATREYLERY 141
              +D +   L +       +ERY
Sbjct: 76  GKRLDLKH-RLFLYTMKD--VERY 96

>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 = 44.9 bits (107), Expect = 4e-06
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 54  QTKVYVGKIAPTADSDFVLSVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
           +  +Y+G +      + +   +   G   +   K  +  +NG  KGF      S     +
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 112 ALRLLNKFNIDGQELMLKVDQAT 134
            + LL K  + GQ     V  + 
Sbjct: 61  LMDLLPKRELHGQN--PVVTPSN 81

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 45.0 bits (107), Expect = 5e-06
 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 2/87 (2%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
                K++VG +      + VL + +  G +          +G+ KG  F +F S     
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDE-CTVLRGPDGSSKGCAFVKFSSHTEAQ 70

Query: 111 RALRLLN-KFNIDGQELMLKVDQATRE 136
            A+  L+    + G    L V  A  +
Sbjct: 71  AAIHALHGSQTMPGASSSLVVKFADTD 97

>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 = 49.1 bits (116), Expect = 6e-06
 Identities = 69/461 (14%), Positives = 139/461 (30%), Gaps = 123/461 (26%)

Query: 385 DEEEDEDDSRKRWRRSVLEEKRRKRIREKE-EDLADEVREEEEI-AVAKRRAEEEQ---- 438
           D E  E   + +   SV E+        K+ +D+   +  +EEI  +   +         
Sbjct: 8   DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL 67

Query: 439 ---LQQQQRDALKLLSDNAVN---GSLAEESAVESKGMDVEHDYHDDSIRENHMAGDPSS 492
              L  +Q + ++   +  +      L      E +   +    + +    + +  D   
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR--DRLYNDNQV 125

Query: 493 QNGNGDESTNVPI---------AASDMRQSGNVPARKLGFGLVGSGKRTAVPSV------ 537
                    NV           A  ++R + NV    L  G++GSGK      V      
Sbjct: 126 F-----AKYNVSRLQPYLKLRQALLELRPAKNV----LIDGVLGSGKTWVALDVCLSYKV 176

Query: 538 -----FHV-------EDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAE 585
                F +        +  +      +  L  + Y  +    ++   S      + +   
Sbjct: 177 QCKMDFKIFWLNLKNCNSPETV----LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 586 FAKRI-------------SNVNSKE--EKSDAE-R----ERSRRLHDR-SSQREKDRSDE 624
             +R+              NV + +     +   +     R +++ D  S+      S +
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 625 DNNR--TRDEHKE---KILDRDRD---RE----HGL----------DKVKTPDNKKLLDA 662
            ++   T DE K    K LD       RE    +            D + T DN K ++ 
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352

Query: 663 KQLIDMIPKTKEELFSYEI-----NWAVYDKHELHERMRPWISKKITEFL-GEEETTLVD 716
            +L  +I  +   L   E        +V+            I   +   +  +   + V 
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA-------HIPTILLSLIWFDVIKSDVM 405

Query: 717 YIV------SSTQDHVKASQM------LELLQTILDDEAEM 745
            +V      S  +   K S +      LEL   + ++E  +
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL-ENEYAL 445

>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 = 43.7 bits (102), Expect = 3e-04
 Identities = 61/447 (13%), Positives = 123/447 (27%), Gaps = 145/447 (32%)

Query: 30  GVRPIMP-PVVRPVPLPTVTPA---EKPQTKVYV------GKIAPTADSDFVLSVLKVCG 79
             +      V R  P   +  A    +P   V +      GK           + +    
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK-----------TWV-ALD 169

Query: 80  TVKSWKRAQYPSNG----TPKGFGFCEFESAEGVLRAL-RLLNKFNIDGQEL-------M 127
              S+K                   C   S E VL  L +LL + + +            
Sbjct: 170 VCLSYKVQCKMDFKIFWLN---LKNCN--SPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224

Query: 128 LKVDQATREYLERYV----------------DKKTENT-----KKLKETQDAG----AGK 162
           L++    +  L R +                + K  N      K L  T+          
Sbjct: 225 LRIHSI-QAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA 283

Query: 163 EDESVQSVEKNEPTKSPENLKD---NETGNKE--------SHDPTNFGVVTEEDRKA--- 208
              +  S++ +  T +P+ +K         +         + +P    ++ E  R     
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343

Query: 209 ----DQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGI--SNSELPAK------ARDGD 256
                    +KLT ++E  L  N L P   +   D   +   ++ +P             
Sbjct: 344 WDNWKHVNCDKLTTIIESSL--NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIK 401

Query: 257 SDVDMIRNDIAEDKLDDETTSDTKASDHD---RPETSSPDRSRVHDR--------RGRDK 305
           SDV ++ N + +  L ++   ++  S        +    +   +H          +  D 
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461

Query: 306 ERDLKREKE------------REIDRYEREAE-----------RERVRKE---------- 332
           + DL                 + I+  ER               +++R +          
Sbjct: 462 D-DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSI 520

Query: 333 -------REQRRKIEEAEREYERCLKD 352
                  +  +  I + + +YER +  
Sbjct: 521 LNTLQQLKFYKPYICDNDPKYERLVNA 547

>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 = 45.0 bits (107), Expect = 6e-06
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 39  VRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGF 98
           +R +P+ +     +P   +Y+  ++P      ++S+       K          G  +G 
Sbjct: 10  IRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQ 69

Query: 99  GFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 136
            F  F + E   +AL L+N + + G+   L ++    +
Sbjct: 70  AFITFPNKEIAWQALHLVNGYKLYGKI--LVIEFGKNK 105

>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 = 44.5 bits (106), Expect = 6e-06
 Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 16/108 (14%)

Query: 31  VRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP 90
           +R           LP       P    ++G +      + +    +    + + +  + P
Sbjct: 1   MRGSHHHHHHRSRLPK-----SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP 54

Query: 91  SN-GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM---LKVDQAT 134
           SN    KGFG+ EFE  + +L AL L      + + L    ++VD A 
Sbjct: 55  SNPERLKGFGYAEFEDLDSLLSALSL------NEESLGNRRIRVDVAD 96

>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 = 45.1 bits (107), Expect = 7e-06
 Identities = 17/115 (14%), Positives = 33/115 (28%), Gaps = 2/115 (1%)

Query: 22  RPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTV 81
             P             + R            P   + V  ++       +  V    G +
Sbjct: 14  LVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPI 73

Query: 82  KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 136
                     +   +GF F  FE+ +    A    N   +DG+   ++VD +  +
Sbjct: 74  ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR--IRVDFSITK 126

>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 = 46.9 bits (111), Expect = 7e-06
 Identities = 26/209 (12%), Positives = 57/209 (27%), Gaps = 27/209 (12%)

Query: 5   AFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAP 64
           +         G++P  +      IPG+                       + + V  + P
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGRIAIPGLAGA------------------GNSVLLVSNLNP 44

Query: 65  -TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG 123
                  +  +  V G V+  K          K     +         A+  LN   + G
Sbjct: 45  ERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAMSHLNGHKLHG 99

Query: 124 QELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSP--EN 181
           + + + + +     L R   +    TK    +      K   S        P+ +    N
Sbjct: 100 KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK-PGSKNFQNIFPPSATLHLSN 158

Query: 182 LKDNETGNKESHDPTNFGVVTEEDRKADQ 210
           +  + +        ++ G V +  +   +
Sbjct: 159 IPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187

>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 = 46.6 bits (110), Expect = 8e-06
 Identities = 15/133 (11%), Positives = 30/133 (22%), Gaps = 15/133 (11%)

Query: 13  PVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTK-----------VYVGK 61
            + V  S     +PG            +            P+             ++   
Sbjct: 71  KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFN 130

Query: 62  IAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI 121
                  +    +    G  +      +         G  E++S    L  L  LN + +
Sbjct: 131 APLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQM 190

Query: 122 DGQ----ELMLKV 130
                     LK+
Sbjct: 191 KNPNGPYPYTLKL 203

>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 = 44.6 bits (106), Expect = 8e-06
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT--PKGFGFCEFESAEGV 109
               K+++G +    +   + +V    G +          + T   +GF F  FE+    
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISE---VLLIKDRTSKSRGFAFITFENPADA 61

Query: 110 LRALRLLNKFNIDGQELMLKVDQATR 135
             A + +N  ++ G+   +KV+QA +
Sbjct: 62  KNAAKDMNGKSLHGKA--IKVEQAKK 85

>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 = 44.6 bits (106), Expect = 9e-06
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
             E+  T +Y+  +  + D   + ++LK  G V S  R    S+GT +G GF   ES E 
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTEK 78

Query: 109 VLRALRLLNKFNIDGQEL 126
               +   N   I     
Sbjct: 79  CEAVIGHFNGKFIKTPPG 96

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 44.2 bits (105), Expect = 9e-06
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 8/83 (9%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
            +++++VG + P    + +  + +  G                KGFGF   E+      A
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGE---VFIH---KDKGFGFIRLETRTLAEIA 67

Query: 113 LRLLNKFNIDGQELMLKVDQATR 135
              L+   + G++  L+V  A  
Sbjct: 68  KVELDNMPLRGKQ--LRVRFACH 88

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 43.7 bits (104), Expect = 9e-06
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 10/80 (12%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            K+++G +   A    + S+ +  G V              K +GF   E       A+R
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECD--------IIKNYGFVHIEDKTAAEDAIR 60

Query: 115 LLNKFNIDGQELMLKVDQAT 134
            L+ + + G    + V+ + 
Sbjct: 61  NLHHYKLHGVN--INVEASK 78

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 45.1 bits (107), Expect = 9e-06
 Identities = 23/129 (17%), Positives = 37/129 (28%), Gaps = 9/129 (6%)

Query: 7   PPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTA 66
                  +    S       G    R  M     P       P  +  T + V  +    
Sbjct: 7   HHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPP-------PDVEGMTSLKVDNLTYRT 59

Query: 67  DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 126
             D +  V +  G V      +       +GF F  F        A+  ++   +DG+E 
Sbjct: 60  SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE- 118

Query: 127 MLKVDQATR 135
            L+V  A  
Sbjct: 119 -LRVQMARY 126

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 19/104 (18%), Positives = 41/104 (39%), Gaps = 15/104 (14%)

Query: 47  VTPAEKPQTKVYVGKIAPTADSD-------FVLSVLKVCGTVKSWKRAQYP-SNGTPKGF 98
              A+   + + V  + P    D        +  +    G + +     YP  +G  KG+
Sbjct: 8   PQEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITN---DFYPEEDGKTKGY 63

Query: 99  GFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYV 142
            F E+ S    + A++  + + +D Q    +V+  T    ++Y+
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQH-TFRVNLFTD--FDKYM 104

>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 = 44.5 bits (105), Expect = 1e-05
 Identities = 15/97 (15%), Positives = 34/97 (35%), Gaps = 3/97 (3%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
            + +        V +  +      + ++        V +         G   G  F +F 
Sbjct: 33  GSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFA 92

Query: 105 SAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERY 141
           S E   +AL   +K  I  +   ++V ++++E +  Y
Sbjct: 93  SQELAEKALG-KHKERIGHRY--IEVFKSSQEEVRSY 126

>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 = 44.3 bits (105), Expect = 1e-05
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
                ++V  +   A  + +       G +K+         G  KG+   E+E+ +    
Sbjct: 20  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 79

Query: 112 ALRLLNKFNIDGQELMLKVDQAT 134
           A+  LN  ++ GQ   + VD   
Sbjct: 80  AMEGLNGQDLMGQP--ISVDWCF 100

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 3/97 (3%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
               +    VY+  +   A++  V+   K    V+      Y  NG   G GF EF +  
Sbjct: 19  RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 78

Query: 108 GVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDK 144
               AL   +K  +  +   ++V   T++ +   +D 
Sbjct: 79  DYKAALC-RHKQYMGNRF--IQVHPITKKGMLEKIDM 112

>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 = 42.9 bits (102), Expect = 2e-05
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
            +YVG +  +A S+ V  +    G V + K         PKGFGF E +       A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAK 61

Query: 116 LNKFNIDGQELMLKVDQA 133
           L+  +  G+   ++V +A
Sbjct: 62  LDNTDFMGRT--IRVTEA 77

>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 = 43.4 bits (103), Expect = 2e-05
 Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             V+VG I    D   + S     G+VK  K     + G  KG+GF  F +   V + + 
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68

Query: 115 LLNKFNIDGQELMLKVDQATR 135
             ++ N  G+   LK+  A R
Sbjct: 69  --SQINFHGK--KLKLGPAIR 85

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 16/76 (21%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 56  KVYVGKIAPTADSD-----FVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
           ++YVG I      +     F   +     T               K F F EF S +   
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 111 RALRLLNKFNIDGQEL 126
           +A+   +     GQ L
Sbjct: 68  QAMA-FDGIIFQGQSL 82

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 10/86 (11%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
            + K  TK++VG I+PT  +  + +  +  G V              K + F   E AE 
Sbjct: 5   SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAED 56

Query: 109 VLRALRLLNKFNIDGQELMLKVDQAT 134
            + A+R L+     G+   + V  +T
Sbjct: 57  AVEAIRGLDNTEFQGKR--MHVQLST 80

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN-GTPKGFGFCEFESA 106
           T  +    +++V  I        +  +    G +      +   N    KGFGF  FE++
Sbjct: 23  TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD---VEIIFNERGSKGFGFVTFENS 79

Query: 107 EGVLRALRLLNKFNIDGQELMLKVDQAT 134
               RA   L+   ++G++  ++V+ AT
Sbjct: 80  ADADRAREKLHGTVVEGRK--IEVNNAT 105

>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 = 44.1 bits (105), Expect = 3e-05
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
             +    K++VG I P              GT+   +       G  +GFGF  ++SA+ 
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 109 VLRALRLLNKFNIDGQELMLK 129
           V R        +   +++ +K
Sbjct: 142 VDRVC-QNKFIDFKDRKIEIK 161

>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 = 42.6 bits (101), Expect = 3e-05
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
           P   ++V  ++     +   ++ +        +       G+ KGFGF +F S E    A
Sbjct: 14  PSKTLFVKGLSEDTTEE---TLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70

Query: 113 LRLLNKFNIDGQELMLKVDQAT 134
              +    IDG +  + +D A 
Sbjct: 71  KEAMEDGEIDGNK--VTLDWAK 90

>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 = 42.8 bits (101), Expect = 3e-05
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 50  AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 109
               +   ++  I  +     VL  L+     ++       +NG   G    +F++ +  
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 110 LRALRLLNKFNIDGQELMLKVDQATRE 136
            ++ R L++  ++G+E    V   T E
Sbjct: 71  RKSER-LHRKKLNGRE--AFVHVVTLE 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 5/90 (5%)

Query: 47  VTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 106
             P  +   K+ +  I P    + + S+L   G V+S ++    S           + S 
Sbjct: 8   SVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSK 64

Query: 107 EGVLRALRLLNKFNIDGQELMLKVDQATRE 136
           +   +AL  LN F ++     LKV     E
Sbjct: 65  DQARQALDKLNGFQLENF--TLKVAYIPDE 92

>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 = 42.2 bits (100), Expect = 4e-05
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 4/81 (4%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             +YV  +    D + +       GT+ S K       G  KGFGF  F S E   +A+ 
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVT 73

Query: 115 LLNKFNIDGQELMLKVDQATR 135
            +N   +  +   L V  A R
Sbjct: 74  EMNGRIVATKP--LYVALAQR 92

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 43.8 bits (104), Expect = 5e-05
 Identities = 15/99 (15%), Positives = 35/99 (35%), Gaps = 1/99 (1%)

Query: 32  RPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS 91
           R + P             A     K++VG I    +   +    +  G ++  +      
Sbjct: 82  RVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG 141

Query: 92  NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 130
           +G  +GF F  F+  + V + + +     ++G    ++ 
Sbjct: 142 SGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRK 179

>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 = 44.9 bits (105), Expect = 5e-05
 Identities = 22/135 (16%), Positives = 38/135 (28%), Gaps = 6/135 (4%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           M      P    P G++P     P    PG  P    +   +P         P   +++ 
Sbjct: 154 MHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLT 213

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
            +    +   +  +       K  +              F EF++      A   L  F 
Sbjct: 214 NLPEETNELMLSMLFNQFPGFKEVRLVP-----GRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 121 IDGQELMLKVDQATR 135
           I     M K+  A +
Sbjct: 269 ITQNNAM-KISFAKK 282

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 41.8 bits (97), Expect = 5e-04
 Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 9/93 (9%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVL----KVCGTVKSWKRAQYPSNGTPKGFGFCEF 103
            P  +P   +Y+  +      D +   L       G +          +   +G  F  F
Sbjct: 3   VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIF 59

Query: 104 ESAEGVLRALRLLNKFNIDGQELMLKVDQATRE 136
           +       ALR +  F    +   +++  A  +
Sbjct: 60  KEVSSATNALRSMQGFPFYDKP--MRIQYAKTD 90

>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 = 41.9 bits (99), Expect = 6e-05
 Identities = 17/91 (18%), Positives = 28/91 (30%), Gaps = 8/91 (8%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
             V  +      VY G IA       +       G +      +       KG+ F  F 
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIME---IRVFPE---KGYSFVRFS 69

Query: 105 SAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
           + E    A+  +N   I+G   ++K      
Sbjct: 70  THESAAHAIVSVNGTTIEGH--VVKCYWGKE 98

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 8/72 (11%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           T+++V           +  +    G +K  K           GF F EFE AE   +A+ 
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVK--------ILNGFAFVEFEEAESAAKAIE 83

Query: 115 LLNKFNIDGQEL 126
            ++  +   Q L
Sbjct: 84  EVHGKSFANQPL 95

>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 = 40.7 bits (96), Expect = 1e-04
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 10/81 (12%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            K++VG ++    S  + S+ +  G V              K + F   E       A+ 
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 115 LLNKFNIDGQELMLKVDQATR 135
            LN   + G+   + V+ +T+
Sbjct: 62  QLNGKEVKGKR--INVELSTK 80

>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 = 42.1 bits (99), Expect = 1e-04
 Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 2/87 (2%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
              +  T + V  +      D +  V +  G V      +       +GF F  F     
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATR 135
              A+  ++   +DG+E  L+V  A  
Sbjct: 125 AEDAMDAMDGAVLDGRE--LRVQMARY 149

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 20/103 (19%), Positives = 35/103 (33%), Gaps = 9/103 (8%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
           +     VY+      A  D +   L+  G V + +  +   +   KG  F  F+S E   
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAK 66

Query: 111 RALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLK 153
           + +           +L++            Y  KK E  K+ K
Sbjct: 67  KFVE-TPGQKYKETDLLILFKDD-------YFAKKNEERKQNK 101

>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 = 40.7 bits (96), Expect = 1e-04
 Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 8/81 (9%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             +YV  +  +   + +             +          + + F  F + E  + A++
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMK 69

Query: 115 LLNKFNIDGQELMLKVDQATR 135
            LN   +DG    ++V  A  
Sbjct: 70  ALNGKVLDGSP--IEVTLAKP 88

>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 = 43.1 bits (102), Expect = 2e-04
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            +++VG +      +    + +  G            +   +GFGF   ES      A  
Sbjct: 23  CRLFVGNLPTDITEEDFKRLFERYGEPSE---VFINRD---RGFGFIRLESRTLAEIAKA 76

Query: 115 LLNKFNIDGQELMLKVDQATR 135
            L+   +  +   L++  AT 
Sbjct: 77  ELDGTILKSRP--LRIRFATH 95

>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 = 40.8 bits (96), Expect = 8e-04
 Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 5/77 (6%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               + V  ++P   ++ +       G V+          G   G GF EF +     +A
Sbjct: 95  HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVV-VDDRGRATGKGFVEFAAKPPARKA 153

Query: 113 LRLLNKFNIDGQELMLK 129
           L        DG  L+  
Sbjct: 154 LERCG----DGAFLLTT 166

>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 = 40.5 bits (95), Expect = 2e-04
 Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 6/88 (6%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGT----VKSWKRAQYPSNGTPKGFGFCEFESAEG 108
              ++++G I      + +L  +         V  +  A        +GF F E+ES   
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADK--MKNRGFAFVEYESHRA 64

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATRE 136
              A R L    I      + VD A  E
Sbjct: 65  AAMARRKLMPGRIQLWGHQIAVDWAEPE 92

>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 = 40.5 bits (95), Expect = 2e-04
 Identities = 14/92 (15%), Positives = 32/92 (34%), Gaps = 3/92 (3%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
           P       V +  +      + ++        V +         G   G  F +F S E 
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATREYLER 140
             +AL+  +K  I  +   +++ +++R  +  
Sbjct: 70  AEKALK-KHKERIGHRY--IEIFKSSRAEVRT 98

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 16/82 (19%)

Query: 44  LPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCE 102
           +P V P    + K            + +  +    G + +     YP  +G  KG+ F E
Sbjct: 9   VPQVGPDRLEKLK------------NVIHKIFSKFGKITN---DFYPEEDGKTKGYIFLE 53

Query: 103 FESAEGVLRALRLLNKFNIDGQ 124
           + S    + A++  + + +D Q
Sbjct: 54  YASPAHAVDAVKNADGYKLDKQ 75

>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 = 41.4 bits (97), Expect = 2e-04
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
                ++V  I   A  D +       G +K+         G  KG+   E+E+ +  L 
Sbjct: 70  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129

Query: 112 ALRLLNKFNIDGQELMLKVDQATRE 136
           A   LN   I GQ   ++VD    +
Sbjct: 130 AKEALNGAEIMGQ--TIQVDWCFVK 152

>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 = 41.8 bits (98), Expect = 3e-04
 Identities = 10/76 (13%), Positives = 26/76 (34%), Gaps = 4/76 (5%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
            P   +++  I P+   + +  +    G V    +         +     +  S E  ++
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQ 173

Query: 112 ALRLLNKFNIDGQELM 127
           AL  L+  ++     +
Sbjct: 174 ALIDLHNHDLGENHHL 189

>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 = 4e-04
 Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 3/83 (3%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
                + ++ +  +        +  + +      ++            G G  EF S E 
Sbjct: 23  KLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN---TRDFDGTGALEFPSEEI 79

Query: 109 VLRALRLLNKFNIDGQELMLKVD 131
           ++ AL  LN     G  + ++ D
Sbjct: 80  LVEALERLNNIEFRGSVITVERD 102

>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 = 39.4 bits (92), Expect = 4e-04
 Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 7/88 (7%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
           P+ + + +V V  + P+     +   ++  G V         ++    G G  EF   E 
Sbjct: 10  PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKED 62

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATRE 136
           +  A+R L+       E      +   +
Sbjct: 63  MTYAVRKLDNTKFRSHEGETAYIRVKVD 90

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
             +K  T +YVG +  T     + +     G +++            +   F +F + + 
Sbjct: 7   GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQA 60

Query: 109 VLRAL-RLLNKFNIDGQELMLK 129
              A  +  NK  ++G+ L +K
Sbjct: 61  AEVAAEKSFNKLIVNGRRLNVK 82

>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 = 40.2 bits (94), Expect = 5e-04
 Identities = 12/88 (13%), Positives = 28/88 (31%), Gaps = 3/88 (3%)

Query: 36  PPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP 95
             + R       T        V++  +   A  + + +       V+     +   +G  
Sbjct: 28  QQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRV 85

Query: 96  KGFGFCEFESAEGVLRALRLLNKFNIDG 123
            G    EF + E  + A+   ++ N+  
Sbjct: 86  TGEADVEFATHEEAVAAMS-KDRANMQH 112

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           KVYVG +   A    +       G +++   A       P GF F EFE       A+R 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRG 56

Query: 116 LNKFNIDGQELMLKVDQA 133
           L+   I G    ++V+ +
Sbjct: 57  LDGKVICGSR--VRVELS 72

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 7/72 (9%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           + + V  +   ++   V  +LK           +Y      K   F    + E    A++
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 115 LLNKFNIDGQEL 126
           + ++++  G++L
Sbjct: 59  MFHQYSFRGKDL 70

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 41.7 bits (97), Expect = 7e-04
 Identities = 19/119 (15%), Positives = 52/119 (43%), Gaps = 5/119 (4%)

Query: 327 ERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDE 386
           E  R+ + +    ++ + + +       Y   E ++     + ++KE E ++       E
Sbjct: 296 ELYRRCKLEEMGFKDTDPDSKPFSLQETY---EAKRNEFLGELQKKEEEMRQMFVQRVKE 352

Query: 387 EEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVRE-EEEIAVAKRRAEEEQLQQQQR 444
           +E E    ++       ++ +K  +++++ L D+ +  ++E+   K+R    +L Q Q 
Sbjct: 353 KEAELKEAEK-ELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQG 410

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12 Length = 430

 Score = 41.6 bits (98), Expect = 8e-04
 Identities = 22/131 (16%), Positives = 45/131 (34%), Gaps = 7/131 (5%)

Query: 301 RGRDKERDLKRE----KEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYR 356
             +D    L+ E    K +    ++ + E+   +   E  R  EE     +      EY 
Sbjct: 127 SYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQY---KKEYE 183

Query: 357 EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEED 416
           E + + E+  +   E  + R+R    L   +    +   +  R    ++   R      +
Sbjct: 184 ELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLFQGPRGSRYDEAEGRFEVINNE 243

Query: 417 LADEVREEEEI 427
                 EE++I
Sbjct: 244 TEQLKAEEKKI 254

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	771
3v53_A	119	RNA-binding protein 25; PWI, RNA-binding domain; 2	100.0
1mp1_A	111	Ser/Arg-related nuclear matrix protein; four helix	99.86
1x4q_A	92	U4/U6 small nuclear ribonucleoprotein PRP3; PWI do	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.7
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.69
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.65
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.65
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.65
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.64
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.6
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.6
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.6
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.6
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.6
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.6
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.59
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.59
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.58
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.58
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.58
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.58
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.57
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.57
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.57
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.57
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.57
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.56
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.56
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.56
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.56
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.56
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.56
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.56
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.56
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.56
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.56
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.56
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.56
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.55
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.55
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.55
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.55
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.54
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.54
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.54
2div_A	99	TRNA selenocysteine associated protein; structural	99.54
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.54
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.54
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.54
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.54
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.54
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.54
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.53
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.53
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.53
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.52
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.52
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.52
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.52
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.52
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.52
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.52
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.52
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.52
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.52
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.52
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.52
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.52
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.51
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.51
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.51
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.51
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.51
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.51
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.51
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.51
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.5
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.5
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.5
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.5
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.5
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.5
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.5
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.49
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.49
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.48
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.48
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.48
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.48
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.48
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.47
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.47
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.47
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.47
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.47
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.47
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.47
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.47
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.46
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.46
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.46
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.46
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.46
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.45
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.45
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.45
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.45
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.45
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.44
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.44
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.44
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.44
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.44
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.43
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.43
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.42
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.42
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.42
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.42
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.42
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.41
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.41
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.41
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.41
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.41
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.41
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.41
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.41
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.41
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.41
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.4
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.39
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.38
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.38
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.08
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.38
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.38
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.38
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.38
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.38
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.37
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.37
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.36
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.36
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.35
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.35
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.35
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.34
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.34
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.34
1x5p_A	97	Negative elongation factor E; structure genomics,	99.33
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.33
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.32
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.32
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.32
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.31
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.31
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.31
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.31
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.31
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.3
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.29
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.29
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.28
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.28
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.28
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.28
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.28
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.27
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.26
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.26
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.26
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.25
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.25
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.24
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.24
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.24
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.23
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.22
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.2
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.19
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.19
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.12
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.11
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.07
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.06
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.03
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.03
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.98
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.98
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.96
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.82
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.72
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.71
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.69
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.63
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.41
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.15
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.59
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.62
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	94.65
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.42
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	93.1
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	92.51
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	91.96
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	91.03
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	87.87
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	85.76
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	84.04
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	81.17

>3v53_A RNA-binding protein 25; PWI, RNA-binding domain; 2.90A {Homo sapiens}

Probab=100.00  E-value=7.3e-38  Score=287.90  Aligned_cols=107  Identities=44%  Similarity=0.875  Sum_probs=101.7

Q ss_pred             hhHHhhhhcCCCCchhhhcccccccccchhhHhhhhhhhHHHHHHhhcCcchhHHHHHHHHhhhccCCHHHHHHHHHHhh
Q 004150          660 LDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTIL  739 (771)
Q Consensus       660 ~~~~~l~~~ip~~k~~lf~~~i~w~~~d~~~~~~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~~~~p~~l~~~l~~~l  739 (771)
                      .++++||++||++|++||+|+|+|++||.++|+++|+|||++||+||||++|++||+||+++|..|.+|+.|+++|++||
T Consensus        12 ~~~k~li~~IP~~Ke~Lf~~~i~W~~vd~~~i~~~lkPWI~kKI~E~LG~eEd~LVdfI~~~L~~~~~pk~l~~~L~~~L   91 (119)
T 3v53_A           12 KHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVL   91 (119)
T ss_dssp             HSSHHHHHHSCSSHHHHHHSCCCTTTSCHHHHHHTHHHHHHHHHHHHTC---CHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHhcccCChhhhhHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhccc
Q 004150          740 DDEAEMFVLKMWRMLIFEIKKVETGLA  766 (771)
Q Consensus       740 de~a~~fv~klWrllife~~~~~~gl~  766 (771)
                      |++|+.||.+||||||||+++++.||+
T Consensus        92 DeeA~~FV~kLWrlLIfe~ea~~~Gl~  118 (119)
T 3v53_A           92 DEEAEVFIVKMWRLLIYETEAKKIGLV  118 (119)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHHcCcc
Confidence            999999999999999999999999997

>1mp1_A Ser/Arg-related nuclear matrix protein; four helix bundle, RNA binding protein; NMR {Homo sapiens} SCOP: a.188.1.1

Probab=99.86  E-value=1.7e-22  Score=184.34  Aligned_cols=91  Identities=21%  Similarity=0.448  Sum_probs=83.0

Q ss_pred             CCchhhhcccccccccchhhHhhhhhhhHHHHHHhhcCcchhHHHHHHHHhhhc-cCCHHHHHHHHHHhhh-HHHHHHHH
Q 004150          671 KTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQD-HVKASQMLELLQTILD-DEAEMFVL  748 (771)
Q Consensus       671 ~~k~~lf~~~i~w~~~d~~~~~~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~-~~~p~~l~~~l~~~ld-e~a~~fv~  748 (771)
                      +.++.+|+++|||..|+..    .|+|||++||++|||++|++|||||+++|.. +.+|+.|+++|++||+ ++|..||.
T Consensus         5 ~kfp~~f~~kVD~~kV~l~----~ikpWI~kki~e~LG~EDdvlid~i~~~L~~~~~dpk~lqi~L~gFL~~e~a~~Fv~   80 (111)
T 1mp1_A            5 LKFAECLEKKVDMSKVNLE----VIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMG   80 (111)
T ss_dssp             CCCCSGGGGCCCTTTSCSG----GGHHHHHHHHHHHHSSCCSHHHHHHHHHTTSSSCCHHHHHHHHTTTSCSHHHHHHHH
T ss_pred             ccCCHHHhccccHHHhhHH----HHHHHHHHHHHHHcCCccHHHHHHHHHHhhccCCCHHHHHHHHHHHhCcccHHHHHH
Confidence            3467899999999999865    4799999999999999999999999999987 6899999999999999 99999999


Q ss_pred             HHHHHHHHHHHhhhhccc
Q 004150          749 KMWRMLIFEIKKVETGLA  766 (771)
Q Consensus       749 klWrllife~~~~~~gl~  766 (771)
                      +||+||||. .+...||.
T Consensus        81 eLW~LLi~a-q~~~~GIP   97 (111)
T 1mp1_A           81 ELWPLLLSA-QENIAGIP   97 (111)
T ss_dssp             HHHHHHHHH-TTSSSSCC
T ss_pred             HHHHHHHHh-hcCCcCcC
Confidence            999999975 67777775

>1x4q_A U4/U6 small nuclear ribonucleoprotein PRP3; PWI domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.9e-20  Score=165.16  Aligned_cols=73  Identities=22%  Similarity=0.369  Sum_probs=68.2

Q ss_pred             cchhhHh-hhhhhhHHHHHHhhcCcchhHHHHHHHHhhhccCCHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 004150          686 YDKHELH-ERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEI  758 (771)
Q Consensus       686 ~d~~~~~-~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~~~~p~~l~~~l~~~lde~a~~fv~klWrllife~  758 (771)
                      ||.+.++ +.|+|||++||++|||++|++||+||+++|..|.+|+.|+++|++|||++|+.||.+||+|||+-+
T Consensus         8 ~d~~kv~l~~lkpWI~kkv~e~LG~eD~~lVd~i~~~l~~~~dpk~l~~~L~~fLd~~a~~Fv~eLW~lL~~aq   81 (92)
T 1x4q_A            8 MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAVEEGR   81 (92)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHTTCCHHHHHHHHTTTTGGGTHHHHHHHHHHHHHHS
T ss_pred             ccchHHhHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Confidence            5555555 789999999999999999999999999999999999999999999999999999999999999765

>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=99.70  E-value=9e-17  Score=180.58  Aligned_cols=82  Identities=18%  Similarity=0.406  Sum_probs=78.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.|++.+|..+|+.||.|..|.|+.++.+|+++|||||+|.+.++|..||..|||+.|+|+.|.|.|+
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            45689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       180 ~~  181 (437)
T 3pgw_S          180 RG  181 (437)
T ss_pred             CC
Confidence            75

>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=99.69  E-value=9.5e-17  Score=144.22  Aligned_cols=82  Identities=21%  Similarity=0.323  Sum_probs=78.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            44689999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      .+
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            65

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.65  E-value=1.2e-15  Score=140.15  Aligned_cols=82  Identities=17%  Similarity=0.270  Sum_probs=78.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ee
Q 004150          130 VD  131 (771)
Q Consensus       130 ~a  131 (771)
                      |+
T Consensus       116 ~a  117 (118)
T 2khc_A          116 LK  117 (118)
T ss_dssp             EC
T ss_pred             ec
Confidence            86

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.65  E-value=6.8e-16  Score=150.13  Aligned_cols=83  Identities=23%  Similarity=0.344  Sum_probs=77.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G--~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...++|||||||+.+++.+|+.+|+.||  .|..|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             Eehhh
Q 004150          130 VDQAT  134 (771)
Q Consensus       130 ~a~~~  134 (771)
                      ++...
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98753

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.65  E-value=9.5e-16  Score=140.46  Aligned_cols=85  Identities=15%  Similarity=0.242  Sum_probs=80.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ++.++|||+|||+.+++.+|+.+|+.||.|.++.|+.++.||+++|||||+|.+.++|..||..|||..|+|+.|.|.++
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            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhHH
Q 004150          132 QATRE  136 (771)
Q Consensus       132 ~~~kk  136 (771)
                      .....
T Consensus        84 ~~~~~   88 (110)
T 3s8s_A           84 IKGQQ   88 (110)
T ss_dssp             STTHH
T ss_pred             CCCcH
Confidence            76543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.64  E-value=2.1e-15  Score=142.30  Aligned_cols=85  Identities=24%  Similarity=0.354  Sum_probs=80.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           49 PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        49 ~~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      +...+.++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34566899999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .++..
T Consensus       117 ~~a~~  121 (139)
T 1u6f_A          117 ALAAS  121 (139)
T ss_dssp             EESSC
T ss_pred             EECCC
Confidence            98875

>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=99.60  E-value=2.1e-15  Score=137.73  Aligned_cols=83  Identities=18%  Similarity=0.263  Sum_probs=78.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            345789999999999999999999999999999999999888999999999999999999999 8999999999999999


Q ss_pred             ehhh
Q 004150          131 DQAT  134 (771)
Q Consensus       131 a~~~  134 (771)
                      +...
T Consensus       101 a~~~  104 (114)
T 2cq4_A          101 SQAE  104 (114)
T ss_dssp             HHHH
T ss_pred             cCCC
Confidence            8753

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.60  E-value=7.3e-16  Score=138.25  Aligned_cols=87  Identities=17%  Similarity=0.203  Sum_probs=81.5

Q ss_pred             CCCCEEEEcCCCC------CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC-e
Q 004150           52 KPQTKVYVGKIAP------TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG-Q  124 (771)
Q Consensus        52 ~~~~tVfVgNLp~------~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G-r  124 (771)
                      ...++|||+|||+      .+++.+|+.+|+.||.|.++.++.++.||+++|||||+|.+.++|..||..|||..|+| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      99999999999999999999999998899999999999999999999999999999999 9


Q ss_pred             EEEEEEehhhHHHH
Q 004150          125 ELMLKVDQATREYL  138 (771)
Q Consensus       125 ~L~V~~a~~~kk~l  138 (771)
                      .|.|.++....+|.
T Consensus        84 ~l~V~~a~~~~~~~   97 (100)
T 3ns6_A           84 RLFLYTMKDVERYN   97 (100)
T ss_dssp             BCEEEESHHHHHHH
T ss_pred             EEEEEECchhhhhh
Confidence            99999998866654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.60  E-value=2.7e-15  Score=133.58  Aligned_cols=81  Identities=14%  Similarity=0.226  Sum_probs=76.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--------WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s--------~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ..+.++|||||||+.+++.+|+.+|+.||.|..        +.++.++.+|.++|||||+|.+.++|..|+..|||..|+
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            344789999999999999999999999999999        999999889999999999999999999999999999999


Q ss_pred             CeEEEEEEe
Q 004150          123 GQELMLKVD  131 (771)
Q Consensus       123 Gr~L~V~~a  131 (771)
                      |+.|.|.++
T Consensus        90 g~~l~V~~A   98 (99)
T 2la6_A           90 GNPIKVSFA   98 (99)
T ss_dssp             SSBCEEEEC
T ss_pred             CcEEEEEec
Confidence            999999986

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.60  E-value=2.1e-16  Score=139.65  Aligned_cols=81  Identities=21%  Similarity=0.343  Sum_probs=75.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEEEe
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELMLKVD  131 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G-~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L-ng~~I~Gr~L~V~~a  131 (771)
                      +++|||+|||+.+++++|+.+|+.|| .|.+++++.++.+|.++|||||+|.+.++|.+||..| |+..|+|+.|.|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 7999999999999999999999999999999999876 567899999999998


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      .+.
T Consensus        81 ~~~   83 (91)
T 2lxi_A           81 DPK   83 (91)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            763

>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=99.60  E-value=4e-15  Score=128.74  Aligned_cols=82  Identities=16%  Similarity=0.320  Sum_probs=76.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||..+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        84 ~~   85 (87)
T 3bs9_A           84 TR   85 (87)
T ss_dssp             C-
T ss_pred             CC
Confidence            65

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=6.6e-15  Score=129.39  Aligned_cols=82  Identities=15%  Similarity=0.229  Sum_probs=77.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .++.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..||+..|+|+.|.|.|
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            34578999999999999999999999999999999999988899999999999999999999999999999999999998


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +.
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.59  E-value=3.8e-15  Score=128.33  Aligned_cols=82  Identities=21%  Similarity=0.357  Sum_probs=77.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +.
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.59  E-value=4.7e-15  Score=127.13  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=76.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++..
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            36899999999999999999999999999999999988999999999999999999999999999999999999999875

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.59  E-value=2.3e-15  Score=134.66  Aligned_cols=83  Identities=19%  Similarity=0.370  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCc----eeCCe
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT--VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF----NIDGQ  124 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~--V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~----~I~Gr  124 (771)
                      ...-.||||+|||+.+|+++|+.+|+.||.  +..++++.|+.+|.++|||||+|.+.++|..||..|||.    .|+|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            345679999999999999999999999995  679999999999999999999999999999999999986    59999


Q ss_pred             EEEEEEehh
Q 004150          125 ELMLKVDQA  133 (771)
Q Consensus       125 ~L~V~~a~~  133 (771)
                      .|.|.|+..
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999864

>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=99.58  E-value=6.6e-15  Score=130.35  Aligned_cols=82  Identities=27%  Similarity=0.427  Sum_probs=78.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
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            46899999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      ..
T Consensus        81 ~~   82 (96)
T 2x1f_A           81 NS   82 (96)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=8.7e-15  Score=128.68  Aligned_cols=82  Identities=16%  Similarity=0.209  Sum_probs=77.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34578999999999999999999999999999999999988899999999999999999999999999999999999998


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +.
T Consensus        92 a~   93 (95)
T 2cqc_A           92 PS   93 (95)
T ss_dssp             CS
T ss_pred             cC
Confidence            75

>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=99.58  E-value=1.1e-14  Score=133.16  Aligned_cols=83  Identities=17%  Similarity=0.274  Sum_probs=78.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       102 a~~  104 (115)
T 2cpz_A          102 KRS  104 (115)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.58  E-value=6.3e-15  Score=132.28  Aligned_cols=83  Identities=20%  Similarity=0.401  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..||+..|+|+.|.|.+
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            34578999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        92 a~~   94 (105)
T 1x5u_A           92 ASA   94 (105)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            875

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=8.5e-15  Score=130.22  Aligned_cols=82  Identities=23%  Similarity=0.381  Sum_probs=77.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||. ||+..|+|+.|.|.+
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            4457899999999999999999999999999999999998899999999999999999999999 999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        86 a~~   88 (99)
T 2dgs_A           86 AEP   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.57  E-value=8.1e-15  Score=132.82  Aligned_cols=83  Identities=22%  Similarity=0.235  Sum_probs=78.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       103 a~~  105 (110)
T 1oo0_B          103 CFV  105 (110)
T ss_dssp             SEE
T ss_pred             ccc
Confidence            864

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=7.9e-15  Score=129.13  Aligned_cols=82  Identities=23%  Similarity=0.431  Sum_probs=78.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
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            45789999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        83 ~~   84 (95)
T 2dnz_A           83 TE   84 (95)
T ss_dssp             SC
T ss_pred             cc
Confidence            64

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.57  E-value=1.6e-14  Score=131.99  Aligned_cols=83  Identities=16%  Similarity=0.315  Sum_probs=79.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            45578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        92 a~~   94 (115)
T 2dgo_A           92 ATR   94 (115)
T ss_dssp             SSC
T ss_pred             ccC
Confidence            875

>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=99.57  E-value=6.1e-15  Score=134.24  Aligned_cols=84  Identities=23%  Similarity=0.428  Sum_probs=79.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.
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            34557899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus       102 ~a~~  105 (108)
T 2jrs_A          102 HVTE  105 (108)
T ss_dssp             CSCS
T ss_pred             Eccc
Confidence            8764

>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=1.3e-14  Score=128.94  Aligned_cols=83  Identities=16%  Similarity=0.256  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        85 a~~   87 (99)
T 1whw_A           85 STI   87 (99)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            875

>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=99.56  E-value=1.4e-14  Score=125.66  Aligned_cols=80  Identities=24%  Similarity=0.380  Sum_probs=75.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||. +++..|+|+.|.|.+
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            4567899999999999999999999999999999999998899999999999999999999997 688999999999987


Q ss_pred             e
Q 004150          131 D  131 (771)
Q Consensus       131 a  131 (771)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=6.3e-15  Score=132.01  Aligned_cols=83  Identities=20%  Similarity=0.326  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            44578999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        90 a~~   92 (103)
T 2dnm_A           90 ARY   92 (103)
T ss_dssp             CSS
T ss_pred             CCc
Confidence            865

>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=99.56  E-value=8.2e-15  Score=134.66  Aligned_cols=78  Identities=18%  Similarity=0.378  Sum_probs=73.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||||||+.+++.+|+.+|+.||.|.+|+|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.++..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5689999999999999999999999999999999983  55899999999999999999999999999999999998764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=7.1e-15  Score=132.19  Aligned_cols=82  Identities=17%  Similarity=0.187  Sum_probs=78.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|..+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            44689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       101 ~~  102 (106)
T 1p27_B          101 FV  102 (106)
T ss_dssp             EE
T ss_pred             cC
Confidence            64

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=9e-15  Score=130.61  Aligned_cols=83  Identities=20%  Similarity=0.354  Sum_probs=78.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..||+..|+|+.|.|.|
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            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        89 a~~   91 (102)
T 2cqb_A           89 AKP   91 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>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=1.1e-14  Score=130.38  Aligned_cols=83  Identities=18%  Similarity=0.292  Sum_probs=79.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            44578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        92 a~~   94 (103)
T 2cq0_A           92 AKP   94 (103)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            865

>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=99.56  E-value=2.1e-15  Score=132.31  Aligned_cols=80  Identities=19%  Similarity=0.296  Sum_probs=72.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G--~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .+|||||||+.+++.+|+.+|+.||  .|.++.++.++.+|+++|||||+|.+.++|..||..|||..|+|+.|.|.++.
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            5799999999999999999999999  99999999998899999999999999999999999999999999999999887


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      ..
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>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=2.1e-14  Score=127.91  Aligned_cols=82  Identities=17%  Similarity=0.358  Sum_probs=77.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..+.++.++ +|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        14 ~~~~~~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           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999996 999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        93 a~~   95 (100)
T 2do4_A           93 SNS   95 (100)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.56  E-value=1.4e-14  Score=131.05  Aligned_cols=83  Identities=18%  Similarity=0.348  Sum_probs=78.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC------CceeCCe
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN------KFNIDGQ  124 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln------g~~I~Gr  124 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..|.++.++.+|.++|||||+|.+.++|..||..||      +..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            3457899999999999999999999999999999999998899999999999999999999999999      9999999


Q ss_pred             EEEEEEehh
Q 004150          125 ELMLKVDQA  133 (771)
Q Consensus       125 ~L~V~~a~~  133 (771)
                      .|.|.++..
T Consensus        92 ~l~v~~a~~  100 (111)
T 1x4h_A           92 QLKVDLAVT  100 (111)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEEECCC
Confidence            999998865

>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=99.56  E-value=2.2e-15  Score=134.83  Aligned_cols=81  Identities=20%  Similarity=0.423  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~-~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ....++|||||||+.+++.+|+.+|+.|| |..+.++.++ .+|+++|||||+|.+.++|..|| .|||..|+|+.|.|.
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            34478999999999999999999999999 9999999987 58999999999999999999999 799999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus        94 ~a~~   97 (100)
T 2j76_E           94 VADQ   97 (100)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            9865

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=8e-15  Score=129.34  Aligned_cols=82  Identities=17%  Similarity=0.370  Sum_probs=78.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~-kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .+.++|||+|||+.+++.+|..+|+.||.|..+ .++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            357899999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        83 a~~   85 (96)
T 1x5t_A           83 AFK   85 (96)
T ss_dssp             SCC
T ss_pred             ecc
Confidence            865

>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=99.56  E-value=1.7e-14  Score=129.93  Aligned_cols=81  Identities=17%  Similarity=0.231  Sum_probs=77.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..+.++.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3557899999999999999999999999999999999996 999999999999999999999999999999999999998


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            74

>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=1.5e-14  Score=130.10  Aligned_cols=83  Identities=20%  Similarity=0.417  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec-CCCCCCceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQY-PSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d-~~tGk~kGfGFVeF~~~esA~~Al~~L-ng~~I~Gr~L~V  128 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..|.++.+ ..+|.++|||||+|.+.++|..||..| |+..|+|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            455789999999999999999999999999999999998 679999999999999999999999999 999999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus        92 ~~a~~   96 (107)
T 2cph_A           92 EWADS   96 (107)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            99875

>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=99.55  E-value=1.2e-14  Score=128.02  Aligned_cols=81  Identities=23%  Similarity=0.444  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++ +|.++|||||+|.+.++|..||..||+..|+|+.|.|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3457899999999999999999999999999999999996 599999999999999999999999999999999999998


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +.
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=99.55  E-value=1.1e-14  Score=130.90  Aligned_cols=83  Identities=17%  Similarity=0.281  Sum_probs=78.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee---CCeEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI---DGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I---~Gr~L~  127 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..||+..+   +|+.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            44578999999999999999999999999999999999988999999999999999999999999999988   899999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus        90 v~~a~~   95 (106)
T 2dgp_A           90 VKPADS   95 (106)
T ss_dssp             EEECCC
T ss_pred             EEECCc
Confidence            999875

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.4e-14  Score=129.42  Aligned_cols=83  Identities=18%  Similarity=0.356  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..||+..|+|+.|.|.+
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            44578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        89 a~~   91 (102)
T 1x5s_A           89 AGK   91 (102)
T ss_dssp             EEC
T ss_pred             CCC
Confidence            865

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.9e-14  Score=130.99  Aligned_cols=83  Identities=19%  Similarity=0.331  Sum_probs=78.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--------SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~--------s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|.        .+.++.++.+|.++|||||+|.+.++|..||..|||..|+
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            45578999999999999999999999999999        6999999889999999999999999999999999999999


Q ss_pred             CeEEEEEEehh
Q 004150          123 GQELMLKVDQA  133 (771)
Q Consensus       123 Gr~L~V~~a~~  133 (771)
                      |+.|.|.++..
T Consensus        92 g~~l~V~~a~~  102 (113)
T 2cpe_A           92 GSKLKVSLARK  102 (113)
T ss_dssp             TEECEEECSSC
T ss_pred             CCEEEEEECCC
Confidence            99999998765

>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=5.1e-14  Score=126.03  Aligned_cols=81  Identities=21%  Similarity=0.311  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..|.++.+.  +.++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            4557899999999999999999999999999999999984  34689999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        90 a~~   92 (103)
T 2cqi_A           90 ATT   92 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.54  E-value=6.5e-14  Score=131.60  Aligned_cols=82  Identities=21%  Similarity=0.356  Sum_probs=77.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.
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            34568999999999999999999999999999999999998899999999999999999999999999999999999998


Q ss_pred             Ee
Q 004150          130 VD  131 (771)
Q Consensus       130 ~a  131 (771)
                      |+
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.4e-14  Score=128.58  Aligned_cols=83  Identities=20%  Similarity=0.365  Sum_probs=78.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee-EEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE----
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK-SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE----  125 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~-s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~----  125 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|. .+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34578999999999999999999999999999 9999999889999999999999999999999999999999999    


Q ss_pred             EEEEEehh
Q 004150          126 LMLKVDQA  133 (771)
Q Consensus       126 L~V~~a~~  133 (771)
                      |.|.|+..
T Consensus        86 l~v~~a~~   93 (99)
T 2div_A           86 FKLNYATY   93 (99)
T ss_dssp             CCEEETTC
T ss_pred             EEEeecCC
Confidence            99988764

>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=2.5e-14  Score=128.41  Aligned_cols=82  Identities=21%  Similarity=0.352  Sum_probs=77.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC---eEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG---QELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G---r~L~  127 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..+.++.++ +|.++|||||+|.+.++|..||..|||..|.|   +.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3457899999999999999999999999999999999996 89999999999999999999999999999998   9999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.|+..
T Consensus        91 V~~a~~   96 (105)
T 2dnh_A           91 VKFADT   96 (105)
T ss_dssp             EEESCS
T ss_pred             EEECcc
Confidence            999875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.54  E-value=1e-13  Score=128.45  Aligned_cols=83  Identities=16%  Similarity=0.223  Sum_probs=78.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+. +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999997 99999999999999999999999999999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus       110 ~a~~  113 (124)
T 2kt5_A          110 LVAS  113 (124)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9865

>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=99.54  E-value=1.8e-14  Score=124.75  Aligned_cols=81  Identities=25%  Similarity=0.430  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC-CceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT-PKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk-~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..++|||+|||+.+++.+|..+|+.||.|..+.++.+..++. ++|||||+|.+.++|..|+..|||..|+|+.|.|.++
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            468999999999999999999999999999999999876665 8999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=1.5e-14  Score=128.20  Aligned_cols=82  Identities=20%  Similarity=0.405  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---CCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPS---NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~---tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.   +|.++|||||+|.+.++|..||..|||..|+|+.|.|
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            4578999999999999999999999999999999998865   5689999999999999999999999999999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .++..
T Consensus        83 ~~a~~   87 (98)
T 2cpf_A           83 RISER   87 (98)
T ss_dssp             ECSSC
T ss_pred             EEccC
Confidence            98865

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.54  E-value=1.7e-14  Score=131.35  Aligned_cols=83  Identities=20%  Similarity=0.322  Sum_probs=74.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..+ +..|+|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3456789999999999999999999999999999999999889999999999999999999999965 599999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus       100 ~a~~  103 (109)
T 2rs2_A          100 VAFP  103 (109)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            8865

>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=99.54  E-value=1.4e-14  Score=134.35  Aligned_cols=83  Identities=17%  Similarity=0.186  Sum_probs=78.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34478999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        99 a~~  101 (126)
T 3ex7_B           99 CFV  101 (126)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            864

>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=99.53  E-value=2.6e-14  Score=124.07  Aligned_cols=79  Identities=24%  Similarity=0.417  Sum_probs=75.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+ .|||..|+|+.|.|.++..
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            579999999999999999999999999999999999889999999999999999999999 8999999999999998764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2e-14  Score=130.76  Aligned_cols=81  Identities=19%  Similarity=0.243  Sum_probs=75.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||..+++.+|+.+|+.||.|..+.++.+.  +.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        26 ~~~~~~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           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4557899999999999999999999999999999999883  45899999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       104 a~~  106 (109)
T 2err_A          104 ATA  106 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=3.5e-14  Score=127.24  Aligned_cols=80  Identities=18%  Similarity=0.321  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|+.|| |..|.++.++.+|.++|||||+|.+.++|..|| .||+..|+|+.|.|.++
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            4478999999999999999999999997 999999999889999999999999999999999 79999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        91 ~~   92 (103)
T 2dng_A           91 EG   92 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.52  E-value=1.1e-14  Score=131.54  Aligned_cols=82  Identities=13%  Similarity=0.276  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 004150           51 EKPQTKVYVGKIAPTA------DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ  124 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~v------te~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr  124 (771)
                      ....++|||||||+.+      ++.+|+.+|+.||.|..|.++.  .+|.++|||||+|.+.++|..||..|||..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3447899999999999      7899999999999999999883  6899999999999999999999999999999998


Q ss_pred             -EEEEEEehhh
Q 004150          125 -ELMLKVDQAT  134 (771)
Q Consensus       125 -~L~V~~a~~~  134 (771)
                       .|.|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999988654

>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=99.52  E-value=3.8e-14  Score=138.19  Aligned_cols=83  Identities=22%  Similarity=0.235  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..|.|+.++.+|.++|||||+|.+..+|..||..|||..|+|+.|.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       149 a~~  151 (165)
T 1rk8_A          149 CFV  151 (165)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            875

>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=99.52  E-value=3.9e-14  Score=127.20  Aligned_cols=80  Identities=23%  Similarity=0.449  Sum_probs=75.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC-CCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN-GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~t-Gk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .+.++|||+|||+.+++.+|+.+|..|| |..|.++.++.+ |.++|||||+|.+.++|..|| .||+..|+|+.|.|.+
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            3468999999999999999999999999 999999999877 999999999999999999999 8999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        91 a~~   93 (104)
T 1wi8_A           91 ADQ   93 (104)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            865

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=5.9e-14  Score=128.46  Aligned_cols=82  Identities=18%  Similarity=0.290  Sum_probs=77.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..|.++.++.+|.++|||||+|.+.++|..||..|++ .|+|+.|.|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            45579999999999999999999999999999999999988999999999999999999999999998 89999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        93 a~~   95 (116)
T 2cqd_A           93 AYL   95 (116)
T ss_dssp             STT
T ss_pred             ccc
Confidence            864

>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=99.52  E-value=2.3e-14  Score=127.00  Aligned_cols=81  Identities=21%  Similarity=0.227  Sum_probs=76.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|..||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
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            44689999999999999999999999999998888888889999999999999999999999999999999999999987


Q ss_pred             h
Q 004150          132 Q  132 (771)
Q Consensus       132 ~  132 (771)
                      .
T Consensus        93 ~   93 (98)
T 2cqp_A           93 S   93 (98)
T ss_dssp             S
T ss_pred             C
Confidence            5

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.52  E-value=9.4e-15  Score=137.19  Aligned_cols=82  Identities=17%  Similarity=0.368  Sum_probs=77.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCc----eeCCe
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF----NIDGQ  124 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s--~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~----~I~Gr  124 (771)
                      ..+.++|||||||+.+++++|+.+|..||.|..  |+|+.++.+|+++|||||+|.+. +|..||..|||.    .|+|+
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            345789999999999999999999999999977  99999988999999999999999 999999999999    99999


Q ss_pred             EEEEEEehh
Q 004150          125 ELMLKVDQA  133 (771)
Q Consensus       125 ~L~V~~a~~  133 (771)
                      .|.|.++..
T Consensus        99 ~l~V~~a~~  107 (131)
T 2m2b_A           99 TINVEFAKG  107 (131)
T ss_dssp             CCCCEECCC
T ss_pred             EEEEEECCC
Confidence            999998875

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.52  E-value=3.1e-14  Score=124.51  Aligned_cols=81  Identities=25%  Similarity=0.419  Sum_probs=76.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+  +|.++|||||+|.+.++|..|+..||+..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999999884  899999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        83 a~~   85 (92)
T 2dgv_A           83 DRN   85 (92)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            865

>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=1.7e-14  Score=135.72  Aligned_cols=83  Identities=16%  Similarity=0.221  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44578999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       123 a~~  125 (129)
T 2kxn_B          123 SIT  125 (129)
T ss_dssp             CSS
T ss_pred             ecC
Confidence            865

>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=99.52  E-value=3.1e-14  Score=131.25  Aligned_cols=82  Identities=15%  Similarity=0.318  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..+.++.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999999996 999999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        83 a~~   85 (116)
T 2fy1_A           83 AKK   85 (116)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=9.4e-14  Score=124.32  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=75.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..|.++.+.  +.++|||||+|.+.++|..||..||+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC--CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4457899999999999999999999999999999999884  34899999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        90 a~~   92 (103)
T 2cq3_A           90 ATA   92 (103)
T ss_dssp             CCS
T ss_pred             ccc
Confidence            865

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=3.2e-14  Score=127.38  Aligned_cols=81  Identities=25%  Similarity=0.341  Sum_probs=76.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+  +|.++|||||+|.+.++|..||..||+..|+|+.|.|.|
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 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345789999999999999999999999999999999997  899999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        90 a~~   92 (103)
T 2d9p_A           90 AQR   92 (103)
T ss_dssp             CSS
T ss_pred             ecc
Confidence            875

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.5e-14  Score=131.01  Aligned_cols=80  Identities=18%  Similarity=0.160  Sum_probs=75.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||||||+.+++++|..+|+.||.|.+|.++.++. |.++|||||+|.+.++|..||. +++..|+|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4468999999999999999999999999999999999965 9999999999999999999999 9999999999999876


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            54

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.52  E-value=1.6e-14  Score=133.64  Aligned_cols=80  Identities=19%  Similarity=0.370  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.+++++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.++.
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            4689999999999999999999999999999999999889999999999999999999999 699999999999999876


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus       114 ~  114 (124)
T 2jwn_A          114 T  114 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.51  E-value=9.3e-14  Score=124.33  Aligned_cols=81  Identities=19%  Similarity=0.247  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..|.++.++.+|.++|||||+|.+.++|..||.  ++..|+|+.|.|.+
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            4557899999999999999999999999999999999998899999999999999999999998  57899999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        90 a~~   92 (103)
T 2cqg_A           90 PNS   92 (103)
T ss_dssp             CCT
T ss_pred             cCC
Confidence            865

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=6.9e-14  Score=127.33  Aligned_cols=82  Identities=17%  Similarity=0.286  Sum_probs=77.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..|.++.++ +|.++|||||+|.+.++|..||..||+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3457899999999999999999999999999999999995 799999999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        91 a~~   93 (114)
T 2do0_A           91 DER   93 (114)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            764

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.9e-14  Score=130.49  Aligned_cols=81  Identities=21%  Similarity=0.336  Sum_probs=76.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|..||.|..|.++.++.+|.++|||||+|.+.++|..||.. ++..|+|+.|.|.++
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            4468999999999999999999999999999999999988999999999999999999999996 999999999999988


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       104 ~~  105 (116)
T 1x4b_A          104 VA  105 (116)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=2.2e-14  Score=128.56  Aligned_cols=82  Identities=21%  Similarity=0.355  Sum_probs=77.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce-eCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKV-CGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN-IDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~-~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~-I~Gr~L~V  128 (771)
                      ..+.++|||+|||+.+++.+|..+|+. ||.|..+.++.++ +|.++|||||+|.+.++|..||..||+.. |+|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            345789999999999999999999999 9999999999997 99999999999999999999999999999 99999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .++..
T Consensus        85 ~~a~~   89 (104)
T 2dhg_A           85 SVAIP   89 (104)
T ss_dssp             CBCCC
T ss_pred             EEccC
Confidence            88764

>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=6.9e-14  Score=124.16  Aligned_cols=79  Identities=14%  Similarity=0.199  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~----~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ...++|||+|||+.+++.+|+    .+|+.||.|..+.++.++.+   +|||||+|.+.++|..||..|||..|+|+.|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            346899999999999999999    99999999999999988544   78999999999999999999999999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus        84 V~~a~~   89 (96)
T 2dgx_A           84 VSLATG   89 (96)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            999864

>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=3.7e-14  Score=127.38  Aligned_cols=82  Identities=20%  Similarity=0.297  Sum_probs=77.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..|.++.++.+|.++|||||+|.+.++|..||.. |+..|+|+.|.|.+
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            45578999999999999999999999999999999999988999999999999999999999997 99999999999988


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        92 a~~   94 (105)
T 2dh8_A           92 CTP   94 (105)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            764

>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=99.51  E-value=6.5e-14  Score=134.79  Aligned_cols=83  Identities=18%  Similarity=0.270  Sum_probs=79.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       147 a~~  149 (158)
T 2kn4_A          147 ARY  149 (158)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            875

>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=99.51  E-value=2e-14  Score=128.56  Aligned_cols=83  Identities=29%  Similarity=0.536  Sum_probs=78.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
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            34689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      ...
T Consensus        86 ~~~   88 (104)
T 1p1t_A           86 ASE   88 (104)
T ss_dssp             TCT
T ss_pred             CCc
Confidence            764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=7.2e-15  Score=126.88  Aligned_cols=80  Identities=18%  Similarity=0.292  Sum_probs=75.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+.
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            45789999999999999999999999999999999999889999999999999999999999999999999999888654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=9.8e-14  Score=121.42  Aligned_cols=80  Identities=16%  Similarity=0.226  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|+.+|+.| .|..+.++.+ .+|.++|||||+|.+.++|..||. |||..|+|+.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            4457899999999999999999999999 9999999999 799999999999999999999999 999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        84 a~~   86 (91)
T 2dgw_A           84 EKS   86 (91)
T ss_dssp             ESS
T ss_pred             CCc
Confidence            865

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.50  E-value=1.7e-14  Score=121.60  Aligned_cols=75  Identities=21%  Similarity=0.313  Sum_probs=72.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      +|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+. ||+..|+|+.|.|.++
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            58999999999999999999999999999999998899999999999999999999998 9999999999999875

>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=99.50  E-value=2.1e-14  Score=126.36  Aligned_cols=80  Identities=21%  Similarity=0.217  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.++|||+|||+.+++.+|+.+|..||.|..+.++.+..+|.++|||||+|.+.++|..||..||+..|+|+.|.|.++.
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            46899999999999999999999999999988888888899999999999999999999999999999999999998865

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.50  E-value=4.8e-14  Score=132.69  Aligned_cols=85  Identities=12%  Similarity=0.257  Sum_probs=75.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  126 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~----~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L  126 (771)
                      ..+.++|||||||+.+++++|+    .+|+.||.|..|.+.   .+|+++|||||+|.+.++|..||..|||..|.|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3447899999999999998765    799999999998774   378999999999999999999999999999999999


Q ss_pred             EEEEehhhHHHH
Q 004150          127 MLKVDQATREYL  138 (771)
Q Consensus       127 ~V~~a~~~kk~l  138 (771)
                      .|.|+......+
T Consensus       103 ~V~~a~~~~~~~  114 (127)
T 2a3j_A          103 VITFSETPQSQV  114 (127)
T ss_dssp             EEEECCCCCHHH
T ss_pred             EEEEccCcchhc
Confidence            999998754443

>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=99.50  E-value=9.3e-14  Score=133.85  Aligned_cols=83  Identities=20%  Similarity=0.292  Sum_probs=79.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..|.|+.++.++.++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       116 a~~  118 (156)
T 1h2v_Z          116 DAG  118 (156)
T ss_dssp             ESC
T ss_pred             CCC
Confidence            875

>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=99.50  E-value=2.1e-13  Score=123.43  Aligned_cols=80  Identities=19%  Similarity=0.357  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..|.+..   ++.++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999865   466899999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        96 a~~   98 (109)
T 1x4a_A           96 PRS   98 (109)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            865

>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=99.49  E-value=6.7e-14  Score=128.26  Aligned_cols=81  Identities=16%  Similarity=0.185  Sum_probs=75.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCe-eEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTV-KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V-~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.| ..|.|+.++ +|.++|||||+|.+.++|..||.. |+..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3457899999999999999999999999999 899999997 999999999999999999999995 9999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus        90 ~a~~   93 (114)
T 2cpy_A           90 VVTL   93 (114)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9865

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=1.7e-14  Score=121.95  Aligned_cols=76  Identities=22%  Similarity=0.359  Sum_probs=73.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..++ ..|+|+.|.|.++
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            579999999999999999999999999999999998899999999999999999999999898 9999999999886

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.48  E-value=9e-14  Score=128.47  Aligned_cols=81  Identities=17%  Similarity=0.150  Sum_probs=75.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT---VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~---V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.   |..|.++.++ +|+++|||||+|.+.++|..||. ||+..|+|+.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~-~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS-SSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC-CCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            345789999999999999999999999999   8999999996 49999999999999999999999 999999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus        92 V~~a~~   97 (118)
T 2db1_A           92 VFKSHR   97 (118)
T ss_dssp             EEEECH
T ss_pred             EEECCH
Confidence            998864

>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=99.48  E-value=6.3e-14  Score=126.59  Aligned_cols=82  Identities=17%  Similarity=0.274  Sum_probs=76.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEe-ecCCCCCCceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRA-QYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELM  127 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~-V~s~kiv-~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln--g~~I~Gr~L~  127 (771)
                      .+.++|||+|||+.+++++|+.+|..||. |..+.++ .+..+|.++|||||+|.+.++|..|+..||  ++.|+|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45789999999999999999999999998 9999998 777889999999999999999999999996  5999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.|+..
T Consensus        86 V~~a~~   91 (109)
T 2dis_A           86 VDWAEP   91 (109)
T ss_dssp             EEESCS
T ss_pred             EEEcCC
Confidence            999865

>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=1.9e-13  Score=124.52  Aligned_cols=82  Identities=26%  Similarity=0.356  Sum_probs=76.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee--------C
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI--------D  122 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I--------~  122 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|..+.++.++ +|.++|||||+|.+.++|..||..|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            4457899999999999999999999999999999999996 999999999999999999999999999999        5


Q ss_pred             CeEEEEEEehh
Q 004150          123 GQELMLKVDQA  133 (771)
Q Consensus       123 Gr~L~V~~a~~  133 (771)
                      ++.|.|.|+.+
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            78899998864

>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=99.48  E-value=4.1e-14  Score=145.80  Aligned_cols=82  Identities=18%  Similarity=0.284  Sum_probs=77.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCG--TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G--~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..++|||+||++.+++.+|+.+|+.||  .|..|.|+.++.+|+++|||||+|.+.++|..||..||+..|+|+.|.|.+
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            578999999999999999999999999  999999999989999999999999999999999999999999999999999


Q ss_pred             ehhh
Q 004150          131 DQAT  134 (771)
Q Consensus       131 a~~~  134 (771)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.48  E-value=1.3e-14  Score=129.37  Aligned_cols=81  Identities=21%  Similarity=0.360  Sum_probs=74.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|.. .++.+..+|.++|||||+|.+.++|..||. |||..|+|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            344789999999999999999999999999888 666766789999999999999999999999 999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        92 a~~   94 (101)
T 1fj7_A           92 PKG   94 (101)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            865

>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=99.47  E-value=1.5e-14  Score=126.24  Aligned_cols=79  Identities=25%  Similarity=0.404  Sum_probs=74.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehhh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQAT  134 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~~  134 (771)
                      ++|||||||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.+ |..|+..|||..|+|+.|.|.++...
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            68999999999999999999999999999999999889999999999999999 99999999999999999999998764

>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=99.47  E-value=5.3e-14  Score=130.72  Aligned_cols=83  Identities=20%  Similarity=0.246  Sum_probs=75.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|..+|..||.|..+.++.+..+|.++|||||+|.+.++|..||. ||+..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999999886666666799999999999999999999999 999999999999999


Q ss_pred             ehhh
Q 004150          131 DQAT  134 (771)
Q Consensus       131 a~~~  134 (771)
                      +...
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8763

>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=5.1e-14  Score=124.40  Aligned_cols=83  Identities=13%  Similarity=0.306  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  126 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~----~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L  126 (771)
                      ..+.++|||+|||+.+++.+|+    .+|+.||.|..+.++.   +|.++|||||+|.+.++|..|+..|||..|+|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            4457899999999999999999    9999999999998874   57888999999999999999999999999999999


Q ss_pred             EEEEehhhHH
Q 004150          127 MLKVDQATRE  136 (771)
Q Consensus       127 ~V~~a~~~kk  136 (771)
                      .|.++.....
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999876533

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.47  E-value=1.7e-13  Score=120.86  Aligned_cols=75  Identities=12%  Similarity=0.217  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..+.-||||||++.+++..|+.+|..||.|.+++++.      ++|||||+|.+.++|..|+..||+..|+|+.|.|+++
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            3467899999999999999999999999999999865      5799999999999999999999999999999999998


Q ss_pred             h
Q 004150          132 Q  132 (771)
Q Consensus       132 ~  132 (771)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.47  E-value=1.5e-13  Score=129.11  Aligned_cols=91  Identities=12%  Similarity=0.210  Sum_probs=78.9

Q ss_pred             CCEEEEcCC----CCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCC----HHH----HHHHHH--HhCCc
Q 004150           54 QTKVYVGKI----APTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFES----AEG----VLRALR--LLNKF  119 (771)
Q Consensus        54 ~~tVfVgNL----p~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~----~es----A~~Al~--~Lng~  119 (771)
                      ++.||||||    |+.+++..|+.+|+.||.|.+|.++.|+.||.++|||||+|.+    +..    |..|+.  .|+|.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            378999999    9999999999999999999999999999999999999999996    433    778887  78999


Q ss_pred             eeCCeEEEEEEehhh--HHHHHHHHHh
Q 004150          120 NIDGQELMLKVDQAT--REYLERYVDK  144 (771)
Q Consensus       120 ~I~Gr~L~V~~a~~~--kk~le~~k~k  144 (771)
                      .|+|+.|.|.++...  .++++....+
T Consensus        82 ~I~Gr~irV~ln~~g~~~~~~~~~i~~  108 (136)
T 2j8a_A           82 FIMGFKFEVILNKHSILNNIISKFVEI  108 (136)
T ss_dssp             EETTEEEEEEECCTTHHHHHHHHHHHH
T ss_pred             eecCcEEEEEECcccHHHHHHHHHHHH
Confidence            999999999998754  4566666543

>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=99.47  E-value=1.9e-13  Score=121.86  Aligned_cols=75  Identities=16%  Similarity=0.386  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      .++.++|||||||+ .+++.+|+.+|+.||.|..+.+.        +|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44578999999998 99999999999999999999883        5899999999999999999999999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus        91 ~a~~   94 (97)
T 2xnq_A           91 VSSS   94 (97)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            9864

>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=99.47  E-value=1.4e-13  Score=125.69  Aligned_cols=81  Identities=14%  Similarity=0.271  Sum_probs=74.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|..+|+.||.|..+.++.+   +.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            34689999999999999999999999999999999865   566899999999999999999999999999999999999


Q ss_pred             hhhH
Q 004150          132 QATR  135 (771)
Q Consensus       132 ~~~k  135 (771)
                      ....
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            8643

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.47  E-value=5.6e-14  Score=125.36  Aligned_cols=76  Identities=20%  Similarity=0.341  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||||||..+++.+|+.+|+.||.|..+.++      .++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            346899999999999999999999999999999987      34699999999999999999999999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.46  E-value=3.8e-13  Score=133.30  Aligned_cols=84  Identities=15%  Similarity=0.221  Sum_probs=78.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..|.++.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999996 99999999999999999999999999999999999999


Q ss_pred             Eehhh
Q 004150          130 VDQAT  134 (771)
Q Consensus       130 ~a~~~  134 (771)
                      |+...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            98753

>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=99.46  E-value=6.3e-14  Score=127.80  Aligned_cols=82  Identities=20%  Similarity=0.322  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|..+|..||.|..+.+..+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45789999999999999999999999999843322222237899999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       103 ~~  104 (115)
T 2cpx_A          103 KN  104 (115)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.46  E-value=4.5e-14  Score=121.21  Aligned_cols=73  Identities=15%  Similarity=0.334  Sum_probs=68.0

Q ss_pred             CCEEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCe-EE
Q 004150           54 QTKVYVGKIAPTA------DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ-EL  126 (771)
Q Consensus        54 ~~tVfVgNLp~~v------te~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr-~L  126 (771)
                      .++|||||||+.+      ++.+|+.+|+.||.|.++.++.  .+|.++|||||+|.+.++|..|+..|||..|+|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3789999999999      7799999999999999999873  6899999999999999999999999999999999 88


Q ss_pred             EE
Q 004150          127 ML  128 (771)
Q Consensus       127 ~V  128 (771)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>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=99.46  E-value=4.6e-14  Score=118.77  Aligned_cols=75  Identities=21%  Similarity=0.345  Sum_probs=71.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      +|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+. +++..|+|+.|.|.++
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            69999999999999999999999999999999998899999999999999999999999 5999999999999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.46  E-value=1.9e-13  Score=138.10  Aligned_cols=82  Identities=20%  Similarity=0.349  Sum_probs=77.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.+||||||||+.+++.+|+.+|+.||.|.+|+++.++.+|.++|||||+|.+.++|..||..||+..+.|+.|.|.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      ..
T Consensus        94 ~~   95 (213)
T 4f02_A           94 RD   95 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.45  E-value=1.8e-13  Score=124.73  Aligned_cols=82  Identities=18%  Similarity=0.274  Sum_probs=74.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeecCCCC---CCceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 004150           52 KPQTKVYVGKIAPTADSDFVL---SVLKVCGTVKSWKRAQYPSNG---TPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  125 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~---~lF~~~G~V~s~kiv~d~~tG---k~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~  125 (771)
                      ...++|||+|||+.+++++|.   .+|+.||.|..+.++.+..++   .++|||||+|.+.++|..||..|||..|+|+.
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            346799999999999999999   999999999999999886544   56699999999999999999999999999999


Q ss_pred             EEEEEehh
Q 004150          126 LMLKVDQA  133 (771)
Q Consensus       126 L~V~~a~~  133 (771)
                      |.|.|+..
T Consensus        93 l~V~~a~~  100 (111)
T 2cpi_A           93 LKASLGTT  100 (111)
T ss_dssp             EEEESCCC
T ss_pred             EEEEeccc
Confidence            99998865

>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=99.45  E-value=8.9e-13  Score=137.98  Aligned_cols=77  Identities=12%  Similarity=0.211  Sum_probs=71.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr~L~V~  129 (771)
                      ..+.++|||+|||..+++.+|+.+|+.||.|..+.++.+.     +|||||+|.+.++|..||..|||..|+ |+.|.|.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            4567899999999999999999999999999999998652     589999999999999999999999999 9999999


Q ss_pred             Eeh
Q 004150          130 VDQ  132 (771)
Q Consensus       130 ~a~  132 (771)
                      |+.
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            975

>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=99.45  E-value=4.8e-13  Score=121.24  Aligned_cols=75  Identities=21%  Similarity=0.285  Sum_probs=70.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC-----eEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG-----QEL  126 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G-----r~L  126 (771)
                      ...++|||+|||+.+++.+|+.+|..||.|..|.++.+       |||||+|.+.++|..||..||+..|+|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            34789999999999999999999999999999999876       899999999999999999999999999     999


Q ss_pred             EEEEehh
Q 004150          127 MLKVDQA  133 (771)
Q Consensus       127 ~V~~a~~  133 (771)
                      .|.++..
T Consensus        86 ~V~~a~~   92 (108)
T 1x4c_A           86 RVKVDGP   92 (108)
T ss_dssp             EEEESSC
T ss_pred             EEEeCCC
Confidence            9998875

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.45  E-value=2.1e-13  Score=124.13  Aligned_cols=77  Identities=22%  Similarity=0.325  Sum_probs=71.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||||||+.+++.+|+.+|+.||.|..+.++        +|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34557899999999999999999999999999999987        5899999999999999999999999999999999


Q ss_pred             Eehhh
Q 004150          130 VDQAT  134 (771)
Q Consensus       130 ~a~~~  134 (771)
                      ++...
T Consensus        99 ~a~~~  103 (108)
T 2jvo_A           99 YSKLP  103 (108)
T ss_dssp             SCSCC
T ss_pred             EecCC
Confidence            98653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.7e-13  Score=124.89  Aligned_cols=77  Identities=16%  Similarity=0.181  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln--g~~I~Gr~L~V  128 (771)
                      ..+.++|||+|||+.+++++|+.+|+.||.|.++.++.+      +|||||+|.+.++|..||..|+  +..|+|+.|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345789999999999999999999999999999999875      5999999999999999999886  47899999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus        87 ~~A~~   91 (105)
T 1sjq_A           87 QFSNH   91 (105)
T ss_dssp             CCCSS
T ss_pred             EEcCC
Confidence            98764

>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=1.9e-13  Score=123.24  Aligned_cols=81  Identities=15%  Similarity=0.105  Sum_probs=74.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS-WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s-~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ....++|||+|||+.+++.+|+.+|..||.|.. +.|+.+ .+|+++|||||+|.+.++|..||.. |+..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            345789999999999999999999999999987 888888 7999999999999999999999996 9999999999998


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus        90 ~~~~   93 (104)
T 1wg5_A           90 KSSR   93 (104)
T ss_dssp             EECT
T ss_pred             ECCH
Confidence            7653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.4e-13  Score=120.21  Aligned_cols=79  Identities=25%  Similarity=0.391  Sum_probs=72.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|..||.|   .++.+ .+|.++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4457999999999999999999999999987   56666 6899999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        88 a~~   90 (101)
T 2fc9_A           88 QGP   90 (101)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            865

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.44  E-value=6.3e-14  Score=132.74  Aligned_cols=83  Identities=18%  Similarity=0.270  Sum_probs=78.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       124 a~~  126 (135)
T 2lea_A          124 ARY  126 (135)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.44  E-value=4.5e-13  Score=121.08  Aligned_cols=78  Identities=13%  Similarity=0.163  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELM  127 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L--ng~~I~Gr~L~  127 (771)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+..|  ++..|+|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3455789999999999999999999999999999988764      699999999999999999976  57889999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.|+..
T Consensus        85 V~~a~~   90 (101)
T 2cq1_A           85 IQYSNH   90 (101)
T ss_dssp             EEECSC
T ss_pred             EEEcCc
Confidence            999864

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.1e-13  Score=120.52  Aligned_cols=80  Identities=20%  Similarity=0.356  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.|+   .+.++.+..+|.++|||||+|.+.++|..||..||+..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34578999999999999999999999774   677888878999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        89 a~~   91 (102)
T 2fc8_A           89 AKP   91 (102)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            875

>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=99.43  E-value=4.6e-13  Score=115.32  Aligned_cols=75  Identities=21%  Similarity=0.301  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L-ng~~I~Gr~L~V~  129 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+..| ++..|+|+.|.|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            345789999999999999999999999999999999874      589999999999999999988 9999999999999


Q ss_pred             Ee
Q 004150          130 VD  131 (771)
Q Consensus       130 ~a  131 (771)
                      |+
T Consensus        83 ~a   84 (85)
T 2ytc_A           83 WG   84 (85)
T ss_dssp             EC
T ss_pred             ec
Confidence            86

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.43  E-value=9.1e-14  Score=125.94  Aligned_cols=81  Identities=14%  Similarity=0.121  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT---VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~---V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.   |..+.++.++. |.++|||||+|.+.++|..||. ||+..|+|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            456789999999999999999999999998   89999999965 9999999999999999999999 999999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            998765

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.42  E-value=5e-13  Score=120.77  Aligned_cols=77  Identities=14%  Similarity=0.148  Sum_probs=70.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce--eCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN--IDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~--I~Gr~L~V  128 (771)
                      .+++++|||+|||+.+++.+|..+|+.||.|.++.++.+      +|||||+|.+.++|..|+..|++..  |+|+.|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            446789999999999999999999999999999998753      5899999999999999999998875  88999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .++..
T Consensus        92 ~~S~~   96 (100)
T 3r27_A           92 NYSTS   96 (100)
T ss_dssp             EECSC
T ss_pred             Eeccc
Confidence            99865

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.42  E-value=9e-13  Score=125.61  Aligned_cols=82  Identities=17%  Similarity=0.319  Sum_probs=78.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            44578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eh
Q 004150          131 DQ  132 (771)
Q Consensus       131 a~  132 (771)
                      +.
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            75

>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=2.4e-13  Score=129.40  Aligned_cols=81  Identities=15%  Similarity=0.120  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGT---VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~---V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.   |..+.++.++. |+++|||||+|.+.++|..||. ||+..|+|+.|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            455789999999999999999999999999   89999999965 9999999999999999999999 999999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            998754

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=4.7e-13  Score=118.70  Aligned_cols=77  Identities=17%  Similarity=0.285  Sum_probs=70.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|. +.++.    +.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3468999999999999999999999999996 66654    467899999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        92 ~~   93 (97)
T 2e5j_A           92 RQ   93 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.42  E-value=5.4e-13  Score=120.82  Aligned_cols=77  Identities=19%  Similarity=0.311  Sum_probs=72.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.|..|.++.+      +|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            345789999999999999999999999999999999875      58999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        96 a~~   98 (109)
T 1x4g_A           96 GKE   98 (109)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=6.5e-13  Score=121.68  Aligned_cols=78  Identities=17%  Similarity=0.110  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.+++.+|+.+|+.| .|..+.|+.++ +|+++|||||+|.+.++|..|| .||+..|+|+.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            35799999999999999999999999 89999999995 5999999999999999999999 599999999999998775


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        92 ~   92 (109)
T 2dnn_A           92 E   92 (109)
T ss_dssp             H
T ss_pred             c
Confidence            4

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.41  E-value=4.9e-13  Score=122.98  Aligned_cols=78  Identities=15%  Similarity=0.168  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G-~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...++|||+|||+.+++.+|+.+|+.|| .|..+.++.    +.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3468999999999999999999999999 899998854    35789999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       102 a~~  104 (111)
T 2jvr_A          102 DDN  104 (111)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            764

>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=99.41  E-value=3.3e-13  Score=122.37  Aligned_cols=76  Identities=12%  Similarity=0.112  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEE
Q 004150           52 KPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK--FNIDGQELML  128 (771)
Q Consensus        52 ~~~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng--~~I~Gr~L~V  128 (771)
                      .+.++|||+|||+ .+++.+|+.+|+.||.|.++.++.++      |||||+|.+.++|..||..||+  ..|+|+.|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            4578999999999 99999999999999999999998763      8999999999999999998886  4699999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .++..
T Consensus        87 ~~a~~   91 (102)
T 1x4d_A           87 HLSQK   91 (102)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            99875

>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=99.41  E-value=1.9e-13  Score=123.21  Aligned_cols=79  Identities=15%  Similarity=0.135  Sum_probs=72.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++++|+.+|..|| +..+.|+.++ +|+++|||||+|.+.++|..||. +|+..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3468999999999999999999999999 4599999996 99999999999999999999996 8999999999999876


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        90 ~~   91 (102)
T 1wez_A           90 ST   91 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.41  E-value=8.6e-13  Score=116.87  Aligned_cols=76  Identities=16%  Similarity=0.395  Sum_probs=70.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC--CeEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID--GQELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~--Gr~L~V~  129 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+..||+..|+  |+.|.|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            34689999999999999999999999999999988754      589999999999999999999999999  9999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      |+..
T Consensus        89 ~a~~   92 (97)
T 1why_A           89 FAKS   92 (97)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9865

>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=7.4e-14  Score=132.62  Aligned_cols=84  Identities=15%  Similarity=0.269  Sum_probs=73.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE--Ee---ecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWK--RA---QYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  125 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~k--iv---~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~  125 (771)
                      ..+.++|||||||+.+++.+|..+|+.||.|..+.  ++   ....+|.++|||||+|.+.++|..||..|||..|+|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            45578999999999999999999999999988751  11   11247999999999999999999999999999999999


Q ss_pred             EEEEEehhh
Q 004150          126 LMLKVDQAT  134 (771)
Q Consensus       126 L~V~~a~~~  134 (771)
                      |.|.++...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999998653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=5.6e-13  Score=116.48  Aligned_cols=75  Identities=19%  Similarity=0.395  Sum_probs=70.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++        +|||||+|.+.++|..|+..||+..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3457899999999999999999999999999999987        47999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        77 a~~   79 (90)
T 2dnq_A           77 SKN   79 (90)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            865

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.41  E-value=2.1e-13  Score=120.34  Aligned_cols=78  Identities=17%  Similarity=0.249  Sum_probs=71.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+     ..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4467899999999999999999999999988766     25789999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        88 a~~   90 (96)
T 1fjc_A           88 TGE   90 (96)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            864

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.41  E-value=1.7e-13  Score=122.38  Aligned_cols=80  Identities=26%  Similarity=0.377  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|..+|+.||.|..+.++.++ +|.++|||||+|.+.++|..|+.  ++..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            346899999999999999999999999999999999997 99999999999999999999999  999999999999988


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      ...
T Consensus        84 ~~~   86 (102)
T 2xs2_A           84 IRK   86 (102)
T ss_dssp             EEC
T ss_pred             CcC
Confidence            754

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=1.1e-12  Score=114.96  Aligned_cols=75  Identities=24%  Similarity=0.426  Sum_probs=70.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.        +||||+|.+.++|..|+..||+..|+|+.|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45578999999999999999999999999999999875        3999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        79 a~~   81 (92)
T 2dgt_A           79 STS   81 (92)
T ss_dssp             SSC
T ss_pred             ccC
Confidence            865

>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=99.40  E-value=1e-12  Score=125.38  Aligned_cols=81  Identities=16%  Similarity=0.318  Sum_probs=77.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
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            36899999999999999999999999999999999998899999999999999999999999999999999999999886


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        81 ~   81 (167)
T 1fxl_A           81 P   81 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.39  E-value=8.1e-13  Score=117.47  Aligned_cols=77  Identities=18%  Similarity=0.311  Sum_probs=71.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            345789999999999999999999999999999998764      58999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        86 a~~   88 (99)
T 2cpj_A           86 ACH   88 (99)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            865

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.5e-12  Score=113.76  Aligned_cols=75  Identities=17%  Similarity=0.322  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.        +||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34578999999999999999999999999999999874        3999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        78 a~~   80 (90)
T 2dnp_A           78 STK   80 (90)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            865

>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=99.38  E-value=9.1e-13  Score=126.07  Aligned_cols=78  Identities=24%  Similarity=0.382  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||||||+.+++.+|+.+|+.||.|.++.++.+     ++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            455789999999999999999999999999999999876     579999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       145 a~~  147 (150)
T 2i2y_A          145 SNG  147 (150)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.38  E-value=6.7e-13  Score=123.63  Aligned_cols=77  Identities=16%  Similarity=0.181  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln--g~~I~Gr~L~V  128 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+..|+  +..|+|+.|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345789999999999999999999999999999999875      5999999999999999999887  46899999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus       102 ~~a~~  106 (119)
T 2ad9_A          102 QFSNH  106 (119)
T ss_dssp             EECSS
T ss_pred             EEccC
Confidence            99864

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.08  E-value=3.6e-14  Score=130.06  Aligned_cols=82  Identities=13%  Similarity=0.220  Sum_probs=77.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKS--------WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  123 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s--------~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G  123 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..        +.++.++.+|.++|||||+|.+.++|..||..|||..|+|
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            45789999999999999999999999999998        8899988889999999999999999999999999999999


Q ss_pred             eEEEEEEehh
Q 004150          124 QELMLKVDQA  133 (771)
Q Consensus       124 r~L~V~~a~~  133 (771)
                      +.|.|.++..
T Consensus        85 ~~l~V~~a~~   94 (116)
T 2lcw_A           85 NPIKVSFATR   94 (116)
Confidence            9999998765

>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=99.38  E-value=1e-12  Score=125.83  Aligned_cols=81  Identities=16%  Similarity=0.343  Sum_probs=77.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|+|..|+|+.|.|.++.
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            47899999999999999999999999999999999998899999999999999999999999999999999999999886


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        82 ~   82 (168)
T 1b7f_A           82 P   82 (168)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.38  E-value=1.7e-12  Score=117.73  Aligned_cols=74  Identities=18%  Similarity=0.306  Sum_probs=68.9

Q ss_pred             CCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~-vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...++|||+|||+. +++.+|+.+|+.||.|..|.+        ++|||||+|.+.++|..||..||+..|+|+.|.|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34689999999999 999999999999999999988        358999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        97 a~~   99 (110)
T 1wf1_A           97 AGE   99 (110)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            863

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.38  E-value=4.4e-13  Score=119.49  Aligned_cols=74  Identities=27%  Similarity=0.408  Sum_probs=70.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ++|||+|||+.+++.+|+.+|+.||.|..+.++.+     ++|||||+|.+.++|..|+..|||..|+|+.|.|.++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   74 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTG   74 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccC
Confidence            58999999999999999999999999999999876     779999999999999999999999999999999999875

>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=99.38  E-value=2.1e-12  Score=115.81  Aligned_cols=74  Identities=15%  Similarity=0.404  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|..||.|..+.++.        +||||+|.+.++|..||..||+..|+|+.|.|.|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            4578999999999999999999999999999999874        59999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        81 ~~   82 (103)
T 2dgu_A           81 KP   82 (103)
T ss_dssp             CC
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=99.38  E-value=1.6e-12  Score=125.23  Aligned_cols=80  Identities=21%  Similarity=0.439  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||.|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            34789999999999999999999999999999999999889999999999999999999999999999999999999986

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=1e-12  Score=115.91  Aligned_cols=78  Identities=19%  Similarity=0.215  Sum_probs=70.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~-kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..+ .++.++.+|    +|||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346899999999999999999999999999999 487775443    399999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        89 a~~   91 (96)
T 2e44_A           89 IPD   91 (96)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            865

>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=99.37  E-value=5.8e-13  Score=121.70  Aligned_cols=76  Identities=12%  Similarity=0.073  Sum_probs=70.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..|.++.      ++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999999998864      4589999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        82 ~~   83 (111)
T 1whx_A           82 PI   83 (111)
T ss_dssp             ET
T ss_pred             CC
Confidence            64

>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=99.36  E-value=1.5e-12  Score=118.29  Aligned_cols=77  Identities=16%  Similarity=0.197  Sum_probs=69.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK--FNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng--~~I~Gr~L~V  128 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+..|++  ..|+|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345789999999999999999999999999999988764      58999999999999999998865  4599999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus        86 ~~a~~   90 (104)
T 1wex_A           86 NYSTS   90 (104)
T ss_dssp             EECSS
T ss_pred             EEccC
Confidence            99864

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=4.6e-12  Score=112.58  Aligned_cols=75  Identities=17%  Similarity=0.374  Sum_probs=69.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVC--GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~--G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.|  |.|..+.++        +|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3457899999999999999999999999  999998875        369999999999999999999999999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .++..
T Consensus        84 ~~a~~   88 (99)
T 2cpd_A           84 TLAKP   88 (99)
T ss_dssp             ECCCC
T ss_pred             EECCC
Confidence            98865

>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=99.35  E-value=1.1e-12  Score=120.92  Aligned_cols=77  Identities=13%  Similarity=0.228  Sum_probs=69.2

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~-vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln--g~~I~Gr~L~  127 (771)
                      ..+.++|||+|||+. +++.+|+.+|+.||.|..+.++..      +|||||+|.+.++|..||..|+  +..|+|+.|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            445789999999998 999999999999999999998753      5999999999999999999885  4569999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus        96 V~~a~~  101 (112)
T 1x4f_A           96 VDLSEK  101 (112)
T ss_dssp             EEEECS
T ss_pred             EEECcc
Confidence            999864

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.35  E-value=4.5e-12  Score=124.81  Aligned_cols=83  Identities=20%  Similarity=0.435  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       191 a~~  193 (198)
T 2yh0_A          191 ASV  193 (198)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            865

>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=99.35  E-value=2e-12  Score=127.17  Aligned_cols=82  Identities=20%  Similarity=0.353  Sum_probs=77.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..||. +++..|+|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHh-cCCCEECCEEeeeec
Confidence            4457899999999999999999999999999999999998899999999999999999999998 599999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        89 ~~~   91 (196)
T 1l3k_A           89 AVS   91 (196)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            765

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.34  E-value=1.1e-12  Score=116.15  Aligned_cols=75  Identities=17%  Similarity=0.407  Sum_probs=69.1

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ..+.++|||+|||+ .+++.+|..+|+.||.|..+.+.        +|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45588999999999 99999999999999999999884        4899999999999999999999999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus        79 ~a~~   82 (96)
T 2kvi_A           79 VSSS   82 (96)
T ss_dssp             EEEC
T ss_pred             EcCc
Confidence            9865

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=2.4e-12  Score=113.52  Aligned_cols=75  Identities=17%  Similarity=0.238  Sum_probs=67.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||||||+.+++.+|+.+|+.||.|..|  +.++.+|.   ||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            346799999999999999999999999999987  55555665   99999999999999999 9999999999999765


Q ss_pred             h
Q 004150          132 Q  132 (771)
Q Consensus       132 ~  132 (771)
                      .
T Consensus        80 ~   80 (94)
T 2e5g_A           80 E   80 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.34  E-value=2.2e-12  Score=113.21  Aligned_cols=75  Identities=15%  Similarity=0.332  Sum_probs=67.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCC-ceeCCeEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK-FNIDGQELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~-V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng-~~I~Gr~L~V~  129 (771)
                      .+.++|||+|||+.+++++|+.+|+.||. |..+.+.       ++|||||+|.+.++|..||..||| ..|+|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45689999999999999999999999999 5555553       358999999999999999999999 99999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus        79 ~a~~   82 (93)
T 2cqh_A           79 YSVS   82 (93)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            9865

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=7.3e-12  Score=110.99  Aligned_cols=75  Identities=15%  Similarity=0.278  Sum_probs=68.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+||  .+++.+|+.+|..||.|..|.+.      .++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345789999996  89999999999999999999884      4568999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        84 a~~   86 (97)
T 1x5p_A           84 ARK   86 (97)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            865

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.33  E-value=2.9e-12  Score=127.99  Aligned_cols=82  Identities=29%  Similarity=0.497  Sum_probs=78.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus       203 ~~  204 (216)
T 2qfj_A          203 VT  204 (216)
T ss_dssp             SS
T ss_pred             cC
Confidence            65

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.32  E-value=4e-12  Score=128.40  Aligned_cols=80  Identities=18%  Similarity=0.360  Sum_probs=74.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.+++.+|+.+|+.||.|..+.|+.+  .+.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d--~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE--TTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeecc--CCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999999998  35579999999999999999999999999999999999987


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      ..
T Consensus       180 ~~  181 (213)
T 4f02_A          180 SR  181 (213)
T ss_dssp             CH
T ss_pred             CC
Confidence            63

>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=99.32  E-value=2.8e-12  Score=111.75  Aligned_cols=75  Identities=15%  Similarity=0.298  Sum_probs=69.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|+.| .|..+.+.      .++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            356899999999999999999999999 99999884      56799999999999999999999999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        76 ~~   77 (88)
T 1wg1_A           76 PT   77 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.32  E-value=2e-12  Score=121.02  Aligned_cols=80  Identities=23%  Similarity=0.219  Sum_probs=72.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCe----eEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTV----KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V----~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|    ..+.|+.+ .+|+++|||||+|.+.++|..||. .|+..|+|+.|.
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~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALR-KHKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHT-TTTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHH-hCCCeeCCeEEE
Confidence            457899999999999999999999999875    68999998 599999999999999999999999 499999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |..+..
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            987753

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=2.7e-12  Score=117.46  Aligned_cols=78  Identities=21%  Similarity=0.328  Sum_probs=69.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC---CCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSN---GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~t---Gk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ...++|||||||+.+++.+|+.+|+.||.|. +.++.+..+   |.++|||||+|.+.++|..||..|+  .++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4578999999999999999999999999999 888887666   8999999999999999999999885  488888888


Q ss_pred             EEeh
Q 004150          129 KVDQ  132 (771)
Q Consensus       129 ~~a~  132 (771)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6443

>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=99.31  E-value=1.9e-12  Score=121.65  Aligned_cols=79  Identities=15%  Similarity=0.113  Sum_probs=71.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCee--EEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~--s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...++|||+|||+.+++.+|+.+|+.| .|.  .|.|+.++. |+++|||||+|.+.++|..||. +++..|+|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            456889999999999999999999999 577  899999964 9999999999999999999999 58899999999998


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      .+..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            7753

>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=99.31  E-value=1.9e-12  Score=124.04  Aligned_cols=80  Identities=21%  Similarity=0.382  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.++|||+|||+.+++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+. ++|..|+|+.|.|.|+.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            46799999999999999999999999999999999998899999999999999999999998 99999999999999986


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      +
T Consensus       165 p  165 (167)
T 2cjk_A          165 P  165 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.31  E-value=6.1e-12  Score=110.51  Aligned_cols=75  Identities=16%  Similarity=0.219  Sum_probs=62.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce--eCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN--IDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~--I~Gr~L~V  128 (771)
                      ..+.++|||||||+.+++++|+.+|+.||.|.++.++.+     ++|||||+|.+.++|..    |++..  ++|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            345789999999999999999999999999999999874     78999999999999873    45554  55999999


Q ss_pred             EEehhh
Q 004150          129 KVDQAT  134 (771)
Q Consensus       129 ~~a~~~  134 (771)
                      .++.+.
T Consensus        79 ~~a~~k   84 (89)
T 3d2w_A           79 SNAEPK   84 (89)
T ss_dssp             EECC--
T ss_pred             EEcCCC
Confidence            988764

>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=99.31  E-value=5.3e-12  Score=124.14  Aligned_cols=82  Identities=15%  Similarity=0.331  Sum_probs=75.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..+.++.+..+|.++|||||.|.+.++|.+||.. +|..|+|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            3468999999999999999999999999999999999988999999999999999999999984 899999999999998


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      ...
T Consensus       181 ~~k  183 (196)
T 1l3k_A          181 LSK  183 (196)
T ss_dssp             C--
T ss_pred             CCh
Confidence            864

>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=99.30  E-value=7.5e-12  Score=119.81  Aligned_cols=80  Identities=21%  Similarity=0.366  Sum_probs=75.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G--r~L~V~  129 (771)
                      .+.++|||+|||..+++.+|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|+|  +.|.|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            456899999999999999999999999999999999997799999999999999999999999999999988  999998


Q ss_pred             Ee
Q 004150          130 VD  131 (771)
Q Consensus       130 ~a  131 (771)
                      ||
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.29  E-value=6.1e-12  Score=119.79  Aligned_cols=78  Identities=19%  Similarity=0.290  Sum_probs=73.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ++|||+|||+.+++.+|..+|+.||.|.++.++.++ +|+++|||||+|.+.++|..|+..|||..|+|+.|.|.++..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCC
Confidence            589999999999999999999999999999999984 788999999999999999999999999999999999998754

>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=99.29  E-value=2.4e-12  Score=118.26  Aligned_cols=73  Identities=23%  Similarity=0.314  Sum_probs=65.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE-----EE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE-----LM  127 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~-----L~  127 (771)
                      ..++|||+|||+.+++.+|+.+|..||.|..|.++.+       |||||+|.+.++|..||..|||..|+|+.     |.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            4689999999999999999999999999999999875       89999999999999999999999999988     56


Q ss_pred             EEEeh
Q 004150          128 LKVDQ  132 (771)
Q Consensus       128 V~~a~  132 (771)
                      |..+.
T Consensus        88 v~~~~   92 (115)
T 3beg_B           88 VKVDG   92 (115)
T ss_dssp             EEECC
T ss_pred             eccCC
Confidence            65443

>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=99.28  E-value=1.1e-12  Score=125.41  Aligned_cols=80  Identities=14%  Similarity=0.126  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++++|+.+|+.|| |..+.|+.++ +|+++|||||+|.+.++|..|| .+|+..|+|+.|.|.+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~-~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS-SSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC-CCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999 7799999996 5999999999999999999999 6999999999999987


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       120 a~~  122 (139)
T 2hgn_A          120 NST  122 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.28  E-value=6.1e-12  Score=125.59  Aligned_cols=83  Identities=24%  Similarity=0.330  Sum_probs=75.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+|.++|||||.|.+.++|..||..||+..|+|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34689999999999999999999999999999999999889999999999999999999999999999999999999887


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      ...
T Consensus       106 ~~~  108 (216)
T 2qfj_A          106 SNI  108 (216)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            543

>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=99.28  E-value=7.7e-12  Score=107.93  Aligned_cols=71  Identities=24%  Similarity=0.418  Sum_probs=65.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVC----G-------TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  120 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~----G-------~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~  120 (771)
                      .+.++|||+|||+.+++.+|+.+|+.|    |       .|.++.+..+      +|||||+|.+.++|..|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       8999988754      599999999999999999 899999


Q ss_pred             eCCeEEEEE
Q 004150          121 IDGQELMLK  129 (771)
Q Consensus       121 I~Gr~L~V~  129 (771)
                      |+|+.|.|.
T Consensus        77 ~~g~~l~V~   85 (87)
T 2hzc_A           77 FQGQSLKIR   85 (87)
T ss_dssp             ETTEECEEE
T ss_pred             ECCeEEEEe
Confidence            999999986

>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=99.28  E-value=8.2e-12  Score=115.40  Aligned_cols=76  Identities=22%  Similarity=0.338  Sum_probs=68.4

Q ss_pred             CCCCEEEE--cCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee-----CCe
Q 004150           52 KPQTKVYV--GKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI-----DGQ  124 (771)
Q Consensus        52 ~~~~tVfV--gNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I-----~Gr  124 (771)
                      .+..+|||  |||++.+++++|+.+|+.||.|..+.++.+      +|||||+|.+.++|..|+..|||..|     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            44678999  889999999999999999999999887542      58999999999999999999999998     689


Q ss_pred             EEEEEEehh
Q 004150          125 ELMLKVDQA  133 (771)
Q Consensus       125 ~L~V~~a~~  133 (771)
                      .|.|.++..
T Consensus        97 ~l~v~~a~~  105 (114)
T 2cq2_A           97 TLYLNFVEK  105 (114)
T ss_dssp             ECEEEEESC
T ss_pred             EEEEEeccc
Confidence            999998764

>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=99.28  E-value=9.5e-12  Score=118.59  Aligned_cols=80  Identities=18%  Similarity=0.276  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE--EEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE--LMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~--L~V~  129 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|+|+.  |.|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            34688999999999999999999999999999999999889999999999999999999999999999999965  7777


Q ss_pred             Ee
Q 004150          130 VD  131 (771)
Q Consensus       130 ~a  131 (771)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>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=99.27  E-value=8e-12  Score=120.23  Aligned_cols=80  Identities=13%  Similarity=0.303  Sum_probs=74.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQELML  128 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~---Gr~L~V  128 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..+.++.+ .+|.++|||||+|.+.++|..|+..|||..+.   |+.|.|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC-TTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEEC-CCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            35789999999999999999999999999999999998 47999999999999999999999999998776   499999


Q ss_pred             EEeh
Q 004150          129 KVDQ  132 (771)
Q Consensus       129 ~~a~  132 (771)
                      .|++
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>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=99.26  E-value=1.2e-11  Score=125.23  Aligned_cols=77  Identities=22%  Similarity=0.235  Sum_probs=71.4

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIA-PTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp-~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .+.++|||+||| +.+++++|..+|+.||.|.+++++.+     .+|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            357899999999 89999999999999999999999875     369999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        77 s~~   79 (205)
T 3tyt_A           77 SKQ   79 (205)
T ss_dssp             CSC
T ss_pred             ccC
Confidence            754

>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=99.26  E-value=1.4e-11  Score=120.77  Aligned_cols=78  Identities=14%  Similarity=0.113  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLK  129 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G--r~L~V~  129 (771)
                      ....+|||+||++.+++++|+.+|+.||.|..+.++..    .++|||||+|.+.++|..|+..|||..|.|  +.|.|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34578999999999999999999999999999998654    357899999999999999999999999965  999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      |+..
T Consensus       120 ~Ak~  123 (164)
T 1sjr_A          120 FSKL  123 (164)
T ss_dssp             ECSS
T ss_pred             EecC
Confidence            9875

>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=99.26  E-value=9.1e-12  Score=119.32  Aligned_cols=79  Identities=24%  Similarity=0.408  Sum_probs=74.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +.++|||+|||+.+++.+|+.+|+.||.|.++.++.++.+|.++|||||.|.+.++|..|+.  ++..|+|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            46899999999999999999999999999999999998899999999999999999999998  4678999999998876


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
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=99.25  E-value=9.9e-12  Score=110.72  Aligned_cols=71  Identities=17%  Similarity=0.289  Sum_probs=63.7

Q ss_pred             CCE-EEEcCCCCCCCHHH----HHHHHHhc-CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           54 QTK-VYVGKIAPTADSDF----VLSVLKVC-GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        54 ~~t-VfVgNLp~~vte~~----L~~lF~~~-G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ..| |||+|||+.++.+.    |..+|+.| |.|..+       +|   |||||.|.+.++|.+|+..|+|..|.|+.|.
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            445 99999999999887    66899999 599887       34   9999999999999999999999999999999


Q ss_pred             EEEehhh
Q 004150          128 LKVDQAT  134 (771)
Q Consensus       128 V~~a~~~  134 (771)
                      |.++...
T Consensus        78 v~~A~~~   84 (96)
T 2diu_A           78 VSFTPKN   84 (96)
T ss_dssp             EESSCCS
T ss_pred             EEecCCC
Confidence            9988753

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.25  E-value=2.1e-11  Score=115.17  Aligned_cols=78  Identities=17%  Similarity=0.177  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGF-GFCEFESAEGVLRALRLLNKFNIDG--QELML  128 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGf-GFVeF~~~esA~~Al~~Lng~~I~G--r~L~V  128 (771)
                      .....|||+||++.++++.|..+|+.||.|.++.++..     .+|| |||+|.+.++|..|+..|||..|.|  +.|.|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            34568999999999999999999999999999988764     2577 9999999999999999999999988  89999


Q ss_pred             EEehhh
Q 004150          129 KVDQAT  134 (771)
Q Consensus       129 ~~a~~~  134 (771)
                      .|+...
T Consensus       101 ~~ak~~  106 (130)
T 3zzy_A          101 DFSKLT  106 (130)
T ss_dssp             EECSCS
T ss_pred             EecCCC
Confidence            998753

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.24  E-value=3.5e-11  Score=109.34  Aligned_cols=82  Identities=17%  Similarity=0.083  Sum_probs=72.8

Q ss_pred             CCCCEEEEcCCCC-----CCCHHHHHHHHHhcCCeeEEEEeecCC-CCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 004150           52 KPQTKVYVGKIAP-----TADSDFVLSVLKVCGTVKSWKRAQYPS-NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  125 (771)
Q Consensus        52 ~~~~tVfVgNLp~-----~vte~~L~~lF~~~G~V~s~kiv~d~~-tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~  125 (771)
                      .++++|+|.||..     ..++.+|+.+|++||.|.++.++.++. ++.++|||||+|.+.++|..|+..|||..++|+.
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            4578999999973     236789999999999999999998864 4789999999999999999999999999999999


Q ss_pred             EEEEEehh
Q 004150          126 LMLKVDQA  133 (771)
Q Consensus       126 L~V~~a~~  133 (771)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999875

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.24  E-value=4.9e-11  Score=111.83  Aligned_cols=74  Identities=20%  Similarity=0.177  Sum_probs=66.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGF-GFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  130 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGf-GFVeF~~~esA~~Al~~Lng~~I~G--r~L~V~~  130 (771)
                      ...|||+||++.++++.|..+|+.||.|..+.++..  +    || |||+|.+.++|..|+..|||..|.|  +.|.|.+
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~--~----Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR--N----GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES--S----SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC--C----CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            345789999999999999999999999999998652  2    76 9999999999999999999999987  6899988


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        99 Ak~  101 (124)
T 2e5i_A           99 ARP  101 (124)
T ss_dssp             CSC
T ss_pred             ecC
Confidence            865

>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=99.24  E-value=2.5e-11  Score=126.96  Aligned_cols=84  Identities=13%  Similarity=0.305  Sum_probs=76.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE  125 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~----~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~  125 (771)
                      ...+.++|||+|||+.+++++|+    .+|+.||.|..|.++.   +|+++|||||+|.+.++|..||..|||..|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34568999999999999999966    8999999999998875   7889999999999999999999999999999999


Q ss_pred             EEEEEehhhHH
Q 004150          126 LMLKVDQATRE  136 (771)
Q Consensus       126 L~V~~a~~~kk  136 (771)
                      |.|.|+.....
T Consensus        82 l~v~~a~~~~~   92 (282)
T 3pgw_A           82 MRIQYAKTDSD   92 (282)
T ss_pred             EEEEEeccCcc
Confidence            99999866443

>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=99.23  E-value=1.7e-11  Score=117.87  Aligned_cols=81  Identities=19%  Similarity=0.275  Sum_probs=72.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC--CCceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG--TPKGFGFCEFESAEGVLRALRLLNKFNID---GQELM  127 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tG--k~kGfGFVeF~~~esA~~Al~~Lng~~I~---Gr~L~  127 (771)
                      ..++|||+|||+.+++.+|..+|+.||.|.++.++.++.+|  .++|||||+|.+.++|..|+..|||..+.   ++.+.
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            46899999999999999999999999999999999997666  89999999999999999999999998776   56777


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus        82 ~~~~~~   87 (175)
T 3nmr_A           82 MKPADS   87 (175)
T ss_dssp             EEECGG
T ss_pred             Eccccc
Confidence            766543

>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=99.22  E-value=2.2e-11  Score=122.17  Aligned_cols=79  Identities=18%  Similarity=0.169  Sum_probs=72.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.++..+|+.+|+.||.|..+.++.+. +|.++|||||+|.+.++|..||..+ +..|+|+.|.|.+..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            35899999999999999999999999999999999984 7999999999999999999999855 569999999998765


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus       186 ~  186 (193)
T 2voo_A          186 D  186 (193)
T ss_dssp             T
T ss_pred             H
Confidence            3

>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=99.20  E-value=3.4e-11  Score=116.54  Aligned_cols=78  Identities=17%  Similarity=0.249  Sum_probs=71.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+     ..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            3457899999999999999999999999988766     36899999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       171 a~~  173 (175)
T 1fje_B          171 TGE  173 (175)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            864

>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=99.19  E-value=2.9e-11  Score=123.51  Aligned_cols=78  Identities=14%  Similarity=0.235  Sum_probs=72.6

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ..+.++|||+|||+ .+++.+|+.+|+.||.|..+.++.++     +|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34578999999999 99999999999999999999998873     7899999999999999999999999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus       106 ~a~~  109 (229)
T 2adc_A          106 LSKH  109 (229)
T ss_dssp             CCSC
T ss_pred             EecC
Confidence            8864

>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=99.19  E-value=1.4e-11  Score=107.05  Aligned_cols=75  Identities=15%  Similarity=0.196  Sum_probs=63.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++++|+.+|+.||.|..+.++.+     ++|||||+|.+.++|..|+.  .++.++|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEec
Confidence            34789999999999999999999999999999998764     67999999999999975432  234568999999887


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        76 ~~   77 (88)
T 1wf0_A           76 EP   77 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.19  E-value=6.7e-11  Score=123.83  Aligned_cols=81  Identities=17%  Similarity=0.279  Sum_probs=77.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.+++.+|..+|+.||.|..+.++.+..+|.++|||||.|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            46799999999999999999999999999999999998899999999999999999999999999999999999999986


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus       174 ~  174 (284)
T 3smz_A          174 A  174 (284)
T ss_dssp             G
T ss_pred             C
Confidence            5

>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=99.18  E-value=4.2e-11  Score=125.89  Aligned_cols=82  Identities=12%  Similarity=0.235  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCC-CCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPS-NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~-vte~~L~~lF~~~G~V~s~kiv~d~~-tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      ..+.++|||+|||+. +++.+|+.+|+.||.|..+.++.+.. ||.++|||||.|.+.++|..|+ .|||..|+|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            445789999999999 99999999999999999999999864 5999999999999999999999 99999999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus       286 ~~a~~  290 (292)
T 2ghp_A          286 SLADK  290 (292)
T ss_dssp             EECCC
T ss_pred             EEecC
Confidence            99875

>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=99.15  E-value=8.6e-11  Score=122.98  Aligned_cols=83  Identities=20%  Similarity=0.228  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCC-CHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTA-DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~v-te~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ....++|||+|||+.+ ++++|..+|+.||.|..+.++.+. +|.++|||||.|.+.++|..|+..|||..|+|+.|.|.
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            3457899999999995 999999999999999999999985 89999999999999999999999999999999999999


Q ss_pred             Eehhh
Q 004150          130 VDQAT  134 (771)
Q Consensus       130 ~a~~~  134 (771)
                      |+...
T Consensus       260 ~a~~~  264 (284)
T 3smz_A          260 FCAPG  264 (284)
T ss_dssp             ECCSS
T ss_pred             EecCC
Confidence            99764

>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=99.14  E-value=1.8e-11  Score=118.47  Aligned_cols=82  Identities=21%  Similarity=0.355  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           50 AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ...+.++|||+|||+.+++.+|+.+|..||.+.. .++.+..+|.++|||||+|.+.++|..||. |||..|+|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            3456899999999999999999999999998766 334444688999999999999999999995 99999999999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      ++..
T Consensus        87 ~~~~   90 (175)
T 1fje_B           87 KPKG   90 (175)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8865

>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=99.12  E-value=9e-11  Score=118.66  Aligned_cols=78  Identities=17%  Similarity=0.207  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCe--eEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCe----E
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTV--KSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQ----E  125 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V--~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr----~  125 (771)
                      .+.++|||+|||+.+++++|+.+|+.||.|  .+++++.+.  |..+|||||+|.+.++|..||..|||..|+|.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            457899999999999999999999999999  899988873  66679999999999999999999999999876    5


Q ss_pred             EEEEEe
Q 004150          126 LMLKVD  131 (771)
Q Consensus       126 L~V~~a  131 (771)
                      +.|+||
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777765

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.12  E-value=6.6e-11  Score=122.80  Aligned_cols=80  Identities=19%  Similarity=0.270  Sum_probs=71.1

Q ss_pred             CCCCCCEEEEcCCCCCC---------CHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce
Q 004150           50 AEKPQTKVYVGKIAPTA---------DSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  120 (771)
Q Consensus        50 ~~~~~~tVfVgNLp~~v---------te~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~  120 (771)
                      .....++||||||+..+         ++..|+.+|+.||.|.++.|+.+      +|||||+|.+.++|..|+..|+|..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            35568999999999998         79999999999999999999864      5999999999999999999999999


Q ss_pred             e------------CCeEEEEEEehhhH
Q 004150          121 I------------DGQELMLKVDQATR  135 (771)
Q Consensus       121 I------------~Gr~L~V~~a~~~k  135 (771)
                      |            +|+.|.|.|+....
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             EeccccccccccCCCCEEEEEEccCCC
Confidence            9            89999999997643

>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=99.11  E-value=1.8e-10  Score=120.04  Aligned_cols=77  Identities=16%  Similarity=0.219  Sum_probs=71.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||||||+.+++.+|..+|+.||.|..+.+..+      +|||||.|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            455789999999999999999999999999999998654      59999999999999999999999999999999998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.09  E-value=8.9e-11  Score=116.21  Aligned_cols=76  Identities=14%  Similarity=0.253  Sum_probs=71.2

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           54 QTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .++|||+|||+ .+++.+|..+|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            58999999999 99999999999999999999998863     6899999999999999999999999999999999987


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      ..
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.07  E-value=2.8e-10  Score=112.59  Aligned_cols=78  Identities=18%  Similarity=0.299  Sum_probs=71.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G-~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr~L~V  128 (771)
                      .++.++|||+|||..+++.+|+.+|+.|| .|..+.++.+     .+|||||+|.+.++|..|+..|||..|+ |+.|.|
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  191 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  191 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEE
Confidence            35679999999999999999999999999 9999998764     2689999999999999999999999999 999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+.+
T Consensus       192 ~~a~~  196 (198)
T 1qm9_A          192 SFSKS  196 (198)
T ss_dssp             EEECC
T ss_pred             Eeecc
Confidence            99864

>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=99.07  E-value=2.6e-10  Score=104.02  Aligned_cols=78  Identities=12%  Similarity=0.136  Sum_probs=67.7

Q ss_pred             CCCCEEEEcCCCCCCC-----------HHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce
Q 004150           52 KPQTKVYVGKIAPTAD-----------SDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  120 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vt-----------e~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~  120 (771)
                      .+.++|+|.||.....           +++|+.+|++||.|..+.| .+.   .++|||||+|.+.++|..|+..|||..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            4578999999955433           4799999999999999955 443   378999999999999999999999999


Q ss_pred             eCCeEEEEEEehh
Q 004150          121 IDGQELMLKVDQA  133 (771)
Q Consensus       121 I~Gr~L~V~~a~~  133 (771)
                      |+|+.|.|.++..
T Consensus        89 ~~gr~l~v~~a~~  101 (112)
T 2dit_A           89 FGGRQITAQAWDG  101 (112)
T ss_dssp             ETTEECEEEECCS
T ss_pred             ECCcEEEEEEeCC
Confidence            9999999999865

>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=99.06  E-value=2.6e-10  Score=119.83  Aligned_cols=81  Identities=17%  Similarity=0.280  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G-~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..++|||+|||+.+++.+|..+|+.|| .|..+.++.+. .|.++|||||.|.+.++|..|+..|||..|+|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 99999999885 5889999999999999999999999999999999999998


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      ...
T Consensus       195 ~~~  197 (292)
T 2ghp_A          195 NPL  197 (292)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.05  E-value=4e-10  Score=117.34  Aligned_cols=81  Identities=15%  Similarity=0.213  Sum_probs=73.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC-CceeC---CeEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN-KFNID---GQELM  127 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln-g~~I~---Gr~L~  127 (771)
                      .+.++|||+|||+.+++.+|..+|+.||.|..+.++.+ .+|.++|||||+|.+.++|..||..|| +..+.   |+.|.
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence            45789999999999999999999999999999999999 699999999999999999999999994 55554   99999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.++..
T Consensus       173 v~~~~~  178 (261)
T 3sde_A          173 VEPMEQ  178 (261)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            988764

>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=99.03  E-value=7.2e-10  Score=100.59  Aligned_cols=82  Identities=17%  Similarity=0.078  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCC--CCC--------HHHHHHHHHhcCCeeEEEEeecCCC--CCCceEEEEEeCCHHHHHHHHHHhCCc
Q 004150           52 KPQTKVYVGKIAP--TAD--------SDFVLSVLKVCGTVKSWKRAQYPSN--GTPKGFGFCEFESAEGVLRALRLLNKF  119 (771)
Q Consensus        52 ~~~~tVfVgNLp~--~vt--------e~~L~~lF~~~G~V~s~kiv~d~~t--Gk~kGfGFVeF~~~esA~~Al~~Lng~  119 (771)
                      .+++.|.+.|+-.  .+.        .++|+..|++||.|.++.|+.+..+  +.++|||||+|.+.++|.+|+..|||.
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            4567889999843  232        3689999999999999999988643  468999999999999999999999999


Q ss_pred             eeCCeEEEEEEehh
Q 004150          120 NIDGQELMLKVDQA  133 (771)
Q Consensus       120 ~I~Gr~L~V~~a~~  133 (771)
                      .++|+.|.|.+...
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            99999999999865

>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=99.03  E-value=1.8e-10  Score=104.41  Aligned_cols=72  Identities=14%  Similarity=0.139  Sum_probs=64.6

Q ss_pred             EcCCCCCCCHHHHHHHH------------HhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 004150           59 VGKIAPTADSDFVLSVL------------KVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  126 (771)
Q Consensus        59 VgNLp~~vte~~L~~lF------------~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L  126 (771)
                      ++|||..+++.+|+.+|            ++||.|.++.++.+. +|.++|||||.|.+.++|.+|+..|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56788888887777666            999999999999884 68999999999999999999999999999999999


Q ss_pred             EEEEe
Q 004150          127 MLKVD  131 (771)
Q Consensus       127 ~V~~a  131 (771)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99886

>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=99.00  E-value=8.5e-10  Score=112.53  Aligned_cols=78  Identities=18%  Similarity=0.299  Sum_probs=71.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCG-TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G-~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr~L~V  128 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.|| .|..+.++..     .+|||||+|.+.++|..|+..|||..|+ |+.|.|
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v  222 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  222 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEE
Confidence            34579999999999999999999999999 9999998653     3589999999999999999999999999 999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+.+
T Consensus       223 ~~a~~  227 (229)
T 2adc_A          223 SFSKS  227 (229)
T ss_dssp             EECSS
T ss_pred             EEecC
Confidence            99865

>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=98.98  E-value=8.1e-10  Score=106.16  Aligned_cols=73  Identities=22%  Similarity=0.402  Sum_probs=64.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVC----G-------TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  121 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~----G-------~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I  121 (771)
                      +.++|||+|||+.+++.+|+.+|+.|    |       .|..+.+.      .++|||||+|.+.++|..|+ .|||..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       66666554      34699999999999999999 7999999


Q ss_pred             CCeEEEEEEeh
Q 004150          122 DGQELMLKVDQ  132 (771)
Q Consensus       122 ~Gr~L~V~~a~  132 (771)
                      +|+.|.|.++.
T Consensus        76 ~g~~i~v~~~~   86 (172)
T 2g4b_A           76 QGQSLKIRRPH   86 (172)
T ss_dssp             TTEECEEECCS
T ss_pred             cCceeeecCCc
Confidence            99999998754

>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=98.98  E-value=1.3e-09  Score=101.26  Aligned_cols=81  Identities=17%  Similarity=0.080  Sum_probs=70.8

Q ss_pred             CCCEEEEcCCCCC-----CCHHHHHHHHHhcCCeeEEEEeecCC----CCCCceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 004150           53 PQTKVYVGKIAPT-----ADSDFVLSVLKVCGTVKSWKRAQYPS----NGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  123 (771)
Q Consensus        53 ~~~tVfVgNLp~~-----vte~~L~~lF~~~G~V~s~kiv~d~~----tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G  123 (771)
                      ++++|++.|+-..     --+++|+..|++||.|.++.|+.++.    ++.++||+||+|.+.++|..|+..|||..++|
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            4788999998532     23579999999999999999998853    45678999999999999999999999999999


Q ss_pred             eEEEEEEehh
Q 004150          124 QELMLKVDQA  133 (771)
Q Consensus       124 r~L~V~~a~~  133 (771)
                      +.|.|.+...
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.96  E-value=1.1e-09  Score=107.75  Aligned_cols=74  Identities=22%  Similarity=0.385  Sum_probs=64.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVC----G-------TVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  121 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~----G-------~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I  121 (771)
                      ..++|||+|||+.+++.+|..+|+.|    |       .|..+.+      +.++|||||+|.+.++|..|| .|||..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    4       4555544      456799999999999999999 7999999


Q ss_pred             CCeEEEEEEehh
Q 004150          122 DGQELMLKVDQA  133 (771)
Q Consensus       122 ~Gr~L~V~~a~~  133 (771)
                      +|+.|.|.++..
T Consensus        76 ~g~~i~v~~~~~   87 (198)
T 2yh0_A           76 QGQSLKIRRPHD   87 (198)
T ss_dssp             TTEEEEEECCCC
T ss_pred             cCceEEEeCCCC
Confidence            999999987754

>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=98.82  E-value=6.6e-09  Score=113.15  Aligned_cols=77  Identities=23%  Similarity=0.357  Sum_probs=65.6

Q ss_pred             CCCCCCEEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC---Ce
Q 004150           50 AEKPQTKVYVGK--IAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID---GQ  124 (771)
Q Consensus        50 ~~~~~~tVfVgN--Lp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~---Gr  124 (771)
                      ...+..+|||||  |++.+++++|+.+|+.||.|.++.+..      ++|||||+|.+.++|..||..|||..+.   |+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            355678999999  589999999999999999999887643      4689999999999999999999999883   44


Q ss_pred             --EEEEEEeh
Q 004150          125 --ELMLKVDQ  132 (771)
Q Consensus       125 --~L~V~~a~  132 (771)
                        .|.|.++.
T Consensus        88 ~~~ly~~~~~   97 (345)
T 3tht_A           88 KITLYLNFVE   97 (345)
T ss_dssp             EEECEEEECS
T ss_pred             ceEEEEEEee
Confidence              57777764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.72  E-value=4e-08  Score=88.51  Aligned_cols=63  Identities=16%  Similarity=0.148  Sum_probs=56.0

Q ss_pred             CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           64 PTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        64 ~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ..+++.+|+.+|+.||.|..+.|+     +.++|||||+|.+.++|..||..+++  +.|+.|.|.|+..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~   89 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEG   89 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccC
Confidence            568999999999999999999987     47889999999999999999997554  6799999998764

>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=98.71  E-value=6.3e-08  Score=89.28  Aligned_cols=82  Identities=12%  Similarity=0.072  Sum_probs=66.5

Q ss_pred             CCEEEEcCCCCCCC----------HHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 004150           54 QTKVYVGKIAPTAD----------SDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  123 (771)
Q Consensus        54 ~~tVfVgNLp~~vt----------e~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G  123 (771)
                      ++.|.+.|+-....          .++|+..|++||.|.++.+..+.    ++|||||.|.+.++|..|+..|||..++|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            45677777644322          24889999999999999987652    58999999999999999999999999999


Q ss_pred             eEEEEEEehhhHHHHHH
Q 004150          124 QELMLKVDQATREYLER  140 (771)
Q Consensus       124 r~L~V~~a~~~kk~le~  140 (771)
                      +.|.|.++.. ..|...
T Consensus        83 R~i~v~~~~~-~~y~~~   98 (114)
T 3s6e_A           83 KMITAAYVPL-PTYHNL   98 (114)
T ss_dssp             EECEEEEECH-HHHHHH
T ss_pred             EEEEEEEEcH-HHHHHh
Confidence            9999999864 344433

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.69  E-value=5.7e-08  Score=90.55  Aligned_cols=89  Identities=15%  Similarity=0.142  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCC-HHHHHHHHHHhC--CceeCCeEE
Q 004150           51 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFES-AEGVLRALRLLN--KFNIDGQEL  126 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~-vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~-~esA~~Al~~Ln--g~~I~Gr~L  126 (771)
                      -++++.|||+||++. ++..+|+.+|+.||.|..|.++.+.      ..|||.|.+ +.+|..|+..|+  +..|+|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~------~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC------SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC------CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            456899999999999 9999999999999999999998875      369999999 899999999994  788999888


Q ss_pred             EEEEehh--hHHHHHHHHHhh
Q 004150          127 MLKVDQA--TREYLERYVDKK  145 (771)
Q Consensus       127 ~V~~a~~--~kk~le~~k~kk  145 (771)
                      .+.+...  -+.|+.+..+.+
T Consensus        89 ~~evL~GeeE~~yw~Ki~ed~  109 (121)
T 1owx_A           89 TWEVLEGEVEKEALKKIIEDQ  109 (121)
T ss_dssp             EEEECCHHHHHHHHHHHHHHH
T ss_pred             EEEECCCHHHHHHHHHHHHHH
Confidence            8877644  466776665533

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.63  E-value=6.4e-08  Score=85.46  Aligned_cols=74  Identities=15%  Similarity=0.117  Sum_probs=62.5

Q ss_pred             CCCCCEEEEcCCC----CCCCH----HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           51 EKPQTKVYVGKIA----PTADS----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        51 ~~~~~tVfVgNLp----~~vte----~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      .++..||+|...+    .+...    ..|...|..||.|..++++.+        .+||+|.+.++|.+||. |||+.|+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d--------~~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED--------KMWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS--------SEEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC--------CEEEEECChHHHHHHHh-cCCeEeC
Confidence            3456788888776    23333    589999999999999999987        38999999999999999 9999999


Q ss_pred             CeEEEEEEehh
Q 004150          123 GQELMLKVDQA  133 (771)
Q Consensus       123 Gr~L~V~~a~~  133 (771)
                      |+.|+|.++..
T Consensus        75 Gr~LkV~lkt~   85 (91)
T 2dnr_A           75 NRTITIALKSP   85 (91)
T ss_dssp             TEEEEEEECCC
T ss_pred             CeEEEEEeCCC
Confidence            99999987654

>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=98.41  E-value=4.2e-07  Score=80.74  Aligned_cols=71  Identities=17%  Similarity=0.225  Sum_probs=61.1

Q ss_pred             CCCCCEEEEcCCCCC------CCH---HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee
Q 004150           51 EKPQTKVYVGKIAPT------ADS---DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  121 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~------vte---~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I  121 (771)
                      .++..||+|..++..      ..+   ..|.+.|..||.|..++++.+.        +||+|.+.++|++||. |||..|
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            445779999888743      332   4689999999999999999882        9999999999999999 999999


Q ss_pred             CCeEEEEEE
Q 004150          122 DGQELMLKV  130 (771)
Q Consensus       122 ~Gr~L~V~~  130 (771)
                      +|+.|+|.+
T Consensus        83 ~Gr~L~V~~   91 (95)
T 1ufw_A           83 KGRAVKISG   91 (95)
T ss_dssp             TTEEEEEEC
T ss_pred             CCeEEEEec
Confidence            999999975

>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=98.15  E-value=2.9e-06  Score=85.80  Aligned_cols=68  Identities=19%  Similarity=0.073  Sum_probs=60.8

Q ss_pred             CCHHHHHHHHHhcCCeeEEEEeecC----CCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           66 ADSDFVLSVLKVCGTVKSWKRAQYP----SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        66 vte~~L~~lF~~~G~V~s~kiv~d~----~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      -.+.+|...|++||.|.++.++.+.    .+|.++||+||+|.+.++|.+|+..|||..++|+.|.|.+...
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            3456899999999999999998553    4558999999999999999999999999999999999999764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.59  E-value=0.00032  Score=63.77  Aligned_cols=74  Identities=9%  Similarity=0.056  Sum_probs=67.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhc-----CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVC-----GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  126 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~-----G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L  126 (771)
                      ...++|-+-|||..+++..|+.|+..+     |.+..+.++.|.      +-++|+|.+...|.+|.-.|+|.+|+|++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            346789999999999999999999999     999999998884      679999999999999998899999999999


Q ss_pred             EEEEe
Q 004150          127 MLKVD  131 (771)
Q Consensus       127 ~V~~a  131 (771)
                      .|.-.
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            99643

>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=96.62  E-value=0.0035  Score=56.51  Aligned_cols=75  Identities=13%  Similarity=0.010  Sum_probs=63.8

Q ss_pred             CCCEEEEcCCCCCCCH-----HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           53 PQTKVYVGKIAPTADS-----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte-----~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      -+++|+|.||+..+-.     ..++.+|..|+.+.+|.....-      .-..|.|.++++|.+|-..||+..++|+.|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            4678999999876532     4789999999999999877641      3568999999999999999999999999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |-+++.
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            988874

>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=94.65  E-value=0.1  Score=46.00  Aligned_cols=68  Identities=12%  Similarity=0.169  Sum_probs=56.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCC--ceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP--KGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~--kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ++|.|.+||+++|++.+...++.++.+..+..+....+.+.  .+-|||.|.+.+++......++|..+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            57999999999999999999999988776666665433333  356899999999999999999998763

>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=94.42  E-value=0.16  Score=45.32  Aligned_cols=54  Identities=11%  Similarity=0.070  Sum_probs=44.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL  116 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L  116 (771)
                      .+-++| +.|..+...+|..+|+.||. ..+..+-|       ..|||.|.+++.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD-------TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET-------TEEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC-------CeEEEEecCHHHHHHHHHhc
Confidence            344555 99999999999999999983 34555566       58999999999999999876

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.10  E-value=0.34  Score=43.59  Aligned_cols=69  Identities=22%  Similarity=0.336  Sum_probs=55.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHh----c-CCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKV----C-GTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~----~-G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      ...+|.|.|||+.+.++.|.-+|..    . |.|..|....        +-|+|+|.+...|.+.|. -..+.|+|..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEE
Confidence            4678999999999999999999986    2 4777776532        468999999999988876 336778888888


Q ss_pred             EEE
Q 004150          128 LKV  130 (771)
Q Consensus       128 V~~  130 (771)
                      |.-
T Consensus        78 V~P   80 (104)
T 2dhx_A           78 LRP   80 (104)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            753

>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=92.51  E-value=0.42  Score=44.07  Aligned_cols=71  Identities=13%  Similarity=0.073  Sum_probs=57.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC-eEEEEEEe
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG-QELMLKVD  131 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G-r~L~V~~a  131 (771)
                      ..+-|.|-+.|+.. -..|...|..||.|......      ....+-.|.|.+..+|.+||. .||..|+| -.|-|..+
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            36778888888875 56778889999999988752      123689999999999999999 89999984 66666654

>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=91.96  E-value=0.15  Score=45.53  Aligned_cols=53  Identities=11%  Similarity=0.053  Sum_probs=45.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN  117 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln  117 (771)
                      -++| +.|..+...+|..+|+.|| -..+..+-|       ..|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            3455 9999999999999999998 556666676       589999999999999999764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=91.03  E-value=0.28  Score=45.93  Aligned_cols=84  Identities=15%  Similarity=0.105  Sum_probs=56.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-------------CCC-CCceEEEEEeCCHHHHHHHHHHhCCc
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-------------SNG-TPKGFGFCEFESAEGVLRALRLLNKF  119 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~-------------~tG-k~kGfGFVeF~~~esA~~Al~~Lng~  119 (771)
                      .+.|.|-+.|+..+ ..+...|++||.|+.-.-+...             ..+ ....+-.|+|.+..+|.+||. .||.
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            34566777766654 5667789999998772211110             011 123577999999999999999 9999


Q ss_pred             eeCCeEEEEEEehhhHHHHHHH
Q 004150          120 NIDGQELMLKVDQATREYLERY  141 (771)
Q Consensus       120 ~I~Gr~L~V~~a~~~kk~le~~  141 (771)
                      .|+|..|-|..+  ++..+++.
T Consensus        85 ii~G~mIGV~Py--~~~~ve~l  104 (132)
T 3p3d_A           85 VFNGVLLGVIPY--TKDAVERL  104 (132)
T ss_dssp             EETTEECEEEEC--CHHHHHHH
T ss_pred             EeCcEEEEEEEC--CHHHHHHH
Confidence            999986666665  34555443

>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=87.87  E-value=0.4  Score=45.01  Aligned_cols=36  Identities=19%  Similarity=0.051  Sum_probs=29.3

Q ss_pred             EEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCce
Q 004150           83 SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN  120 (771)
Q Consensus        83 s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~  120 (771)
                      .++++.+.  .+++|||||+|.+..+|..|+..+++..
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            46677763  4789999999999999999998777643

>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=85.76  E-value=0.41  Score=44.72  Aligned_cols=46  Identities=22%  Similarity=0.168  Sum_probs=38.3

Q ss_pred             EEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEEEeh
Q 004150           84 WKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELMLKVDQ  132 (771)
Q Consensus        84 ~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L-ng~~I~Gr~L~V~~a~  132 (771)
                      +.+..+  ..+.+|+++|+|.+.+.|.+|+..| ||..|+| .|.|.++.
T Consensus         3 ~al~l~--g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~   49 (150)
T 2i2y_A            3 YKLILN--GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDAT   49 (150)
T ss_dssp             EEEEEC--CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTT
T ss_pred             eEeeec--cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceeccccc
Confidence            444443  4577899999999999999999999 9999999 88887554

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=84.04  E-value=1.2  Score=39.70  Aligned_cols=69  Identities=9%  Similarity=0.096  Sum_probs=49.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCC--ceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP--KGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~--kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      +-+|.|..||+++|++.+...++.+-.+.....+....+-+.  -+-|||.|.+.+++..-...++|..+-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            457999999999999998888776544322222222222222  245799999999999999999998763

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=81.17  E-value=0.84  Score=51.36  Aligned_cols=55  Identities=16%  Similarity=0.149  Sum_probs=41.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHH
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR  114 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~  114 (771)
                      .++|||. .|..++..+|..+|++||.|.++.+..+  .|   .|+.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FG---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SS---EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CC---eEEEEEeCCHHHHHHHHh
Confidence            4789997 7999999999999999999999987664  22   799999999999887754

---

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	771
d1mp1a_	111	a.188.1.1 (A:) Ser/Arg-related nuclear matrix prot	3e-18
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-06
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-06
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	6e-05
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-05
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	0.002
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	9e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.001
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	0.004
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.004

>d1mp1a_ a.188.1.1 (A:) Ser/Arg-related nuclear matrix protein srm160 {Human (Homo sapiens) [TaxId: 9606]} Length = 111

class: All alpha proteins
fold: PWI domain
superfamily: PWI domain
family: PWI domain
domain: Ser/Arg-related nuclear matrix protein srm160
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.6 bits (194), Expect = 3e-18
 Identities = 20/90 (22%), Positives = 50/90 (55%), Gaps = 6/90 (6%)

Query: 675 ELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLEL 734
           E    +++ +  +     E ++PWI+K++TE LG E+  ++++I +  +     S+M+++
Sbjct: 9   ECLEKKVDMSKVNL----EVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQI 64

Query: 735 -LQTILDDE-AEMFVLKMWRMLIFEIKKVE 762
            L   L+ + A  F+ ++W +L+   + + 
Sbjct: 65  NLTGFLNGKNAREFMGELWPLLLSAQENIA 94

>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 = 59.2 bits (143), Expect = 1e-11
 Identities = 18/79 (22%), Positives = 30/79 (37%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           T +YV  +  T   D + ++    G++      +    G P+G  F  +   E    A+ 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 115 LLNKFNIDGQELMLKVDQA 133
            LN    +G    L V  A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 6e-11
 Identities = 15/79 (18%), Positives = 27/79 (34%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             +YV  +  T     +  +    G + + +       G  +G GF  F+       A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 115 LLNKFNIDGQELMLKVDQA 133
            LN     G    + V  A
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 54.3 bits (130), Expect = 1e-09
 Identities = 18/103 (17%), Positives = 40/103 (38%), Gaps = 3/103 (2%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
           +    +Y+  +     ++ +  +    G ++     +  +    +G  +  +E       
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKN 61

Query: 112 ALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKE 154
           A   L+ FN+  + L++    A R + +    KK E  K LKE
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 104

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K+++G ++     + +       G VK     + P     +GFGF  F    GV + L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 116 LNKFNIDGQELMLKV 130
            ++  +D + +  KV
Sbjct: 61  QSRHELDSKTIDPKV 75

>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 = 52.7 bits (126), Expect = 2e-09
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           T + V  +        + ++ +  G + + +  +    G   G+ F +F S     RA++
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 115 LLNKFNIDGQELMLKVDQAT 134
           +LN   +  +   LKV  A 
Sbjct: 63  VLNGITVRNKR--LKVSYAR 80

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.8 bits (124), Expect = 4e-09
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
            +YVG + P      +       G + S +  +        G+ +  F+      RAL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 116 LNKFNIDGQELMLKVDQATRE 136
           +N   I G+   +++  + R+
Sbjct: 62  MNFDVIKGKP--VRIMWSQRD 80

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.0 bits (124), Expect = 4e-09
 Identities = 17/83 (20%), Positives = 30/83 (36%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
           +  +   T + V  +  T   D +L        +      +Y   G P G     FES +
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 108 GVLRALRLLNKFNIDGQELMLKV 130
               A+  LN   I  +++ L +
Sbjct: 63  EATAAVIDLNDRPIGSRKVKLVL 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K+++G +    + D V  +L   G +K++   +  + G  KG+ FCE+       +A+  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 116 LNKFNIDGQELMLKVDQAT 134
           LN   +  ++  L V +A+
Sbjct: 63  LNGMQLGDKK--LLVQRAS 79

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 49  PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
            +E+ Q   VYVG +        +  +    G V +    +    G  +G+GF EF S E
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 108 GVLRALRLLNKFNIDGQELMLKVDQATR 135
               A+++++   + G+   ++V++A+ 
Sbjct: 63  DADYAIKIMDMIKLYGKP--IRVNKASA 88

>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 = 49.3 bits (117), Expect = 3e-08
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 54  QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 113
           +T + V  +      +   S+    G ++S K  +    G   G+GF  +   +   +A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 114 RLLNKFNIDGQELMLKVDQA 133
             LN   +  +   +KV  A
Sbjct: 62  NTLNGLRLQTKT--IKVSYA 79

>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 = 49.2 bits (117), Expect = 4e-08
 Identities = 18/85 (21%), Positives = 32/85 (37%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
           K    +YVG ++     + +  +    G +K           T  GF F E+ S      
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 112 ALRLLNKFNIDGQELMLKVDQATRE 136
           A+R +N   +D + +    D   +E
Sbjct: 65  AMRYINGTRLDDRIIRTDWDAGFKE 89

>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 = 49.0 bits (116), Expect = 7e-08
 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 3/82 (3%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           TK++VG +        +    +  G ++          G  +G+GF          RA +
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 115 LLNKFNIDGQELMLKVDQATRE 136
             N   IDG+     V+ A   
Sbjct: 71  DPNPI-IDGR--KANVNLAYLG 89

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 1e-07
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K++VG ++P    + +       G V+S +          +GF F  F+  E V + +  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 116 LNKFNIDGQELMLKV 130
               N+   +  +KV
Sbjct: 61  KYH-NVGLSKCEIKV 74

>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 = 48.1 bits (114), Expect = 1e-07
 Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 35  MPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT 94
           M   +  VPL      ++   K+++G ++     + + +  +  G +      + P++  
Sbjct: 1   MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR 60

Query: 95  PKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
            +GFGF  F S   V  A+      +IDG+  +++  +A  
Sbjct: 61  SRGFGFVTFSSMAEVDAAMA-ARPHSIDGR--VVEPKRAVA 98

>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 = 47.8 bits (113), Expect = 2e-07
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
           PA     ++YVG + P   +  +  V    G ++        +      F F EFE    
Sbjct: 9   PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI---DLKNRRGGPPFAFVEFEDPRD 65

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATR 135
              A+   + ++ DG  L ++  ++ R
Sbjct: 66  AEDAVYGRDGYDYDGYRLRVEFPRSGR 92

>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 = 46.7 bits (110), Expect = 3e-07
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 54  QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 113
           + K++VG ++   +   +  V    G +      +       +GFGF  FE+ +    A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 114 RLLNKFNIDGQELMLKVDQATR 135
             +N  ++DG++  ++VDQA +
Sbjct: 65  MAMNGKSVDGRQ--IRVDQAGK 84

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.5 bits (110), Expect = 4e-07
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQ-YPSNGTPKGFGFCEFESAE 107
           P ++  +K+ V  I   A+   +  +    G +K+ +  +     G  +GFGF +F + +
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 108 GVLRALR-LLNKFNIDGQELMLKVDQATRE 136
              +A   L +  ++ G+   L ++ A  E
Sbjct: 63  DAKKAFNALCHSTHLYGRR--LVLEWADSE 90

>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 = 46.2 bits (109), Expect = 5e-07
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
            +++V  ++ T+  + +  +    G +             PKGF F  F   E  ++A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 115 LLNKFNIDGQELMLKVDQATRE 136
            ++     G+  ML V  +T +
Sbjct: 69  EVDGQVFQGR--MLHVLPSTIK 88

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 6e-07
 Identities = 13/92 (14%), Positives = 27/92 (29%), Gaps = 4/92 (4%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
             + P  ++ V  +      D +  +    GTV         +    +     ++     
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVS 57

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATREYLER 140
              A   L+  NI      L++D +    L  
Sbjct: 58  AQHAKLSLDGQNIYNACCTLRIDFSKLTSLNV 89

>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 = 45.5 bits (107), Expect = 8e-07
 Identities = 13/74 (17%), Positives = 25/74 (33%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
           P   + V  ++       +  V    G +          +   +GF F  FE+ +    A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 113 LRLLNKFNIDGQEL 126
               N   +DG+ +
Sbjct: 68  KERANGMELDGRRI 81

>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 = 45.0 bits (106), Expect = 1e-06
 Identities = 18/85 (21%), Positives = 35/85 (41%)

Query: 52  KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLR 111
             +  +YVG +A   D   + +     G +   +          +GF F EFE AE    
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 112 ALRLLNKFNIDGQELMLKVDQATRE 136
           A+  +N+  + G+ + + + +  R 
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRI 87

>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 = 45.0 bits (106), Expect = 1e-06
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 58  YVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP---SNGTPKGFGFCEFESAEGVLRALR 114
           ++  +  +   + +  V    G +KS   ++           GFGF E++  E   +AL+
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 115 LLNKFNIDGQELMLKVDQATRE 136
            L    +DG +  L+V  + R 
Sbjct: 62  QLQGHTVDGHK--LEVRISERA 81

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 11/89 (12%)

Query: 48  TPAEKPQTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 106
           T      ++V++G +         V ++    G +              KGF F ++ + 
Sbjct: 9   TDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS--------VHKGFAFVQYVNE 60

Query: 107 EGVLRALRLLNKFNIDGQELMLKVDQATR 135
                A+   +   I GQ  +L ++ A  
Sbjct: 61  RNARAAVAGEDGRMIAGQ--VLDINLAAE 87

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K+++G ++     + + S  +  GT+      + P+    +GFGF  + + E V  A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 116 LNKFNIDGQELMLKVDQA 133
                +DG+  +++  +A
Sbjct: 68  RPH-KVDGR--VVEPKRA 82

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.5 bits (105), Expect = 1e-06
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 3/79 (3%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K+ V  +        +  +    GT+K      Y  +G   G     FE     L+A++ 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKA-AVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 116 LNKFNIDGQELMLKVDQAT 134
            N   +DG+   + +   T
Sbjct: 61  YNGVPLDGRP--MNIQLVT 77

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               +++  +        +L +    G V S K          K FGF  +++      A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 113 LRLLNKFNIDGQELMLKVDQATRE 136
           ++ +N F I  +   LKV     +
Sbjct: 77  IQSMNGFQIGMKR--LKVQLKRSK 98

>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 = 43.6 bits (102), Expect = 3e-06
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKR-AQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           +++G + P  D   +       G +    +  + P  G  KG+ F  F S +    A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 116 LNKFNIDGQELMLKVDQATR 135
           +N   +  +   + V  A +
Sbjct: 61  MNGQYLCNRP--ITVSYAFK 78

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 44.9 bits (105), Expect = 4e-06
 Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 2/96 (2%)

Query: 40  RPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFG 99
           + +P   + P       + V  I  T D   +  + +  G ++S K          +G+G
Sbjct: 28  QHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87

Query: 100 FCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
           F +F+S     +A+  LN FNI  +   LKV  A  
Sbjct: 88  FVKFQSGSSAQQAIAGLNGFNILNKR--LKVALAAS 121

>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 = 43.6 bits (102), Expect = 4e-06
 Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             ++V  I   A  D +       G +K+         G  KG+   E+E+ +  L A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 115 LLNKFNIDGQELMLKVDQAT 134
            LN   I GQ   ++VD   
Sbjct: 68  ALNGAEIMGQT--IQVDWCF 85

>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 = 43.4 bits (102), Expect = 4e-06
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 47  VTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA 106
           V  A +  + + V  +        +       G V   +  +    G  KGFGF  F   
Sbjct: 1   VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 60

Query: 107 EGVLRALRLLNKFNIDGQELMLKV 130
           E  ++ +   +   IDG+    K+
Sbjct: 61  ETQVKVMSQRHM--IDGRWCDCKL 82

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 4e-06
 Identities = 27/150 (18%), Positives = 68/150 (45%), Gaps = 7/150 (4%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVRKE------REQRRKIEEAEREYERCLKDWEYR 356
           +     L  +K +++ +   E  R+ ++ E       + +  + +A  + ++ L + E  
Sbjct: 146 KPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKE 205

Query: 357 -EREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEE 415
            E ER K    +   +   E +RK E + +++E       +     +E  R + ++E+E 
Sbjct: 206 IEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQER 265

Query: 416 DLADEVREEEEIAVAKRRAEEEQLQQQQRD 445
            LA +++E+E++     + E   ++ + +D
Sbjct: 266 TLALKLQEQEQLLKEGFQKESRIMKNEIQD 295

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 6e-05
 Identities = 22/144 (15%), Positives = 55/144 (38%), Gaps = 5/144 (3%)

Query: 307 RDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQY 366
           R   ++ +    +Y  E  +    +E  Q     +          D    E+E+E E + 
Sbjct: 151 RLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVER 210

Query: 367 EKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEE 426
            K +  +   K   E+    E+  +   + +     +E  ++   + E D    ++E+E 
Sbjct: 211 VKAESAQASAKMLHEMQRKNEQMMEQKERSY-----QEHLKQLTEKMENDRVQLLKEQER 265

Query: 427 IAVAKRRAEEEQLQQQQRDALKLL 450
               K + +E+ L++  +   +++
Sbjct: 266 TLALKLQEQEQLLKEGFQKESRIM 289

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 24/140 (17%), Positives = 56/140 (40%), Gaps = 5/140 (3%)

Query: 303 RDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREK 362
            ++ R   + +E      + +        + +Q    +E E E ER   +      +   
Sbjct: 165 YEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLH 224

Query: 363 ERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVR 422
           E Q + E+  E++ +  +E L    E  ++ R +  +   E     +++E+E+ L +  +
Sbjct: 225 EMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKE-QERTLALKLQEQEQLLKEGFQ 283

Query: 423 EEEEIAVAKRRAEEEQLQQQ 442
           +E        + E + LQ +
Sbjct: 284 KESR----IMKNEIQDLQTK 299

>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 = 43.6 bits (102), Expect = 5e-06
 Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
             ++    V+VG I   A  + +  +    G V S++       G PKG+GFCE++  E 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATRE 136
            L A+R LN     G+   L+VD A  E
Sbjct: 63  ALSAMRNLNGREFSGRA--LRVDNAASE 88

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 6e-06
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K+++G ++       +       G V        P  G  +GFGF  F+ +E V + +  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD- 59

Query: 116 LNKFNIDGQELMLKVDQA 133
             +  ++G+   +   +A
Sbjct: 60  QKEHKLNGKV--IDPKRA 75

>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 = 42.7 bits (100), Expect = 1e-05
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
           P T+++VG + P      +            +   +   +     F + ++ES +    A
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFD------RFGSIRTIDHVKGDSFAYIQYESLDAAQAA 69

Query: 113 LRLLNKFNIDGQELMLKVDQATRE 136
              +  F + G +  L+VD A   
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKSG 93

>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 = 42.4 bits (99), Expect = 1e-05
 Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT--PKGFGFCEFESAEGVLRA 112
            ++++G I      + +L  +               +      +GF F E+ES      A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 113 LRLLNKFNIDGQELMLKVDQATRE 136
            R L    I      + VD A  E
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPE 85

>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 = 42.0 bits (98), Expect = 1e-05
 Identities = 12/86 (13%), Positives = 28/86 (32%), Gaps = 3/86 (3%)

Query: 52  KPQTKVYVGKIAPTADSDFV-LSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
           +P   +Y+  +      D +  S+  +              +   +G  F  F+      
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 111 RALRLLNKFNIDGQELMLKVDQATRE 136
            ALR +  F    +   +++  A  +
Sbjct: 61  NALRSMQGFPFYDKP--MRIQYAKTD 84

>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 = 44.2 bits (103), Expect = 1e-05
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 49  PAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEG 108
            A     K++VG I    +   +    +  G ++  +      +G  +GF F  F+  + 
Sbjct: 92  GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

Query: 109 VLRALRLLNKFNIDGQELMLKVDQATRE 136
           V + +       ++G    ++   + +E
Sbjct: 152 VDKIVI-QKYHTVNGHNCEVRKALSKQE 178

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (95), Expect = 2e-04
 Identities = 13/65 (20%), Positives = 28/65 (43%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K+++G ++     + + S  +  GT+      + P+    +GFGF  + + E V  A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 116 LNKFN 120
                
Sbjct: 68  RPHKV 72

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K++VG ++     + V    +  G V         +    +GFGF  FES + V +    
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 116 LNKFNIDGQELMLKVDQA 133
           ++   I+ +   ++  +A
Sbjct: 60  IHFHEINNKM--VECKKA 75

>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 = 40.7 bits (95), Expect = 4e-05
 Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           ++++VG + P    + +  + +  G        +         FGF   E+      A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

Query: 115 LLNKFNIDGQELMLKVDQAT 134
            L+   + G++  L+V  A 
Sbjct: 63  ELDNMPLRGKQ--LRVRFAC 80

>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 = 40.8 bits (95), Expect = 4e-05
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 53  PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
               + V  ++       +  + +  G++     A+  + G  KGF F  F   E   RA
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 113 LRLLNKFNIDGQELMLKVDQA 133
           +  ++ F  D     L V+ A
Sbjct: 67  IAGVSGFGYDHLI--LNVEWA 85

>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 = 40.8 bits (95), Expect = 4e-05
 Identities = 17/87 (19%), Positives = 37/87 (42%), Gaps = 4/87 (4%)

Query: 48  TPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
           + ++    +++V  I        +  +    G +   +          KGFGF  FE++ 
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSA 62

Query: 108 GVLRALRLLNKFNIDGQELMLKVDQAT 134
              RA   L+   ++G++  ++V+ AT
Sbjct: 63  DADRAREKLHGTVVEGRK--IEVNNAT 87

>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 = 40.8 bits (95), Expect = 4e-05
 Identities = 13/91 (14%), Positives = 30/91 (32%), Gaps = 7/91 (7%)

Query: 45  PTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE 104
           P  +   +    +    ++     D +  V +    ++   +     +G  KG  + EF+
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFK 61

Query: 105 SAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
           S     + L       IDG+   + +     
Sbjct: 62  SEADAEKNLEEKQGAEIDGRS--VSLYYTGE 90

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 5e-05
 Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKS-----WKRAQYPSNGTPKGFGFCEFESAEGVL 110
           ++YVG I      + ++        +                   K F F EF S +   
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 111 RALRLLNKFNIDGQELMLK 129
           +A+   +     GQ L ++
Sbjct: 63  QAMA-FDGIIFQGQSLKIR 80

>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 = 40.5 bits (94), Expect = 5e-05
 Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           + + V  +   ++   V  +LK       +           K   F    + E    A++
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-------RNKRTAFVTLLNGEQAQNAIQ 58

Query: 115 LLNKFNIDGQELMLKVDQATRE 136
           + ++++  G++  L V     +
Sbjct: 59  MFHQYSFRGKD--LIVQLQPTD 78

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 5e-05
 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 4/86 (4%)

Query: 51  EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 110
           +     +YVG ++       +L +    G  KS K      + +   + F EF       
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCK--MITEHTSNDPYCFVEFYEHRDAA 62

Query: 111 RALRLLNKFNIDGQELMLKVDQATRE 136
            AL  +N   I G+E  +KV+ AT  
Sbjct: 63  AALAAMNGRKILGKE--VKVNWATTP 86

>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 = 40.1 bits (93), Expect = 6e-05
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 9/80 (11%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K+Y+G ++P   +D +  +        + +           G+ F ++      +RA+  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAIET 56

Query: 116 LN-KFNIDGQELMLKVDQAT 134
           L+ K  + G+   ++VD + 
Sbjct: 57  LSGKVELHGKI--MEVDYSV 74

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 8e-05
 Identities = 14/70 (20%), Positives = 29/70 (41%)

Query: 57  VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 116
           +Y+  + P      ++ + +  G + S K     +    KG+GF +F+S     +A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 117 NKFNIDGQEL 126
               +  Q  
Sbjct: 61  KASGVQAQMA 70

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 8e-05
 Identities = 12/80 (15%), Positives = 21/80 (26%), Gaps = 9/80 (11%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           + V+VG+       D +       G V      +       + F F  F   +       
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCG 60

Query: 115 LLNKFNIDGQELMLKVDQAT 134
                 I G    + +  A 
Sbjct: 61  --EDLIIKGIS--VHISNAE 76

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 9e-05
 Identities = 11/81 (13%), Positives = 22/81 (27%), Gaps = 9/81 (11%)

Query: 54  QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 113
            T V V      + S  +L      G +     +          +    ++S     +AL
Sbjct: 4   DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKAL 56

Query: 114 RLLNKFNIDGQELMLKVDQAT 134
               +       +M+ V    
Sbjct: 57  SKDGRI-FGES-IMIGVKPCI 75

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
           K++VG I    +   +    +  G ++  +      +G  +GF F  F+  + V + +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 116 LNKFNIDGQELMLKVDQA 133
                ++G     +V +A
Sbjct: 63  QKYHTVNGH--NCEVRKA 78

>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 = 38.5 bits (89), Expect = 3e-04
 Identities = 15/82 (18%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
             +++  +  + D+  +       G + S K     +    KG+GF  FE+ E   RA+ 
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIE 66

Query: 115 LLNKFNIDGQELMLKVDQATRE 136
            +N   ++ +++ +   ++ +E
Sbjct: 67  KMNGMLLNDRKVFVGRFKSRKE 88

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 5e-04
 Identities = 14/87 (16%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 50  AEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGV 109
               +   ++  I  +     VL  L+     ++       +NG   G    +F++ +  
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 110 LRALRLLNKFNIDGQELMLKVDQATRE 136
            ++ R L++  ++G+     V   T E
Sbjct: 64  RKSER-LHRKKLNGR--EAFVHVVTLE 87

>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 = 37.3 bits (86), Expect = 8e-04
 Identities = 15/90 (16%), Positives = 25/90 (27%), Gaps = 8/90 (8%)

Query: 46  TVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFES 105
            V  +      VY G IA       +       G +   +            + F  F +
Sbjct: 10  VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFST 63

Query: 106 AEGVLRALRLLNKFNIDGQELMLKVDQATR 135
            E    A+  +N   I+G    +K      
Sbjct: 64  HESAAHAIVSVNGTTIEGHV--VKCYWGKE 91

>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 = 36.6 bits (84), Expect = 8e-04
 Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 55  TKVYVGKIAPTADSDFVLSVL--KVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 112
            ++ +  ++     + +L           K    A    +       F  FE+ +   RA
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 113 LRLLNKFNIDGQELMLKVDQATR 135
           L+ +N+  +  +E  + V  A +
Sbjct: 65  LQ-MNRSLLGNRE--ISVSLADK 84

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.4 bits (83), Expect = 0.001
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 5/80 (6%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           T V V  +  + + + V    K CG +     A          F   EF   +G L A+ 
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT 58

Query: 115 LLNKFNIDGQELMLKVDQAT 134
             +K  +   E  + V   T
Sbjct: 59  KTHKV-VGQNE--IIVSHLT 75

>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 = 36.7 bits (84), Expect = 0.001
 Identities = 24/96 (25%), Positives = 35/96 (36%), Gaps = 11/96 (11%)

Query: 49  PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP--------SNGTPKGFG 99
           P E    + +YV  +  +   D +    K CG VK  KR   P          G PKG  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 100 FCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATR 135
              +E       A+   +  +  G +  LKV  A +
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSK--LKVSLARK 95

>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 = 35.0 bits (80), Expect = 0.004
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 8/78 (10%)

Query: 56  KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 115
            +YV  +  +   + +             +          + + F  F + E  + A++ 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMKA 63

Query: 116 LNKFNIDGQELMLKVDQA 133
           LN   +DG    ++V  A
Sbjct: 64  LNGKVLDGSP--IEVTLA 79

>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 = 35.2 bits (80), Expect = 0.004
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 5/91 (5%)

Query: 49  PAEKPQ-TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 107
           P++  +   V++  ++  ++ + +  VL+  G +K  +   +P     KG  F +F + E
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 108 GVLRALRLLN-KFNIDGQELM---LKVDQAT 134
              + L   + +    G +L    LKVD A 
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 92

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	771
d1mp1a_	111	Ser/Arg-related nuclear matrix protein srm160 {Hum	99.88
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.69
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.68
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.67
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.67
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.66
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.66
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.66
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.65
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.64
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.64
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.64
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.62
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.62
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.61
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.6
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.59
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.59
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.59
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.58
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.58
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.58
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.58
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.58
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.57
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.57
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.56
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.56
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.56
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.54
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.54
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.54
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.53
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.52
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.51
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.5
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.5
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.49
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.47
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.47
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.47
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.47
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.46
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.46
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.45
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.45
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.44
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.44
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.42
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.41
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.41
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.4
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.4
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.39
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.38
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.38
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.38
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.37
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.37
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.37
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.36
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.35
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.35
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.34
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.32
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.32
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.31
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.27
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.25
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.2
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.19
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	99.09
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.07
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.02
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.93
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.87
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.76
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.37
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.74
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	94.66

>d1mp1a_ a.188.1.1 (A:) Ser/Arg-related nuclear matrix protein srm160 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PWI domain
superfamily: PWI domain
family: PWI domain
domain: Ser/Arg-related nuclear matrix protein srm160
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=6.3e-24  Score=190.83  Aligned_cols=90  Identities=21%  Similarity=0.460  Sum_probs=80.3

Q ss_pred             CchhhhcccccccccchhhHhhhhhhhHHHHHHhhcCcchhHHHHHHHHhhhc-cCCHHHHHHHHHHhhh-HHHHHHHHH
Q 004150          672 TKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQD-HVKASQMLELLQTILD-DEAEMFVLK  749 (771)
Q Consensus       672 ~k~~lf~~~i~w~~~d~~~~~~~i~pwi~kki~e~lG~ee~~lv~~i~~~l~~-~~~p~~l~~~l~~~ld-e~a~~fv~k  749 (771)
                      ..+++|+++|||+.|+..+    |+|||++||+||||++|++||+||+++|.. |.+|+.|+++|++||| ++|+.||.+
T Consensus         6 kfp~~f~~kVD~~kV~l~~----ikpWI~kkI~e~LG~EDdvvvd~i~~~L~~~~~dpk~l~i~L~gfLd~k~a~~Fv~e   81 (111)
T d1mp1a_           6 KFAECLEKKVDMSKVNLEV----IKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGE   81 (111)
T ss_dssp             CCCSGGGGCCCTTTSCSGG----GHHHHHHHHHHHHSSCCSHHHHHHHHHTTSSSCCHHHHHHHHTTTSCSHHHHHHHHH
T ss_pred             ccCHHHccccCHHHcCHHH----HHHHHHHHHHHHhCcchHHHHHHHHHHHHccCCCHHHHHHHHHHHhCcccHHHHHHH
Confidence            3568999999999998655    699999999999999999999999999986 5799999999999998 799999999


Q ss_pred             HHHHHHHHHHhhhhccc
Q 004150          750 MWRMLIFEIKKVETGLA  766 (771)
Q Consensus       750 lWrllife~~~~~~gl~  766 (771)
                      ||||||+.+.. ..||.
T Consensus        82 LW~LLi~aq~s-~~GIP   97 (111)
T d1mp1a_          82 LWPLLLSAQEN-IAGIP   97 (111)
T ss_dssp             HHHHHHHHTTS-SSSCC
T ss_pred             HHHHHHHhhcC-CcCCc
Confidence            99999976554 34764

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.69  E-value=1e-16  Score=150.27  Aligned_cols=83  Identities=23%  Similarity=0.332  Sum_probs=78.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||||||+.+++.+|+.+|+.||.|.+|.++.++.+|.++|||||+|.+.++|..||..|||+.|+|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34467899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus       119 a~~  121 (139)
T d1u6fa1         119 AAS  121 (139)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            764

>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=99.68  E-value=5.2e-17  Score=138.58  Aligned_cols=80  Identities=16%  Similarity=0.346  Sum_probs=77.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||+|||+.+++++|..+|+.||.|..++++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.+
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            57899999999999999999999999999999999988999999999999999999999999999999999999999864

>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=99.68  E-value=3.9e-17  Score=145.63  Aligned_cols=86  Identities=17%  Similarity=0.275  Sum_probs=79.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||||||+.+++++|+.+|+.||.|..|.++.+..+|+++|||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            345799999999999999999999999999999999998899999999999999999999996 9999999999999998


Q ss_pred             hhhHHHH
Q 004150          132 QATREYL  138 (771)
Q Consensus       132 ~~~kk~l  138 (771)
                      .+.+.+|
T Consensus        95 ~~~~nr~  101 (101)
T d2cq4a1          95 QAEKNRL  101 (101)
T ss_dssp             HHHHHHH
T ss_pred             CCCCCCC
Confidence            8766543

>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=99.67  E-value=1.4e-16  Score=139.56  Aligned_cols=82  Identities=21%  Similarity=0.307  Sum_probs=78.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ..++||||||||+.+++++|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.5e-16  Score=135.55  Aligned_cols=80  Identities=16%  Similarity=0.320  Sum_probs=76.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||||||+.+++.+|+.+|+.||.|..|.++.+..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+.+
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            46899999999999999999999999999999999988999999999999999999999999999999999999999865

>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=99.66  E-value=8e-17  Score=139.93  Aligned_cols=81  Identities=21%  Similarity=0.363  Sum_probs=77.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||||||+.+++.+|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
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            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      +
T Consensus        84 p   84 (89)
T d2cqba1          84 P   84 (89)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.66  E-value=1.9e-16  Score=137.34  Aligned_cols=82  Identities=22%  Similarity=0.237  Sum_probs=77.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|..+|+.||.|.+++++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
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            34689999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        85 ~~   86 (88)
T d1rk8a_          85 FV   86 (88)
T ss_dssp             EE
T ss_pred             cC
Confidence            64

>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=99.66  E-value=1.3e-16  Score=139.80  Aligned_cols=82  Identities=21%  Similarity=0.400  Sum_probs=78.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||||||+.+++.+|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
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            35799999999999999999999999999999999998999999999999999999999999999999999999999987


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      +.
T Consensus        88 ~~   89 (93)
T d1x5ua1          88 AH   89 (93)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=99.65  E-value=2.6e-16  Score=140.19  Aligned_cols=82  Identities=17%  Similarity=0.281  Sum_probs=78.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ++.++|||+|||+.+++.+|..+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..|||+.|+|+.|.|.|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      .+
T Consensus        96 ~~   97 (102)
T d2cpza1          96 RS   97 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=2.2e-16  Score=137.38  Aligned_cols=82  Identities=18%  Similarity=0.295  Sum_probs=78.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||+.+++.+|..+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            45689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      .+
T Consensus        86 kp   87 (90)
T d2cq0a1          86 KP   87 (90)
T ss_dssp             SC
T ss_pred             eC
Confidence            75

>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=99.64  E-value=2.4e-16  Score=134.15  Aligned_cols=77  Identities=19%  Similarity=0.343  Sum_probs=74.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +|||||||+.+++++|..+|+.||.|.+++++.++.+|+++|||||+|.++++|..|+..|||..|+|+.|.|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.1e-16  Score=133.45  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=73.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      +.++|||+|||+.+++.+|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|
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            4678999999999999999999999999999999999889999999999999999999999999999999999987

>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=99.62  E-value=3.7e-16  Score=133.01  Aligned_cols=79  Identities=19%  Similarity=0.267  Sum_probs=69.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      |||||+|||+.+++++|..+|+.||.|..+.++.+..+|+++|||||+|.+.++|..|+..|||..|+|+.|.|.++.+
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            7999999999999999999999999999998888878999999999999999999999999999999999999999865

>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=4.5e-16  Score=136.59  Aligned_cols=83  Identities=20%  Similarity=0.407  Sum_probs=77.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCCceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLL-NKFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~-~tGk~kGfGFVeF~~~esA~~Al~~L-ng~~I~Gr~L~V  128 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.|..+.++.+. .+|.++|||||.|.+.++|..||..| ||..|+|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            3456789999999999999999999999999999998875 48999999999999999999999988 899999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus        85 ~~A~~   89 (94)
T d2cpha1          85 EWADS   89 (94)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99875

>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=99.62  E-value=4.7e-16  Score=133.90  Aligned_cols=78  Identities=18%  Similarity=0.302  Sum_probs=73.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEEe
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKVD  131 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G--r~L~V~~a  131 (771)
                      .++|||||||+.+++.+|+.+|+.||.|.+++++.++.+|.++|||||+|.+.++|..|+..|||..++|  ++|.|+||
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            5789999999999999999999999999999999998899999999999999999999999999999997  55888885

>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=8.4e-16  Score=135.87  Aligned_cols=82  Identities=16%  Similarity=0.258  Sum_probs=78.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|..||.|..+.++.++.+|.++|||||+|.+.++|..||..||+..|+|+.|.|.++
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            34678999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        86 ~~   87 (99)
T d1whwa_          86 TI   87 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.62  E-value=2e-16  Score=136.31  Aligned_cols=79  Identities=22%  Similarity=0.456  Sum_probs=76.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ++|||||||+.+++.+|..+|+.||.|.+++++.++.||.++|||||+|.++++|..|+..|||..|+|+.|.|.++..
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999999999865

>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=99.62  E-value=6.3e-16  Score=132.93  Aligned_cols=79  Identities=22%  Similarity=0.379  Sum_probs=75.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  130 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G--r~L~V~~  130 (771)
                      ..++|||+|||+.+++.+|+.+|+.||.|..++++.++.+|+++|||||+|.+.++|..||..|||..+.|  ++|.|.|
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            46789999999999999999999999999999999998899999999999999999999999999999976  8899998


Q ss_pred             e
Q 004150          131 D  131 (771)
Q Consensus       131 a  131 (771)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.61  E-value=1.2e-15  Score=129.20  Aligned_cols=76  Identities=18%  Similarity=0.260  Sum_probs=73.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      +|||+|||+.+++.+|..+|+.||.|.++.++.+ .+|+++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCS-SCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe-eccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5999999999999999999999999999999998 599999999999999999999999999999999999999875

>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=99.60  E-value=1.1e-15  Score=131.33  Aligned_cols=78  Identities=21%  Similarity=0.365  Sum_probs=74.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .++|||||||+++++.+|..+|+.||.|..+.++.++.+|.++|||||+|.+.+.|..||. +++..|+|+.|.|+.|.
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            4789999999999999999999999999999999999999999999999999999999998 79999999999998764

>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=7.2e-16  Score=133.76  Aligned_cols=82  Identities=18%  Similarity=0.361  Sum_probs=77.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ....+|||||||+.+++.+|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|..||..|||+.|+|+.|.|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34678999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        83 ~~   84 (90)
T d1x5sa1          83 GK   84 (90)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>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=99.60  E-value=2.5e-16  Score=133.45  Aligned_cols=76  Identities=22%  Similarity=0.383  Sum_probs=73.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      |+|||||||+.+++++|+.+|+.||.|.++.++.++.+|+++|||||+|.+.++|.+||. +++..|+|+.|.|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999998 7999999999999875

>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=3.2e-15  Score=129.88  Aligned_cols=81  Identities=21%  Similarity=0.324  Sum_probs=74.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+++||||||||+.+++.+|+.+|+.||.|..+.++.+..++  +|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999999985443  78999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        83 a~~   85 (90)
T d2cqia1          83 ATT   85 (90)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.59  E-value=2.5e-15  Score=130.96  Aligned_cols=80  Identities=19%  Similarity=0.249  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+++++.+|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..||..  +..|+|+.|.|+++
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            3467899999999999999999999999999999999998999999999999999999999984  45899999999988


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      .+
T Consensus        84 ~~   85 (90)
T d2cqga1          84 NS   85 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            65

>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=99.59  E-value=1.9e-15  Score=134.81  Aligned_cols=81  Identities=19%  Similarity=0.283  Sum_probs=75.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||||||+.+++++|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..+|+ .|+|+.|.|.++
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            3457899999999999999999999999999999999988999999999999999999999998876 799999999988


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        87 ~~   88 (103)
T d2cqda1          87 YL   88 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.58  E-value=3e-15  Score=126.58  Aligned_cols=77  Identities=16%  Similarity=0.362  Sum_probs=73.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .++|||||||+.+++++|+.+|+.||.|..+.++.++.++.++|||||+|.+.+++.+|+. |||..|+|+.|.|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4689999999999999999999999999999999999999999999999999999999997 8999999999999865

>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=9.2e-16  Score=136.73  Aligned_cols=81  Identities=30%  Similarity=0.537  Sum_probs=77.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||+|||+.+++.+|..+|+.||.|.++.++.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++..
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            56899999999999999999999999999999999988999999999999999999999999999999999999999865


Q ss_pred             h
Q 004150          134 T  134 (771)
Q Consensus       134 ~  134 (771)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.3e-15  Score=128.04  Aligned_cols=74  Identities=20%  Similarity=0.375  Sum_probs=70.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .|||||||+++++++|..+|+.||.|..+.++.++.+|+++|||||+|.+.++|..||. +++..|+|+.|.|+.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            48999999999999999999999999999999999999999999999999999999998 899999999999864

>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=99.58  E-value=6e-15  Score=129.01  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=74.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|+.+|+.||.|.+|.++.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4457789999999999999999999999999999999874  44789999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +.+
T Consensus        86 A~~   88 (93)
T d2cq3a1          86 ATA   88 (93)
T ss_dssp             CCS
T ss_pred             cCc
Confidence            875

>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=99.58  E-value=1.6e-15  Score=129.63  Aligned_cols=77  Identities=18%  Similarity=0.397  Sum_probs=72.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           57 VYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        57 VfVgNLp~~vte~~L~~lF~~~G~V~s~-kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      |||||||+++++.+|..+|+.||.|..+ .++.++.+|+++|||||+|.+.++|..||..|||..|+|+.|.|.|+..
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecC
Confidence            7999999999999999999999998765 7888888999999999999999999999999999999999999999864

>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=2.1e-15  Score=129.42  Aligned_cols=77  Identities=21%  Similarity=0.469  Sum_probs=71.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC---CCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           57 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNG---TPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        57 VfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tG---k~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      |||||||+++++++|+.+|+.||.|.++.++.++.++   .++|||||+|.+.++|..|+..|||..|+|+.|.|.|+..
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            7999999999999999999999999999999886554   4689999999999999999999999999999999998754

>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=99.57  E-value=2.4e-15  Score=134.42  Aligned_cols=79  Identities=22%  Similarity=0.341  Sum_probs=75.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      .++|||||||+++++++|+.+|+.||.|..+.|+.++.++.++|||||+|.+.++|..||. +++..|+|+.|.|.++.+
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            4789999999999999999999999999999999998899999999999999999999997 899999999999988765

>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=99.57  E-value=5.1e-15  Score=133.78  Aligned_cols=78  Identities=13%  Similarity=0.235  Sum_probs=72.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .+++|||||||+.+++.+|..+|+.||.|.+|.+..   ++.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            367999999999999999999999999999998875   46778999999999999999999999999999999999986


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            5

>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=99.56  E-value=2.7e-15  Score=130.09  Aligned_cols=79  Identities=18%  Similarity=0.365  Sum_probs=73.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      ..+|||+|||+.+++.+|..+|+.||.|..+.++.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.++..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999984  45789999999999999999999999999999999999875


Q ss_pred             h
Q 004150          134 T  134 (771)
Q Consensus       134 ~  134 (771)
                      .
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=6.4e-15  Score=129.22  Aligned_cols=81  Identities=19%  Similarity=0.363  Sum_probs=75.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhC------CceeCCeEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLN------KFNIDGQEL  126 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Ln------g~~I~Gr~L  126 (771)
                      ..++|||||||+.+++++|+.+|+.||.|..+.++.+..++.++|||||+|.+.++|..||..||      |..|+|+.|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            46789999999999999999999999999999999998899999999999999999999999886      678999999


Q ss_pred             EEEEehh
Q 004150          127 MLKVDQA  133 (771)
Q Consensus       127 ~V~~a~~  133 (771)
                      .|.++..
T Consensus        87 ~v~~a~~   93 (98)
T d1x4ha1          87 KVDLAVT   93 (98)
T ss_dssp             EEECCCC
T ss_pred             EEEECCC
Confidence            9998764

>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=99.56  E-value=1.5e-15  Score=128.02  Aligned_cols=75  Identities=21%  Similarity=0.345  Sum_probs=71.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .|||||||+++++++|+.+|+.||.|..+.++.++.+|+++|||||+|.+.++|.+||. +++..|+|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999998 6778999999998764

>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=7.3e-15  Score=129.66  Aligned_cols=83  Identities=19%  Similarity=0.331  Sum_probs=75.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVK--------SWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~--------s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ....++|||||||+.+++.+|+.+|..||.|.        .+.+..+..+|+++|||||+|.+.++|..||..|||+.|+
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            34578999999999999999999999999874        4566777788999999999999999999999999999999


Q ss_pred             CeEEEEEEehh
Q 004150          123 GQELMLKVDQA  133 (771)
Q Consensus       123 Gr~L~V~~a~~  133 (771)
                      |+.|.|.++..
T Consensus        85 gr~i~V~~a~~   95 (101)
T d2cpea1          85 GSKLKVSLARK   95 (101)
T ss_dssp             TEECEEECSSC
T ss_pred             CEEEEEEEcCC
Confidence            99999999864

>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=99.54  E-value=3.9e-15  Score=124.39  Aligned_cols=75  Identities=21%  Similarity=0.313  Sum_probs=71.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           56 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        56 tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .|||||||+++++++|+.+|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+. |||..|+|+.|.|.+|
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            48999999999999999999999999999999998899999999999999999999997 9999999999999875

>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=99.54  E-value=1.5e-15  Score=134.56  Aligned_cols=82  Identities=20%  Similarity=0.322  Sum_probs=77.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      .+.++|||+|||..+++.+|..+|+.||.|..+.++.+..+|+++|||||.|.+.++|..||..|||..|+|+.|.|.|+
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            34689999999999999999999999999999998888778999999999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        96 k~   97 (102)
T d2cpxa1          96 KN   97 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.53  E-value=1.9e-14  Score=126.20  Aligned_cols=80  Identities=19%  Similarity=0.357  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+.+++.+|+.+|+.||.|..+.+..   ++.+++||||+|.+.++|..||..|||+.|+|++|.|.|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45578999999999999999999999999999988755   456789999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        88 a~~   90 (95)
T d1x4aa1          88 PRS   90 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            864

>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=99.53  E-value=7.9e-15  Score=126.37  Aligned_cols=80  Identities=11%  Similarity=0.225  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCCC-HHHHHHHHHhcCCeeEEEEeec-CCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           53 PQTKVYVGKIAPTAD-SDFVLSVLKVCGTVKSWKRAQY-PSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        53 ~~~tVfVgNLp~~vt-e~~L~~lF~~~G~V~s~kiv~d-~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..++|||+|||+.++ ++.|+.+|+.||.|.++.++.+ ..+|.++|||||+|.+.++|..||. |||..|+|+.|.|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            367999999999876 5679999999999999998764 4689999999999999999999997 999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.52  E-value=2.8e-15  Score=130.86  Aligned_cols=80  Identities=21%  Similarity=0.386  Sum_probs=74.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..+.++.+ .+|+++|||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34679999999999999999999999999999888765 699999999999999999999997 9999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.51  E-value=2.1e-14  Score=123.60  Aligned_cols=77  Identities=18%  Similarity=0.185  Sum_probs=72.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .++|||+|||+.+++.+|..+|+.||.|..|.+..+ .+|.++|||||+|.+.++|.+||. +++..++|+.|.|.|..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            579999999999999999999999999999999887 589999999999999999999997 89999999999998753

>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=99.51  E-value=7.8e-15  Score=130.19  Aligned_cols=82  Identities=24%  Similarity=0.306  Sum_probs=75.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...+++|||||||+.+++.+|..+|+.||.|..+.++.+ .+|.++|||||+|.+.++|..||..|||..|.|++|.|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            344689999999999999999999999999999999888 5899999999999999999999999999999999988876


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +.+
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.50  E-value=2.9e-14  Score=125.51  Aligned_cols=75  Identities=20%  Similarity=0.321  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||||||+.+++.+|+.+|+.||.|.+++++.+      +|||||.|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4679999999999999999999999999999999876      5899999999999999999999999999999999986


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        91 ~   91 (96)
T d1x4ga1          91 E   91 (96)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=3.6e-14  Score=126.14  Aligned_cols=79  Identities=20%  Similarity=0.436  Sum_probs=71.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~-~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      +.++|||+|||+.+++.+|+.+|+.|| +..+.++.+. .+|.++|||||+|.+.++|.+|+. ||+..|+|+.|.|.++
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            458999999999999999999999999 7788877764 578999999999999999987775 9999999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        92 ~~   93 (104)
T d1wi8a_          92 DQ   93 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.49  E-value=4.3e-14  Score=120.82  Aligned_cols=77  Identities=12%  Similarity=0.219  Sum_probs=69.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNID-GQELMLK  129 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~-Gr~L~V~  129 (771)
                      .+|+++|||+|||..+++.+|..+|+.||.|..++++.+     .+|||||+|.+.++|..|+..|||..|. |+.|.|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            345789999999999999999999999999999999764     3589999999999999999999999985 7899999


Q ss_pred             Eeh
Q 004150          130 VDQ  132 (771)
Q Consensus       130 ~a~  132 (771)
                      |+.
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            985

>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=99.47  E-value=3.4e-14  Score=121.97  Aligned_cols=79  Identities=20%  Similarity=0.182  Sum_probs=70.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSW-KRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~-kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      +..++|||+|||+++++++|.++|..||.+... .+..+ .+|.++|||||+|.+.++|..||..||+..|+|++|.|.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345789999999999999999999999998764 44444 6899999999999999999999999999999999999987


Q ss_pred             e
Q 004150          131 D  131 (771)
Q Consensus       131 a  131 (771)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=9.6e-15  Score=121.32  Aligned_cols=71  Identities=20%  Similarity=0.359  Sum_probs=68.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           57 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        57 VfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      |||+|||+++++.+|..+|+.||.|..++++.++.++.++|||||+|.+.++|..|+..|||..|+|+.|+
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            79999999999999999999999999999999988999999999999999999999999999999998763

>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=99.47  E-value=5.7e-14  Score=121.15  Aligned_cols=78  Identities=14%  Similarity=0.247  Sum_probs=69.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee-CCeEEEEEE
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI-DGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I-~Gr~L~V~~  130 (771)
                      +|+++|||||||+.+++++|..+|+.||.|..+.+..    ++.+|||||+|.+.++|..|+..|||..| +|+.|.|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            3468999999999999999999999999998887654    35578999999999999999999999998 589999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            865

>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=99.47  E-value=3.4e-14  Score=123.27  Aligned_cols=76  Identities=17%  Similarity=0.233  Sum_probs=69.0

Q ss_pred             CCEEEEcCCCCCCCHHHH---HHHHHhcCCeeEEEEeecCCCCCC---ceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 004150           54 QTKVYVGKIAPTADSDFV---LSVLKVCGTVKSWKRAQYPSNGTP---KGFGFCEFESAEGVLRALRLLNKFNIDGQELM  127 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L---~~lF~~~G~V~s~kiv~d~~tGk~---kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~  127 (771)
                      .++|||+|||+.+++++|   .++|++||.|..+.++.++.++.+   +|||||+|.+.++|..||..|||..|+|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            467999999999999999   678999999999999998755544   58999999999999999999999999999999


Q ss_pred             EE
Q 004150          128 LK  129 (771)
Q Consensus       128 V~  129 (771)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>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=99.46  E-value=4e-14  Score=124.30  Aligned_cols=78  Identities=17%  Similarity=0.247  Sum_probs=70.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ..+.++|||+|||+++++.+|+.+|..||.|..+.     .+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34578999999999999999999999999876653     3688999999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        88 a~~   90 (96)
T d1fjca_          88 TGE   90 (96)
T ss_dssp             CSS
T ss_pred             eCC
Confidence            875

>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=99.46  E-value=3.5e-14  Score=123.48  Aligned_cols=82  Identities=13%  Similarity=0.297  Sum_probs=72.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVL----SVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML  128 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~----~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V  128 (771)
                      |.+||||||||+.+++++|+    .+|+.||.|.++.+..   ++.++|||||+|.+.++|..|+..|||..|+|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            57899999999999998875    4689999999988754   5778899999999999999999999999999999999


Q ss_pred             EEehhhHHH
Q 004150          129 KVDQATREY  137 (771)
Q Consensus       129 ~~a~~~kk~  137 (771)
                      .|+....++
T Consensus        79 ~~ak~~~~~   87 (91)
T d1nu4a_          79 QYAKTDSDI   87 (91)
T ss_dssp             EECSSCCTH
T ss_pred             EEeCCCchh
Confidence            999765433

>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=99.45  E-value=1e-13  Score=116.43  Aligned_cols=73  Identities=21%  Similarity=0.276  Sum_probs=67.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      +||||+|||+++++++|+.+|+.||.|..+.++.++  +...+||||+|.+.++|.+||. +|+..|+|+.|.|..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~--~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT--TSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeec--cccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEE
Confidence            589999999999999999999999999999999884  3345799999999999999996 899999999999974

>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=99.45  E-value=5.4e-14  Score=123.36  Aligned_cols=80  Identities=18%  Similarity=0.287  Sum_probs=72.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecC-CCCCCceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEEE
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGT-VKSWKRAQYP-SNGTPKGFGFCEFESAEGVLRALRLLN--KFNIDGQELMLK  129 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~-V~s~kiv~d~-~tGk~kGfGFVeF~~~esA~~Al~~Ln--g~~I~Gr~L~V~  129 (771)
                      .|+|||||||..+++++|..+|+.||. |..+.++.+. .+|.++|||||+|.+.++|..|+..|+  ++.++|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999995 8999998875 468999999999999999999999886  456679999999


Q ss_pred             Eehh
Q 004150          130 VDQA  133 (771)
Q Consensus       130 ~a~~  133 (771)
                      |+.+
T Consensus        81 ~A~p   84 (96)
T d2disa1          81 WAEP   84 (96)
T ss_dssp             ESCS
T ss_pred             EcCC
Confidence            9975

>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=99.44  E-value=7.5e-14  Score=120.29  Aligned_cols=75  Identities=19%  Similarity=0.337  Sum_probs=70.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.+++.+|..+|+.||.|.++.+..+      +|||||+|.+.++|..|+..|||..|+|+.|.|.|+.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            4578999999999999999999999999999999865      4899999999999999999999999999999999986


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        81 ~   81 (86)
T d2cpja1          81 H   81 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.44  E-value=7.7e-14  Score=124.93  Aligned_cols=76  Identities=12%  Similarity=0.073  Sum_probs=69.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|+.+|+.||.|..|.|..      .+|||||.|.+.++|..||..|||..|.|+.|.|.|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            3468999999999999999999999999999998743      4689999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        82 ~~   83 (111)
T d1whxa_          82 PI   83 (111)
T ss_dssp             ET
T ss_pred             CC
Confidence            64

>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=99.42  E-value=3.3e-13  Score=115.75  Aligned_cols=75  Identities=13%  Similarity=0.266  Sum_probs=68.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ...+|||||||+.+++.+|..+|+.||.|..+.+.      .++|||||.|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            35789999999999999999999999998877664      346899999999999999999999999999999999986


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      +
T Consensus        81 P   81 (86)
T d2cpda1          81 P   81 (86)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.41  E-value=1.8e-13  Score=120.79  Aligned_cols=74  Identities=18%  Similarity=0.296  Sum_probs=66.8

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           52 KPQTKVYVGKIA-PTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        52 ~~~~tVfVgNLp-~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ...++|||+||| ..+++.+|+.+|++||.|..+.+.        +|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999997 578888999999999999999883        48999999999999999999999999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        85 a~~   87 (98)
T d1wf2a_          85 AAE   87 (98)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            754

>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=99.41  E-value=2e-13  Score=121.15  Aligned_cols=81  Identities=16%  Similarity=0.196  Sum_probs=71.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ....+|||+|||+.+++.+|..+|..||.|..+.++....+|.++|||||+|.+.++|..||. ||+..|+|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345779999999999999999999999998875554444799999999999999999999997 9999999999999887


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            43

>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=99.40  E-value=9.9e-14  Score=117.84  Aligned_cols=73  Identities=15%  Similarity=0.311  Sum_probs=66.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEEEehh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF-NIDGQELMLKVDQA  133 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~-~I~Gr~L~V~~a~~  133 (771)
                      .+|||||||+.+++.+|+.+|+.||.|..+.++..      +|||||+|.+.++|..|+..|||. .|+|+.|.|.|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            47999999999999999999999999877666553      589999999999999999999985 79999999999875

>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=99.40  E-value=2.2e-13  Score=115.32  Aligned_cols=74  Identities=14%  Similarity=0.234  Sum_probs=67.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...+||||+||+  +|+++|+.+|+.||.|.++.+..+      +|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346899999986  899999999999999999988654      479999999999999999999999999999999998


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        75 ~~   76 (79)
T d2bz2a1          75 RK   76 (79)
T ss_dssp             CS
T ss_pred             cC
Confidence            64

>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=99.39  E-value=2.7e-13  Score=121.06  Aligned_cols=74  Identities=15%  Similarity=0.263  Sum_probs=68.6

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           54 QTKVYVGKIAP-TADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~-~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .++|||+|||+ .+++++|..+|+.||.|..|.++.+.     +|||||+|.+.++|.+||..|||..|+|+.|.|.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 69999999999999999999998862     6899999999999999999999999999999999875

>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=99.38  E-value=8.5e-14  Score=120.06  Aligned_cols=71  Identities=20%  Similarity=0.198  Sum_probs=66.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .+|||||||+.+++.+|..+|+.||.|..+.++.+       |||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~   71 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            36999999999999999999999999999998765       899999999999999999999999999999987654

>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=99.38  E-value=4.6e-13  Score=118.18  Aligned_cols=75  Identities=19%  Similarity=0.222  Sum_probs=68.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|..+|+.||.|..+.+..+       |||||+|.+.++|..||..|||..|+|+.|.|.+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc-------ceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            34678999999999999999999999999999998654       89999999999999999999999999999999886


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        86 ~~   87 (98)
T d1wg4a_          86 RV   87 (98)
T ss_dssp             EE
T ss_pred             ec
Confidence            53

>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=99.38  E-value=4.5e-13  Score=119.12  Aligned_cols=81  Identities=15%  Similarity=0.098  Sum_probs=73.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ....+|||+|||+.+++.+|+++|..||.|....++.+..++.++|||||+|.+.++|.+|+. ||+..|+|+.|.|.++
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            345679999999999999999999999999887676766899999999999999999999997 9999999999999877


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      ..
T Consensus        92 ~~   93 (104)
T d1wg5a_          92 SR   93 (104)
T ss_dssp             CT
T ss_pred             CH
Confidence            64

>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=99.37  E-value=3.1e-13  Score=121.05  Aligned_cols=79  Identities=14%  Similarity=0.119  Sum_probs=70.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee--CCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI--DGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I--~Gr~L~V  128 (771)
                      ..+..+|||+|||+.+|+++|..+|+.||.|..+.++.+    +.+|||||+|.+.++|..||..|||..|  +|..|.|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~----~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee----CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            345678999999999999999999999999999999876    3579999999999999999999999998  4788888


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .++..
T Consensus        80 ~~s~~   84 (108)
T d2adba1          80 DFSKL   84 (108)
T ss_dssp             EECSS
T ss_pred             EecCC
Confidence            87754

>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=99.37  E-value=3.6e-13  Score=121.55  Aligned_cols=82  Identities=21%  Similarity=0.247  Sum_probs=72.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||+|||+.+++.+|..+|+.||.+..+.++.+..+|.+.|||||+|.+.++|.+|+. |||..|+|+.|.|.++
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            346789999999999999999999999988765555555799999999999999999999997 9999999999999887


Q ss_pred             hhh
Q 004150          132 QAT  134 (771)
Q Consensus       132 ~~~  134 (771)
                      ...
T Consensus        95 ~~~   97 (112)
T d1wela1          95 TKK   97 (112)
T ss_dssp             CHH
T ss_pred             ChH
Confidence            553

>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=99.37  E-value=1.1e-12  Score=115.15  Aligned_cols=75  Identities=17%  Similarity=0.426  Sum_probs=68.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG--QELMLKV  130 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G--r~L~V~~  130 (771)
                      |.++|||+|||+++++++|+++|+.||.|..+.++.+      ++||||+|.+.++|..|+..||+..|+|  ++|.|.|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4689999999999999999999999999999998765      4899999999999999999999999986  5899998


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        90 ak~   92 (97)
T d1whya_          90 AKS   92 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=5.8e-13  Score=115.10  Aligned_cols=74  Identities=15%  Similarity=0.304  Sum_probs=64.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           53 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        53 ~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..++|||+|||+.+++.+|+.+|..|| +..+.+      +.++|||||+|.+.++|..||..||++.|+|+.|.|.|+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999 222322      3456899999999999999999999999999999999875


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        77 ~   77 (88)
T d1wg1a_          77 T   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.35  E-value=3.2e-13  Score=116.61  Aligned_cols=75  Identities=15%  Similarity=0.199  Sum_probs=67.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           52 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      ...++|||||||+.+++++|+.+|+.||.|..+++.     +.+++||||+|.+.+.|..||.  +++.|+|+.|.|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            347899999999999999999999999999998764     3467899999999999999985  888999999999987


Q ss_pred             hh
Q 004150          132 QA  133 (771)
Q Consensus       132 ~~  133 (771)
                      .+
T Consensus        76 ~~   77 (88)
T d1wf0a_          76 EP   77 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.35  E-value=1.5e-12  Score=112.11  Aligned_cols=77  Identities=13%  Similarity=0.167  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L--ng~~I~Gr~L~V  128 (771)
                      ..|+++|||||||+.+++++|..+|+.||.|..+.++.+      ++||||+|.+.++|..|+..|  ++..|+|+.|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            456889999999999999999999999999999988765      379999999999999999755  678999999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus        79 ~~sk~   83 (88)
T d2cq1a1          79 QYSNH   83 (88)
T ss_dssp             EECSC
T ss_pred             EECCC
Confidence            99864

>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=99.34  E-value=5.5e-13  Score=118.24  Aligned_cols=80  Identities=14%  Similarity=0.104  Sum_probs=71.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      .....+|||+|||+++|+.+|+.+|..|| +..+.++.+ .+|.++|||||+|.+.++|..||. ||+..|+|+.|.|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34467899999999999999999999998 557777777 579999999999999999999997 899999999999988


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +..
T Consensus        89 s~~   91 (102)
T d1weza_          89 NST   91 (102)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            764

>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=99.32  E-value=3.8e-12  Score=122.67  Aligned_cols=82  Identities=15%  Similarity=0.332  Sum_probs=77.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV  130 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~  130 (771)
                      ....++|||+|||+.+++.+|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. +++..|+|+.|.|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            4456899999999999999999999999999999999998899999999999999999999998 799999999999999


Q ss_pred             ehh
Q 004150          131 DQA  133 (771)
Q Consensus       131 a~~  133 (771)
                      +.+
T Consensus       173 A~~  175 (183)
T d1u1qa_         173 ALS  175 (183)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.32  E-value=2.3e-12  Score=108.04  Aligned_cols=70  Identities=14%  Similarity=0.183  Sum_probs=63.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEehh
Q 004150           57 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA  133 (771)
Q Consensus        57 VfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~~  133 (771)
                      |||||||+++++.+|..+|+.|| +..+.      +++++|||||+|.+.++|..|+..|||..++|+.|.|.|+..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~------~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCF------VDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE------EETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee------ecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 44443      345679999999999999999999999999999999999854

>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=99.31  E-value=7.3e-13  Score=117.02  Aligned_cols=78  Identities=14%  Similarity=0.256  Sum_probs=69.4

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHH--HhCCceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR--LLNKFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~-vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~--~Lng~~I~Gr~L~  127 (771)
                      ..++++|||+|||.. +++.+|..+|+.||.|..+.++.+      +|||||+|.+.++|..||.  .+++..|+|+.|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345789999999984 899999999999999999998765      4899999999999999997  4789999999999


Q ss_pred             EEEehhh
Q 004150          128 LKVDQAT  134 (771)
Q Consensus       128 V~~a~~~  134 (771)
                      |.|+...
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9998653

>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=99.27  E-value=3.5e-12  Score=110.43  Aligned_cols=77  Identities=12%  Similarity=0.094  Sum_probs=69.1

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEE
Q 004150           51 EKPQTKVYVGKIAPT-ADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELM  127 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~-vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L--ng~~I~Gr~L~  127 (771)
                      ..++.+|||+|||.. +|+.+|..+|+.||.|..+.++.++      +||||.|.+.++|..|+..|  ++..++|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            345789999999996 7899999999999999999998753      69999999999999999866  78899999999


Q ss_pred             EEEehh
Q 004150          128 LKVDQA  133 (771)
Q Consensus       128 V~~a~~  133 (771)
                      |.|+..
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999864

>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=99.25  E-value=9.9e-12  Score=110.37  Aligned_cols=77  Identities=16%  Similarity=0.184  Sum_probs=69.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEE
Q 004150           51 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL--NKFNIDGQELML  128 (771)
Q Consensus        51 ~~~~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~L--ng~~I~Gr~L~V  128 (771)
                      ..+..+|||+|||+.+++.+|..+|..||.|..+.+..+      ++||||+|.+.++|..||..|  +++.++|++|.|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345789999999999999999999999999999988754      489999999999999999877  567889999999


Q ss_pred             EEehh
Q 004150          129 KVDQA  133 (771)
Q Consensus       129 ~~a~~  133 (771)
                      .|+..
T Consensus        86 ~~s~~   90 (104)
T d1wexa_          86 NYSTS   90 (104)
T ss_dssp             EECSS
T ss_pred             EEcCC
Confidence            98864

>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=99.20  E-value=5.3e-12  Score=112.55  Aligned_cols=76  Identities=13%  Similarity=0.013  Sum_probs=67.6

Q ss_pred             CCCCEEEEcCCCCCCCH-----HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 004150           52 KPQTKVYVGKIAPTADS-----DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL  126 (771)
Q Consensus        52 ~~~~tVfVgNLp~~vte-----~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L  126 (771)
                      ...++|||+||+..+..     ..|..+|+.||.|.+|.+...      ++||||.|.+.++|..|+..|||..|+|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            45789999999997633     569999999999999998753      5899999999999999999999999999999


Q ss_pred             EEEEehh
Q 004150          127 MLKVDQA  133 (771)
Q Consensus       127 ~V~~a~~  133 (771)
                      .|.|+..
T Consensus        77 ~v~~a~~   83 (104)
T d1weya_          77 KLYFAQT   83 (104)
T ss_dssp             EEECCCC
T ss_pred             EEeeccc
Confidence            9999854

>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=99.19  E-value=3.2e-13  Score=116.80  Aligned_cols=74  Identities=20%  Similarity=0.349  Sum_probs=66.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe-----ecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRA-----QYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLK  129 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv-----~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~  129 (771)
                      ++|||||||+.+++++|.++|+.||.+..+.+.     .+..++.++|||||+|.+.++|..|+. |||+.|+|+.|.|.
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            689999999999999999999999987766543     334678899999999999999999996 99999999999995

>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=5.6e-12  Score=112.41  Aligned_cols=76  Identities=14%  Similarity=0.126  Sum_probs=71.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVD  131 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a  131 (771)
                      +.++|.+++..++++.|..+|++||.|.++.|+.+ .+|.++|||||.|.+.++|.+|+..|||..++|+.|.|.++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46889999999999999999999999999999887 69999999999999999999999999999999999999875

>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=99.09  E-value=7.6e-11  Score=106.24  Aligned_cols=75  Identities=11%  Similarity=0.037  Sum_probs=65.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCH-HHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESA-EGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~-esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ...+||||||+.+|+++|+.+|+.||.|.++.++.+      +|||||.|.+. +.|..|+..|++..|.++.+.|.|..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            556799999999999999999999999999999865      58999999985 67889999999999887777777765


Q ss_pred             hh
Q 004150          133 AT  134 (771)
Q Consensus       133 ~~  134 (771)
                      ..
T Consensus        85 ~~   86 (113)
T d1owxa_          85 LE   86 (113)
T ss_dssp             CC
T ss_pred             cc
Confidence            44

>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=99.07  E-value=1.9e-10  Score=110.50  Aligned_cols=78  Identities=21%  Similarity=0.365  Sum_probs=71.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      .++|||||||+.+++.+|..+|+.||.|.++.++.+..+|.++|||||+|.+.++|..|+. +++..++++.+.+....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            3699999999999999999999999999999999998999999999999999999999998 67778888888876544

>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=99.02  E-value=3.7e-10  Score=99.80  Aligned_cols=65  Identities=23%  Similarity=0.371  Sum_probs=57.9

Q ss_pred             CCCCCEEEE--cCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCcee
Q 004150           51 EKPQTKVYV--GKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNI  121 (771)
Q Consensus        51 ~~~~~tVfV--gNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I  121 (771)
                      ..+..++||  ||||+.+++++|+.+|+.||.|..+.++.+      ++||||.|.+.++|..|+..|||..|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            344678888  559999999999999999999999988765      47999999999999999999999987

>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=98.93  E-value=7.2e-10  Score=97.51  Aligned_cols=81  Identities=11%  Similarity=0.135  Sum_probs=68.0

Q ss_pred             CCCCCEEEEcCC--CCCCC---------HHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCc
Q 004150           51 EKPQTKVYVGKI--APTAD---------SDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKF  119 (771)
Q Consensus        51 ~~~~~tVfVgNL--p~~vt---------e~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~  119 (771)
                      .....+|+|.||  |..+.         .++|+..|++||.|..+.+..+    .++|||||.|.+.++|..|+..|||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            345789999999  43321         2578899999999999988654    56799999999999999999999999


Q ss_pred             eeCCeEEEEEEehhhH
Q 004150          120 NIDGQELMLKVDQATR  135 (771)
Q Consensus       120 ~I~Gr~L~V~~a~~~k  135 (771)
                      .++|+.|.|.+.....
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999987643

>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=98.87  E-value=2e-09  Score=91.35  Aligned_cols=72  Identities=13%  Similarity=0.017  Sum_probs=60.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeE-EEEEEeh
Q 004150           54 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQE-LMLKVDQ  132 (771)
Q Consensus        54 ~~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~-L~V~~a~  132 (771)
                      .+.|||+++|+.+++..| .+|+.||.|.++.+..      .++||||.|.+.++|.+||. +||..|+|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999986555 5899999999997643      45899999999999999997 9999999975 5576654


Q ss_pred             h
Q 004150          133 A  133 (771)
Q Consensus       133 ~  133 (771)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=4.4e-09  Score=93.05  Aligned_cols=82  Identities=17%  Similarity=0.086  Sum_probs=68.4

Q ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeecCCC--CCCceEEEEEeCCHHHHHHHHHHhCCc
Q 004150           52 KPQTKVYVGKI--APTAD--------SDFVLSVLKVCGTVKSWKRAQYPSN--GTPKGFGFCEFESAEGVLRALRLLNKF  119 (771)
Q Consensus        52 ~~~~tVfVgNL--p~~vt--------e~~L~~lF~~~G~V~s~kiv~d~~t--Gk~kGfGFVeF~~~esA~~Al~~Lng~  119 (771)
                      +|+..|.|.||  +..+.        .++|+..|++||.|.++.|+.+..+  ....||+||.|.+.++|..|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            45778999999  33332        2468999999999999999876433  344689999999999999999999999


Q ss_pred             eeCCeEEEEEEehh
Q 004150          120 NIDGQELMLKVDQA  133 (771)
Q Consensus       120 ~I~Gr~L~V~~a~~  133 (771)
                      .++|+.|.|.+...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999874

>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=96.37  E-value=0.0042  Score=52.41  Aligned_cols=69  Identities=17%  Similarity=0.226  Sum_probs=55.9

Q ss_pred             CCCEEEEcCCCCC------CCH---HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 004150           53 PQTKVYVGKIAPT------ADS---DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDG  123 (771)
Q Consensus        53 ~~~tVfVgNLp~~------vte---~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~G  123 (771)
                      +.-||.|.=....      ..+   ..|.+.|..||.|.-++++.+        --+|+|.+-.+|++|+. |+|.++.|
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G   84 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcc
Confidence            3557777544432      233   367788899999999999886        78999999999999999 99999999


Q ss_pred             eEEEEEE
Q 004150          124 QELMLKV  130 (771)
Q Consensus       124 r~L~V~~  130 (771)
                      +.|.|..
T Consensus        85 ~~l~It~   91 (95)
T d1ufwa_          85 RAVKISG   91 (95)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEec
Confidence            9999864

>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=95.74  E-value=0.024  Score=45.50  Aligned_cols=61  Identities=13%  Similarity=0.262  Sum_probs=52.0

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCCceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEeh
Q 004150           69 DFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ  132 (771)
Q Consensus        69 ~~L~~lF~~~G~V~s~kiv~d~~tGk~kGfGFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~  132 (771)
                      ..|..+|..||.|.++.+... ..|.  ..|-|...+..+|.-|+..||...|++++|.|.++.
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 QLLQEAFARHGKVKSVELSPH-TDYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSC-CSTT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEec-cCCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            356778889999999988654 3454  478999999999999999999999999999998864

>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=94.66  E-value=0.047  Score=46.00  Aligned_cols=68  Identities=12%  Similarity=0.169  Sum_probs=56.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCC--ceEEEEEeCCHHHHHHHHHHhCCceeC
Q 004150           55 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTP--KGFGFCEFESAEGVLRALRLLNKFNID  122 (771)
Q Consensus        55 ~tVfVgNLp~~vte~~L~~lF~~~G~V~s~kiv~d~~tGk~--kGfGFVeF~~~esA~~Al~~Lng~~I~  122 (771)
                      ++|.|.+||+++|++.+.+.++..|.+..+..+....+.++  -.-|||.|.+.+.+......++|..+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            67999999999999999999999998877776665544333  356899999999999999999998763